Chloroplast genomes: diversity, evolution, and applications in genetic engineering
Identifieur interne : 000719 ( Pmc/Corpus ); précédent : 000718; suivant : 000720Chloroplast genomes: diversity, evolution, and applications in genetic engineering
Auteurs : Henry Daniell ; Choun-Sea Lin ; Ming Yu ; Wan-Jung ChangSource :
- Genome Biology [ 1474-7596 ] ; 2016.
Abstract
Chloroplasts play a crucial role in sustaining life on earth. The availability of over 800 sequenced chloroplast genomes from a variety of land plants has enhanced our understanding of chloroplast biology, intracellular gene transfer, conservation, diversity, and the genetic basis by which chloroplast transgenes can be engineered to enhance plant agronomic traits or to produce high-value agricultural or biomedical products. In this review, we discuss the impact of chloroplast genome sequences on understanding the origins of economically important cultivated species and changes that have taken place during domestication. We also discuss the potential biotechnological applications of chloroplast genomes.
The online version of this article (doi:10.1186/s13059-016-1004-2) contains supplementary material, which is available to authorized users.
Url:
DOI: 10.1186/s13059-016-1004-2
PubMed: 27339192
PubMed Central: 4918201
Links to Exploration step
PMC:4918201Le document en format XML
<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Chloroplast genomes: diversity, evolution, and applications in genetic engineering</title><author><name sortKey="Daniell, Henry" sort="Daniell, Henry" uniqKey="Daniell H" first="Henry" last="Daniell">Henry Daniell</name><affiliation><nlm:aff id="Aff1">Department of Biochemistry, School of Dental Medicine, University of Pennsylvania, South 40th St, Philadelphia, PA 19104-6030 USA</nlm:aff></affiliation></author><author><name sortKey="Lin, Choun Sea" sort="Lin, Choun Sea" uniqKey="Lin C" first="Choun-Sea" last="Lin">Choun-Sea Lin</name><affiliation><nlm:aff id="Aff2">Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan</nlm:aff></affiliation></author><author><name sortKey="Yu, Ming" sort="Yu, Ming" uniqKey="Yu M" first="Ming" last="Yu">Ming Yu</name><affiliation><nlm:aff id="Aff1">Department of Biochemistry, School of Dental Medicine, University of Pennsylvania, South 40th St, Philadelphia, PA 19104-6030 USA</nlm:aff></affiliation></author><author><name sortKey="Chang, Wan Jung" sort="Chang, Wan Jung" uniqKey="Chang W" first="Wan-Jung" last="Chang">Wan-Jung Chang</name><affiliation><nlm:aff id="Aff2">Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan</nlm:aff></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">27339192</idno><idno type="pmc">4918201</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4918201</idno><idno type="RBID">PMC:4918201</idno><idno type="doi">10.1186/s13059-016-1004-2</idno><date when="2016">2016</date><idno type="wicri:Area/Pmc/Corpus">000719</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Chloroplast genomes: diversity, evolution, and applications in genetic engineering</title><author><name sortKey="Daniell, Henry" sort="Daniell, Henry" uniqKey="Daniell H" first="Henry" last="Daniell">Henry Daniell</name><affiliation><nlm:aff id="Aff1">Department of Biochemistry, School of Dental Medicine, University of Pennsylvania, South 40th St, Philadelphia, PA 19104-6030 USA</nlm:aff></affiliation></author><author><name sortKey="Lin, Choun Sea" sort="Lin, Choun Sea" uniqKey="Lin C" first="Choun-Sea" last="Lin">Choun-Sea Lin</name><affiliation><nlm:aff id="Aff2">Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan</nlm:aff></affiliation></author><author><name sortKey="Yu, Ming" sort="Yu, Ming" uniqKey="Yu M" first="Ming" last="Yu">Ming Yu</name><affiliation><nlm:aff id="Aff1">Department of Biochemistry, School of Dental Medicine, University of Pennsylvania, South 40th St, Philadelphia, PA 19104-6030 USA</nlm:aff></affiliation></author><author><name sortKey="Chang, Wan Jung" sort="Chang, Wan Jung" uniqKey="Chang W" first="Wan-Jung" last="Chang">Wan-Jung Chang</name><affiliation><nlm:aff id="Aff2">Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan</nlm:aff></affiliation></author></analytic><series><title level="j">Genome Biology</title><idno type="ISSN">1474-7596</idno><idno type="eISSN">1474-760X</idno><imprint><date when="2016">2016</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>Chloroplasts play a crucial role in sustaining life on earth. The availability of over 800 sequenced chloroplast genomes from a variety of land plants has enhanced our understanding of chloroplast biology, intracellular gene transfer, conservation, diversity, and the genetic basis by which chloroplast transgenes can be engineered to enhance plant agronomic traits or to produce high-value agricultural or biomedical products. In this review, we discuss the impact of chloroplast genome sequences on understanding the origins of economically important cultivated species and changes that have taken place during domestication. We also discuss the potential biotechnological applications of chloroplast genomes.</p><sec><title>Electronic supplementary material</title><p>The online version of this article (doi:10.1186/s13059-016-1004-2) contains supplementary material, which is available to authorized users.</p></sec></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Bobik, K" uniqKey="Bobik K">K Bobik</name></author><author><name sortKey="Burch Smith, Tm" uniqKey="Burch Smith T">TM Burch-Smith</name></author></analytic></biblStruct><biblStruct></biblStruct><biblStruct><analytic><author><name sortKey="Shinozaki, K" uniqKey="Shinozaki K">K Shinozaki</name></author><author><name sortKey="Ohme, M" uniqKey="Ohme M">M Ohme</name></author><author><name sortKey="Tanaka, M" uniqKey="Tanaka M">M Tanaka</name></author><author><name sortKey="Wakasugi, T" uniqKey="Wakasugi T">T Wakasugi</name></author><author><name sortKey="Hayashida, N" uniqKey="Hayashida N">N Hayashida</name></author><author><name sortKey="Matsubayashi, T" uniqKey="Matsubayashi T">T Matsubayashi</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Wambugu, P" uniqKey="Wambugu P">P Wambugu</name></author><author><name sortKey="Brozynska, M" uniqKey="Brozynska M">M Brozynska</name></author><author><name sortKey="Furtado, A" uniqKey="Furtado A">A Furtado</name></author><author><name sortKey="Waters, D" uniqKey="Waters D">D Waters</name></author><author><name sortKey="Henry, R" uniqKey="Henry R">R Henry</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Brozynska, M" uniqKey="Brozynska M">M Brozynska</name></author><author><name sortKey="Furtado, A" uniqKey="Furtado A">A Furtado</name></author><author><name sortKey="Henry, Rj" uniqKey="Henry R">RJ Henry</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Su, J" uniqKey="Su J">J Su</name></author><author><name sortKey="Zhu, L" uniqKey="Zhu L">L Zhu</name></author><author><name sortKey="Sherman, A" uniqKey="Sherman A">A Sherman</name></author><author><name sortKey="Wang, X" uniqKey="Wang X">X Wang</name></author><author><name sortKey="Lin, S" uniqKey="Lin S">S Lin</name></author><author><name sortKey="Kamesh, A" uniqKey="Kamesh A">A Kamesh</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Jansen, Rk" uniqKey="Jansen R">RK Jansen</name></author><author><name sortKey="Wojciechowski, Mf" uniqKey="Wojciechowski M">MF Wojciechowski</name></author><author><name sortKey="Sanniyasi, E" uniqKey="Sanniyasi E">E Sanniyasi</name></author><author><name sortKey="Lee, Sb" uniqKey="Lee S">SB Lee</name></author><author><name sortKey="Daniell, H" uniqKey="Daniell H">H Daniell</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Saski, C" uniqKey="Saski C">C Saski</name></author><author><name sortKey="Lee, Sb" uniqKey="Lee S">SB Lee</name></author><author><name sortKey="Fjellheim, S" uniqKey="Fjellheim S">S Fjellheim</name></author><author><name sortKey="Guda, C" uniqKey="Guda C">C Guda</name></author><author><name sortKey="Jansen, Rk" uniqKey="Jansen R">RK Jansen</name></author><author><name sortKey="Luo, H" uniqKey="Luo H">H Luo</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Ruhlman, T" uniqKey="Ruhlman T">T Ruhlman</name></author><author><name sortKey="Lee, Sb" uniqKey="Lee S">SB Lee</name></author><author><name sortKey="Jansen, Rk" uniqKey="Jansen R">RK Jansen</name></author><author><name sortKey="Hostetler, Jb" uniqKey="Hostetler J">JB Hostetler</name></author><author><name sortKey="Tallon, Lj" uniqKey="Tallon L">LJ Tallon</name></author><author><name sortKey="Town, Cd" uniqKey="Town C">CD Town</name></author><author><name sortKey="Daniell, H" uniqKey="Daniell H">H Daniell</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Samson, N" uniqKey="Samson N">N Samson</name></author><author><name sortKey="Bausher, Mg" uniqKey="Bausher M">MG Bausher</name></author><author><name sortKey="Lee, Sb" uniqKey="Lee S">SB Lee</name></author><author><name sortKey="Jansen, Rk" uniqKey="Jansen R">RK Jansen</name></author><author><name sortKey="Daniell, H" uniqKey="Daniell H">H Daniell</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Lee, Sb" uniqKey="Lee S">SB Lee</name></author><author><name sortKey="Kaittanis, C" uniqKey="Kaittanis C">C Kaittanis</name></author><author><name sortKey="Jansen, Rk" uniqKey="Jansen R">RK Jansen</name></author><author><name sortKey="Hostetler, Jb" uniqKey="Hostetler J">JB Hostetler</name></author><author><name sortKey="Tallon, Lj" uniqKey="Tallon L">LJ Tallon</name></author><author><name sortKey="Town, Cd" uniqKey="Town C">CD Town</name></author><author><name sortKey="Daniell, H" uniqKey="Daniell H">H Daniell</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Bausher, Mg" uniqKey="Bausher M">MG Bausher</name></author><author><name sortKey="Singh, Nd" uniqKey="Singh N">ND Singh</name></author><author><name sortKey="Lee, Sb" uniqKey="Lee S">SB Lee</name></author><author><name sortKey="Jansen, Rk" uniqKey="Jansen R">RK Jansen</name></author><author><name sortKey="Daniell, H" uniqKey="Daniell H">H Daniell</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Daniell, H" uniqKey="Daniell H">H Daniell</name></author><author><name sortKey="Lee, Sb" uniqKey="Lee S">SB Lee</name></author><author><name sortKey="Grevich, J" uniqKey="Grevich J">J Grevich</name></author><author><name sortKey="Saski, C" uniqKey="Saski C">C Saski</name></author><author><name sortKey="Quesada Vargas, T" uniqKey="Quesada Vargas T">T Quesada-Vargas</name></author><author><name sortKey="Guda, C" uniqKey="Guda C">C Guda</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Jansen, Rk" uniqKey="Jansen R">RK Jansen</name></author><author><name sortKey="Saski, C" uniqKey="Saski C">C Saski</name></author><author><name sortKey="Lee, Sb" uniqKey="Lee S">SB Lee</name></author><author><name sortKey="Hansen, Ak" uniqKey="Hansen A">AK Hansen</name></author><author><name sortKey="Daniell, H" uniqKey="Daniell H">H Daniell</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Wolfe, Kh" uniqKey="Wolfe K">KH Wolfe</name></author><author><name sortKey="Morden, Cw" uniqKey="Morden C">CW Morden</name></author><author><name sortKey="Palmer, Jd" uniqKey="Palmer J">JD Palmer</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Bortiri, E" uniqKey="Bortiri E">E Bortiri</name></author><author><name sortKey="Coleman Derr, D" uniqKey="Coleman Derr D">D Coleman-Derr</name></author><author><name sortKey="Lazo, Gr" uniqKey="Lazo G">GR Lazo</name></author><author><name sortKey="Anderson, Od" uniqKey="Anderson O">OD Anderson</name></author><author><name sortKey="Gu, Yq" uniqKey="Gu Y">YQ Gu</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Sato, S" uniqKey="Sato S">S Sato</name></author><author><name sortKey="Nakamura, Y" uniqKey="Nakamura Y">Y Nakamura</name></author><author><name sortKey="Kaneko, T" uniqKey="Kaneko T">T Kaneko</name></author><author><name sortKey="Asamizu, E" uniqKey="Asamizu E">E Asamizu</name></author><author><name sortKey="Tabata, S" uniqKey="Tabata S">S Tabata</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Saski, C" uniqKey="Saski C">C Saski</name></author><author><name sortKey="Lee, Sb" uniqKey="Lee S">SB Lee</name></author><author><name sortKey="Daniell, H" uniqKey="Daniell H">H Daniell</name></author><author><name sortKey="Wood, Tc" uniqKey="Wood T">TC Wood</name></author><author><name sortKey="Tomkins, J" uniqKey="Tomkins J">J Tomkins</name></author><author><name sortKey="Kim, Hg" uniqKey="Kim H">HG Kim</name></author><author><name sortKey="Jansen, Rk" uniqKey="Jansen R">RK Jansen</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Jansen, Rk" uniqKey="Jansen R">RK Jansen</name></author><author><name sortKey="Kaittanis, C" uniqKey="Kaittanis C">C Kaittanis</name></author><author><name sortKey="Saski, C" uniqKey="Saski C">C Saski</name></author><author><name sortKey="Lee, Sb" uniqKey="Lee S">SB Lee</name></author><author><name sortKey="Tomkins, J" uniqKey="Tomkins J">J Tomkins</name></author><author><name sortKey="Alverson, Aj" uniqKey="Alverson A">AJ Alverson</name></author><author><name sortKey="Daniell, H" uniqKey="Daniell H">H Daniell</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Daniell, H" uniqKey="Daniell H">H Daniell</name></author><author><name sortKey="Wurdack, Kj" uniqKey="Wurdack K">KJ Wurdack</name></author><author><name sortKey="Kanagaraj, A" uniqKey="Kanagaraj A">A Kanagaraj</name></author><author><name sortKey="Lee, Sb" uniqKey="Lee S">SB Lee</name></author><author><name sortKey="Saski, C" uniqKey="Saski C">C Saski</name></author><author><name sortKey="Jansen, Rk" uniqKey="Jansen R">RK Jansen</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Wu, J" uniqKey="Wu J">J Wu</name></author><author><name sortKey="Liu, B" uniqKey="Liu B">B Liu</name></author><author><name sortKey="Cheng, F" uniqKey="Cheng F">F Cheng</name></author><author><name sortKey="Ramchiary, N" uniqKey="Ramchiary N">N Ramchiary</name></author><author><name sortKey="Choi, Sr" uniqKey="Choi S">SR Choi</name></author><author><name sortKey="Lim, Yp" uniqKey="Lim Y">YP Lim</name></author><author><name sortKey="Wang, X W" uniqKey="Wang X">X-W Wang</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Grivet, D" uniqKey="Grivet D">D Grivet</name></author><author><name sortKey="Heinze, B" uniqKey="Heinze B">B Heinze</name></author><author><name sortKey="Vendramin, G" uniqKey="Vendramin G">G Vendramin</name></author><author><name sortKey="Petit, R" uniqKey="Petit R">R Petit</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Goremykin, V" uniqKey="Goremykin V">V Goremykin</name></author><author><name sortKey="Hirsch Ernst, K" uniqKey="Hirsch Ernst K">K Hirsch-Ernst</name></author><author><name sortKey="Wolfl, S" uniqKey="Wolfl S">S Wölfl</name></author><author><name sortKey="Hellwig, F" uniqKey="Hellwig F">F Hellwig</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Goremykin, Vv" uniqKey="Goremykin V">VV Goremykin</name></author><author><name sortKey="Hirsch Ernst, Ki" uniqKey="Hirsch Ernst K">KI Hirsch-Ernst</name></author><author><name sortKey="Wolfl, S" uniqKey="Wolfl S">S Wolfl</name></author><author><name sortKey="Hellwig, Fh" uniqKey="Hellwig F">FH Hellwig</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Goremykin, Vv" uniqKey="Goremykin V">VV Goremykin</name></author><author><name sortKey="Hirsch Ernst, Ki" uniqKey="Hirsch Ernst K">KI Hirsch-Ernst</name></author><author><name sortKey="Wolfl, S" uniqKey="Wolfl S">S Wölfl</name></author><author><name sortKey="Hellwig, Fh" uniqKey="Hellwig F">FH Hellwig</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Dhingra, A" uniqKey="Dhingra A">A Dhingra</name></author><author><name sortKey="Folta, Km" uniqKey="Folta K">KM Folta</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Heinze, B" uniqKey="Heinze B">B Heinze</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Wu, Fh" uniqKey="Wu F">FH Wu</name></author><author><name sortKey="Kan, Dp" uniqKey="Kan D">DP Kan</name></author><author><name sortKey="Lee, Sb" uniqKey="Lee S">SB Lee</name></author><author><name sortKey="Daniell, H" uniqKey="Daniell H">H Daniell</name></author><author><name sortKey="Lee, Yw" uniqKey="Lee Y">YW Lee</name></author><author><name sortKey="Lin, Cc" uniqKey="Lin C">CC Lin</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Leseberg, Ch" uniqKey="Leseberg C">CH Leseberg</name></author><author><name sortKey="Duvall, Mr" uniqKey="Duvall M">MR Duvall</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Dong, W" uniqKey="Dong W">W Dong</name></author><author><name sortKey="Xu, C" uniqKey="Xu C">C Xu</name></author><author><name sortKey="Cheng, T" uniqKey="Cheng T">T Cheng</name></author><author><name sortKey="Lin, K" uniqKey="Lin K">K Lin</name></author><author><name sortKey="Zhou, S" uniqKey="Zhou S">S Zhou</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Mardanov, Av" uniqKey="Mardanov A">AV Mardanov</name></author><author><name sortKey="Ravin, Nv" uniqKey="Ravin N">NV Ravin</name></author><author><name sortKey="Kuznetsov, Bb" uniqKey="Kuznetsov B">BB Kuznetsov</name></author><author><name sortKey="Samigullin, Th" uniqKey="Samigullin T">TH Samigullin</name></author><author><name sortKey="Antonov, As" uniqKey="Antonov A">AS Antonov</name></author><author><name sortKey="Kolganova, Tv" uniqKey="Kolganova T">TV Kolganova</name></author><author><name sortKey="Skyabin, Kg" uniqKey="Skyabin K">KG Skyabin</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Lin, Cs" uniqKey="Lin C">CS Lin</name></author><author><name sortKey="Chen, Jj" uniqKey="Chen J">JJ Chen</name></author><author><name sortKey="Huang, Yt" uniqKey="Huang Y">YT Huang</name></author><author><name sortKey="Chan, Mt" uniqKey="Chan M">MT Chan</name></author><author><name sortKey="Daniell, H" uniqKey="Daniell H">H Daniell</name></author><author><name sortKey="Chang, Wj" uniqKey="Chang W">WJ Chang</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Moore, Mj" uniqKey="Moore M">MJ Moore</name></author><author><name sortKey="Dhingra, A" uniqKey="Dhingra A">A Dhingra</name></author><author><name sortKey="Soltis, Ps" uniqKey="Soltis P">PS Soltis</name></author><author><name sortKey="Shaw, R" uniqKey="Shaw R">R Shaw</name></author><author><name sortKey="Farmerie, Wg" uniqKey="Farmerie W">WG Farmerie</name></author><author><name sortKey="Folta, Km" uniqKey="Folta K">KM Folta</name></author><author><name sortKey="Soltis, De" uniqKey="Soltis D">DE Soltis</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Wang, W" uniqKey="Wang W">W Wang</name></author><author><name sortKey="Messing, J" uniqKey="Messing J">J Messing</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Cronn, R" uniqKey="Cronn R">R Cronn</name></author><author><name sortKey="Liston, A" uniqKey="Liston A">A Liston</name></author><author><name sortKey="Parks, M" uniqKey="Parks M">M Parks</name></author><author><name sortKey="Gernandt, Ds" uniqKey="Gernandt D">DS Gernandt</name></author><author><name sortKey="Shen, R" uniqKey="Shen R">R Shen</name></author><author><name sortKey="Mockler, T" uniqKey="Mockler T">T Mockler</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Pan, Ic" uniqKey="Pan I">IC Pan</name></author><author><name sortKey="Liao, Dc" uniqKey="Liao D">DC Liao</name></author><author><name sortKey="Wu, Fh" uniqKey="Wu F">FH Wu</name></author><author><name sortKey="Daniell, H" uniqKey="Daniell H">H Daniell</name></author><author><name sortKey="Singh, Nd" uniqKey="Singh N">ND Singh</name></author><author><name sortKey="Chang, C" uniqKey="Chang C">C Chang</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Atherton, Ra" uniqKey="Atherton R">RA Atherton</name></author><author><name sortKey="Mccomish, Bj" uniqKey="Mccomish B">BJ McComish</name></author><author><name sortKey="Shepherd, Ld" uniqKey="Shepherd L">LD Shepherd</name></author><author><name sortKey="Berry, La" uniqKey="Berry L">LA Berry</name></author><author><name sortKey="Albert, Nw" uniqKey="Albert N">NW Albert</name></author><author><name sortKey="Lockhart, Pj" uniqKey="Lockhart P">PJ Lockhart</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Jackman, Sd" uniqKey="Jackman S">SD Jackman</name></author><author><name sortKey="Warren, Rl" uniqKey="Warren R">RL Warren</name></author><author><name sortKey="Gibb, Ea" uniqKey="Gibb E">EA Gibb</name></author><author><name sortKey="Vandervalk, Bp" uniqKey="Vandervalk B">BP Vandervalk</name></author><author><name sortKey="Mohamadi, H" uniqKey="Mohamadi H">H Mohamadi</name></author><author><name sortKey="Chu, J" uniqKey="Chu J">J Chu</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Ferrarini, M" uniqKey="Ferrarini M">M Ferrarini</name></author><author><name sortKey="Moretto, M" uniqKey="Moretto M">M Moretto</name></author><author><name sortKey="Ward, Ja" uniqKey="Ward J">JA Ward</name></author><author><name sortKey="Surbanovski, N" uniqKey="Surbanovski N">N Šurbanovski</name></author><author><name sortKey="Stevanovi, V" uniqKey="Stevanovi V">V Stevanović</name></author><author><name sortKey="Giongo, L" uniqKey="Giongo L">L Giongo</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Wu, Z" uniqKey="Wu Z">Z Wu</name></author><author><name sortKey="Gui, S" uniqKey="Gui S">S Gui</name></author><author><name sortKey="Quan, Z" uniqKey="Quan Z">Z Quan</name></author><author><name sortKey="Pan, L" uniqKey="Pan L">L Pan</name></author><author><name sortKey="Wang, S" uniqKey="Wang S">S Wang</name></author><author><name sortKey="Ke, W" uniqKey="Ke W">W Ke</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Li, Q" uniqKey="Li Q">Q Li</name></author><author><name sortKey="Li, Y" uniqKey="Li Y">Y Li</name></author><author><name sortKey="Song, J" uniqKey="Song J">J Song</name></author><author><name sortKey="Xu, H" uniqKey="Xu H">H Xu</name></author><author><name sortKey="Xu, J" uniqKey="Xu J">J Xu</name></author><author><name sortKey="Zhu, Y" uniqKey="Zhu Y">Y Zhu</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Redwan, R" uniqKey="Redwan R">R Redwan</name></author><author><name sortKey="Saidin, A" uniqKey="Saidin A">A Saidin</name></author><author><name sortKey="Kumar, S" uniqKey="Kumar S">S Kumar</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Chen, X" uniqKey="Chen X">X Chen</name></author><author><name sortKey="Li, Q" uniqKey="Li Q">Q Li</name></author><author><name sortKey="Li, Y" uniqKey="Li Y">Y Li</name></author><author><name sortKey="Qian, J" uniqKey="Qian J">J Qian</name></author><author><name sortKey="Han, J" uniqKey="Han J">J Han</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Eid, J" uniqKey="Eid J">J Eid</name></author><author><name sortKey="Fehr, A" uniqKey="Fehr A">A Fehr</name></author><author><name sortKey="Gray, J" uniqKey="Gray J">J Gray</name></author><author><name sortKey="Luong, K" uniqKey="Luong K">K Luong</name></author><author><name sortKey="Lyle, J" uniqKey="Lyle J">J Lyle</name></author><author><name sortKey="Otto, G" uniqKey="Otto G">G Otto</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="English, Ac" uniqKey="English A">AC English</name></author><author><name sortKey="Richards, S" uniqKey="Richards S">S Richards</name></author><author><name sortKey="Han, Y" uniqKey="Han Y">Y Han</name></author><author><name sortKey="Wang, M" uniqKey="Wang M">M Wang</name></author><author><name sortKey="Vee, V" uniqKey="Vee V">V Vee</name></author><author><name sortKey="Qu, J" uniqKey="Qu J">J Qu</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Chin, Cs" uniqKey="Chin C">CS Chin</name></author><author><name sortKey="Alexander, Dh" uniqKey="Alexander D">DH Alexander</name></author><author><name sortKey="Marks, P" uniqKey="Marks P">P Marks</name></author><author><name sortKey="Klammer, Aa" uniqKey="Klammer A">AA Klammer</name></author><author><name sortKey="Drake, J" uniqKey="Drake J">J Drake</name></author><author><name sortKey="Heiner, C" uniqKey="Heiner C">C Heiner</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Oldenburg, Dj" uniqKey="Oldenburg D">DJ Oldenburg</name></author><author><name sortKey="Bendich, Aj" uniqKey="Bendich A">AJ Bendich</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Oldenburg, Dj" uniqKey="Oldenburg D">DJ Oldenburg</name></author><author><name sortKey="Bendich, Aj" uniqKey="Bendich A">AJ Bendich</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Jansen, Rk" uniqKey="Jansen R">RK Jansen</name></author><author><name sortKey="Cai, Z" uniqKey="Cai Z">Z Cai</name></author><author><name sortKey="Raubeson, La" uniqKey="Raubeson L">LA Raubeson</name></author><author><name sortKey="Daniell, H" uniqKey="Daniell H">H Daniell</name></author><author><name sortKey="Leebens Mack, J" uniqKey="Leebens Mack J">J Leebens-Mack</name></author><author><name sortKey="Muller, Kf" uniqKey="Muller K">KF Müller</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Pillon, Y" uniqKey="Pillon Y">Y Pillon</name></author><author><name sortKey="Chase, Mw" uniqKey="Chase M">MW Chase</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Chang, Cc" uniqKey="Chang C">CC Chang</name></author><author><name sortKey="Lin, Hc" uniqKey="Lin H">HC Lin</name></author><author><name sortKey="Lin, Ip" uniqKey="Lin I">IP Lin</name></author><author><name sortKey="Chow, Ty" uniqKey="Chow T">TY Chow</name></author><author><name sortKey="Chen, Hh" uniqKey="Chen H">HH Chen</name></author><author><name sortKey="Chen, Wh" uniqKey="Chen W">WH Chen</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Jheng, Cf" uniqKey="Jheng C">CF Jheng</name></author><author><name sortKey="Chen, Tc" uniqKey="Chen T">TC Chen</name></author><author><name sortKey="Lin, Jy" uniqKey="Lin J">JY Lin</name></author><author><name sortKey="Chen, Tc" uniqKey="Chen T">TC Chen</name></author><author><name sortKey="Wu, Wl" uniqKey="Wu W">WL Wu</name></author><author><name sortKey="Chang, Cc" uniqKey="Chang C">CC Chang</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Kim, Gb" uniqKey="Kim G">GB Kim</name></author><author><name sortKey="Kwon, Y" uniqKey="Kwon Y">Y Kwon</name></author><author><name sortKey="Yu, Hj" uniqKey="Yu H">HJ Yu</name></author><author><name sortKey="Lim, Kb" uniqKey="Lim K">KB Lim</name></author><author><name sortKey="Seo, Jh" uniqKey="Seo J">JH Seo</name></author><author><name sortKey="Mun, Jh" uniqKey="Mun J">JH Mun</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Wu, Fh" uniqKey="Wu F">FH Wu</name></author><author><name sortKey="Chan, Mt" uniqKey="Chan M">MT Chan</name></author><author><name sortKey="Liao, Dc" uniqKey="Liao D">DC Liao</name></author><author><name sortKey="Hsu, Ct" uniqKey="Hsu C">CT Hsu</name></author><author><name sortKey="Lee, Yw" uniqKey="Lee Y">YW Lee</name></author><author><name sortKey="Daniell, H" uniqKey="Daniell H">H Daniell</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Yang, Jb" uniqKey="Yang J">JB Yang</name></author><author><name sortKey="Tang, M" uniqKey="Tang M">M Tang</name></author><author><name sortKey="Li, Ht" uniqKey="Li H">HT Li</name></author><author><name sortKey="Zhang, Zr" uniqKey="Zhang Z">ZR Zhang</name></author><author><name sortKey="Li, Dz" uniqKey="Li D">DZ Li</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Luo, J" uniqKey="Luo J">J Luo</name></author><author><name sortKey="Hou, Bw" uniqKey="Hou B">BW Hou</name></author><author><name sortKey="Niu, Zt" uniqKey="Niu Z">ZT Niu</name></author><author><name sortKey="Liu, W" uniqKey="Liu W">W Liu</name></author><author><name sortKey="Xue, Qy" uniqKey="Xue Q">QY Xue</name></author><author><name sortKey="Ding, Xy" uniqKey="Ding X">XY Ding</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Li, J" uniqKey="Li J">J Li</name></author><author><name sortKey="Chen, C" uniqKey="Chen C">C Chen</name></author><author><name sortKey="Wang, Zz" uniqKey="Wang Z">ZZ Wang</name></author></analytic></biblStruct><biblStruct></biblStruct><biblStruct><analytic><author><name sortKey="Tsitrone, A" uniqKey="Tsitrone A">A Tsitrone</name></author><author><name sortKey="Kirkpatrick, M" uniqKey="Kirkpatrick M">M Kirkpatrick</name></author><author><name sortKey="Levin, Da" uniqKey="Levin D">DA Levin</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Soltis, De" uniqKey="Soltis D">DE Soltis</name></author><author><name sortKey="Kuzoff, Rk" uniqKey="Kuzoff R">RK Kuzoff</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Rieseberg, Lh" uniqKey="Rieseberg L">LH Rieseberg</name></author><author><name sortKey="Soltis, De" uniqKey="Soltis D">DE Soltis</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Maier, Rm" uniqKey="Maier R">RM Maier</name></author><author><name sortKey="Neckermann, K" uniqKey="Neckermann K">K Neckermann</name></author><author><name sortKey="Igloi, Gl" uniqKey="Igloi G">GL Igloi</name></author><author><name sortKey="Kossel, H" uniqKey="Kossel H">H Kossel</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Ogihara, Y" uniqKey="Ogihara Y">Y Ogihara</name></author><author><name sortKey="Isono, K" uniqKey="Isono K">K Isono</name></author><author><name sortKey="Kojima, T" uniqKey="Kojima T">T Kojima</name></author><author><name sortKey="Endo, A" uniqKey="Endo A">A Endo</name></author><author><name sortKey="Hanaoka, M" uniqKey="Hanaoka M">M Hanaoka</name></author><author><name sortKey="Shiina, T" uniqKey="Shiina T">T Shiina</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Middleton, Cp" uniqKey="Middleton C">CP Middleton</name></author><author><name sortKey="Senerchia, N" uniqKey="Senerchia N">N Senerchia</name></author><author><name sortKey="Stein, N" uniqKey="Stein N">N Stein</name></author><author><name sortKey="Akhunov, Ed" uniqKey="Akhunov E">ED Akhunov</name></author><author><name sortKey="Keller, B" uniqKey="Keller B">B Keller</name></author><author><name sortKey="Wicker, T" uniqKey="Wicker T">T Wicker</name></author><author><name sortKey="Kilian, B" uniqKey="Kilian B">B Kilian</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Brozynska, M" uniqKey="Brozynska M">M Brozynska</name></author><author><name sortKey="Omar, Es" uniqKey="Omar E">ES Omar</name></author><author><name sortKey="Furtado, A" uniqKey="Furtado A">A Furtado</name></author><author><name sortKey="Crayn, D" uniqKey="Crayn D">D Crayn</name></author><author><name sortKey="Simon, B" uniqKey="Simon B">B Simon</name></author><author><name sortKey="Ishikawa, R" uniqKey="Ishikawa R">R Ishikawa</name></author><author><name sortKey="Henry, Rj" uniqKey="Henry R">RJ Henry</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Waters, Dl" uniqKey="Waters D">DL Waters</name></author><author><name sortKey="Nock, Cj" uniqKey="Nock C">CJ Nock</name></author><author><name sortKey="Ishikawa, R" uniqKey="Ishikawa R">R Ishikawa</name></author><author><name sortKey="Rice, N" uniqKey="Rice N">N Rice</name></author><author><name sortKey="Henry, Rj" uniqKey="Henry R">RJ Henry</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Sotowa, M" uniqKey="Sotowa M">M Sotowa</name></author><author><name sortKey="Ootsuka, K" uniqKey="Ootsuka K">K Ootsuka</name></author><author><name sortKey="Kobayashi, Y" uniqKey="Kobayashi Y">Y Kobayashi</name></author><author><name sortKey="Hao, Y" uniqKey="Hao Y">Y Hao</name></author><author><name sortKey="Tanaka, K" uniqKey="Tanaka K">K Tanaka</name></author><author><name sortKey="Ichitani, K" uniqKey="Ichitani K">K Ichitani</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Xu, Q" uniqKey="Xu Q">Q Xu</name></author><author><name sortKey="Xiong, G" uniqKey="Xiong G">G Xiong</name></author><author><name sortKey="Li, P" uniqKey="Li P">P Li</name></author><author><name sortKey="He, F" uniqKey="He F">F He</name></author><author><name sortKey="Huang, Y" uniqKey="Huang Y">Y Huang</name></author><author><name sortKey="Wang, K" uniqKey="Wang K">K Wang</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Ibrahim, Ri" uniqKey="Ibrahim R">RI Ibrahim</name></author><author><name sortKey="Azuma, J" uniqKey="Azuma J">J Azuma</name></author><author><name sortKey="Sakamoto, M" uniqKey="Sakamoto M">M Sakamoto</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Li, P" uniqKey="Li P">P Li</name></author><author><name sortKey="Li, Z" uniqKey="Li Z">Z Li</name></author><author><name sortKey="Liu, H" uniqKey="Liu H">H Liu</name></author><author><name sortKey="Hua, J" uniqKey="Hua J">J Hua</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Pickersgill, B" uniqKey="Pickersgill B">B Pickersgill</name></author><author><name sortKey="Debouck, Dg" uniqKey="Debouck D">DG Debouck</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Palmer, Jd" uniqKey="Palmer J">JD Palmer</name></author><author><name sortKey="Osorio, B" uniqKey="Osorio B">B Osorio</name></author><author><name sortKey="Thompson, Wf" uniqKey="Thompson W">WF Thompson</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Sherman Broyles, S" uniqKey="Sherman Broyles S">S Sherman-Broyles</name></author><author><name sortKey="Bombarely, A" uniqKey="Bombarely A">A Bombarely</name></author><author><name sortKey="Grimwood, J" uniqKey="Grimwood J">J Grimwood</name></author><author><name sortKey="Schmutz, J" uniqKey="Schmutz J">J Schmutz</name></author><author><name sortKey="Doyle, J" uniqKey="Doyle J">J Doyle</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Sabir, J" uniqKey="Sabir J">J Sabir</name></author><author><name sortKey="Schwarz, E" uniqKey="Schwarz E">E Schwarz</name></author><author><name sortKey="Ellison, N" uniqKey="Ellison N">N Ellison</name></author><author><name sortKey="Zhang, J" uniqKey="Zhang J">J Zhang</name></author><author><name sortKey="Baeshen, Na" uniqKey="Baeshen N">NA Baeshen</name></author><author><name sortKey="Mutwakil, M" uniqKey="Mutwakil M">M Mutwakil</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Cai, Z" uniqKey="Cai Z">Z Cai</name></author><author><name sortKey="Guisinger, M" uniqKey="Guisinger M">M Guisinger</name></author><author><name sortKey="Kim, H G" uniqKey="Kim H">H-G Kim</name></author><author><name sortKey="Ruck, E" uniqKey="Ruck E">E Ruck</name></author><author><name sortKey="Blazier, Jc" uniqKey="Blazier J">JC Blazier</name></author><author><name sortKey="Mcmurtry, V" uniqKey="Mcmurtry V">V McMurtry</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Magee, Am" uniqKey="Magee A">AM Magee</name></author><author><name sortKey="Aspinall, S" uniqKey="Aspinall S">S Aspinall</name></author><author><name sortKey="Rice, Dw" uniqKey="Rice D">DW Rice</name></author><author><name sortKey="Cusack, Bp" uniqKey="Cusack B">BP Cusack</name></author><author><name sortKey="Semon, M" uniqKey="Semon M">M Semon</name></author><author><name sortKey="Perry, As" uniqKey="Perry A">AS Perry</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Bogdanova, Vs" uniqKey="Bogdanova V">VS Bogdanova</name></author><author><name sortKey="Zaytseva, Oo" uniqKey="Zaytseva O">OO Zaytseva</name></author><author><name sortKey="Mglinets, Av" uniqKey="Mglinets A">AV Mglinets</name></author><author><name sortKey="Shatskaya, Nv" uniqKey="Shatskaya N">NV Shatskaya</name></author><author><name sortKey="Kosterin, Oe" uniqKey="Kosterin O">OE Kosterin</name></author><author><name sortKey="Vasiliev, Gv" uniqKey="Vasiliev G">GV Vasiliev</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Guo, X" uniqKey="Guo X">X Guo</name></author><author><name sortKey="Castillo Ramirez, S" uniqKey="Castillo Ramirez S">S Castillo-Ramírez</name></author><author><name sortKey="Gonzalez, V" uniqKey="Gonzalez V">V González</name></author><author><name sortKey="Bustos, P" uniqKey="Bustos P">P Bustos</name></author><author><name sortKey="Fernandez Vazquez, Jl" uniqKey="Fernandez Vazquez J">JL Fernández-Vázquez</name></author><author><name sortKey="Santamaria, Ri" uniqKey="Santamaria R">RI Santamaría</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Tangphatsornruang, S" uniqKey="Tangphatsornruang S">S Tangphatsornruang</name></author><author><name sortKey="Sangsrakru, D" uniqKey="Sangsrakru D">D Sangsrakru</name></author><author><name sortKey="Chanprasert, J" uniqKey="Chanprasert J">J Chanprasert</name></author><author><name sortKey="Uthaipaisanwong, P" uniqKey="Uthaipaisanwong P">P Uthaipaisanwong</name></author><author><name sortKey="Yoocha, T" uniqKey="Yoocha T">T Yoocha</name></author><author><name sortKey="Jomchai, N" uniqKey="Jomchai N">N Jomchai</name></author><author><name sortKey="Tragoonrung, S" uniqKey="Tragoonrung S">S Tragoonrung</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Martin, Ge" uniqKey="Martin G">GE Martin</name></author><author><name sortKey="Rousseau Gueutin, M" uniqKey="Rousseau Gueutin M">M Rousseau-Gueutin</name></author><author><name sortKey="Cordonnier, S" uniqKey="Cordonnier S">S Cordonnier</name></author><author><name sortKey="Lima, O" uniqKey="Lima O">O Lima</name></author><author><name sortKey="Michon Coudouel, S" uniqKey="Michon Coudouel S">S Michon-Coudouel</name></author><author><name sortKey="Naquin, D" uniqKey="Naquin D">D Naquin</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Kazakoff, Sh" uniqKey="Kazakoff S">SH Kazakoff</name></author><author><name sortKey="Imelfort, M" uniqKey="Imelfort M">M Imelfort</name></author><author><name sortKey="Edwards, D" uniqKey="Edwards D">D Edwards</name></author><author><name sortKey="Koehorst, J" uniqKey="Koehorst J">J Koehorst</name></author><author><name sortKey="Biswas, B" uniqKey="Biswas B">B Biswas</name></author><author><name sortKey="Batley, J" uniqKey="Batley J">J Batley</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Schwarz, En" uniqKey="Schwarz E">EN Schwarz</name></author><author><name sortKey="Ruhlman, Ta" uniqKey="Ruhlman T">TA Ruhlman</name></author><author><name sortKey="Sabir, Js" uniqKey="Sabir J">JS Sabir</name></author><author><name sortKey="Hajrah, Nh" uniqKey="Hajrah N">NH Hajrah</name></author><author><name sortKey="Alharbi, Ns" uniqKey="Alharbi N">NS Alharbi</name></author><author><name sortKey="Al Alki, Al" uniqKey="Al Alki A">AL Al‐Malki</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Su, Hj" uniqKey="Su H">HJ Su</name></author><author><name sortKey="Hogenhout, Sa" uniqKey="Hogenhout S">SA Hogenhout</name></author><author><name sortKey="Al Sadi, Am" uniqKey="Al Sadi A">AM Al-Sadi</name></author><author><name sortKey="Kuo, Ch" uniqKey="Kuo C">CH Kuo</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Carbonell Caballero, J" uniqKey="Carbonell Caballero J">J Carbonell-Caballero</name></author><author><name sortKey="Alonso, R" uniqKey="Alonso R">R Alonso</name></author><author><name sortKey="Iba Ez, V" uniqKey="Iba Ez V">V Ibañez</name></author><author><name sortKey="Terol, J" uniqKey="Terol J">J Terol</name></author><author><name sortKey="Talon, M" uniqKey="Talon M">M Talon</name></author><author><name sortKey="Dopazo, J" uniqKey="Dopazo J">J Dopazo</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Caspermeyer, J" uniqKey="Caspermeyer J">J Caspermeyer</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Chen, Sl" uniqKey="Chen S">SL Chen</name></author><author><name sortKey="Xiao, Pg" uniqKey="Xiao P">PG Xiao</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Peng, L" uniqKey="Peng L">L Peng</name></author><author><name sortKey="Yamamoto, H" uniqKey="Yamamoto H">H Yamamoto</name></author><author><name sortKey="Shikanai, T" uniqKey="Shikanai T">T Shikanai</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Ma, Pf" uniqKey="Ma P">PF Ma</name></author><author><name sortKey="Zhang, Yx" uniqKey="Zhang Y">YX Zhang</name></author><author><name sortKey="Guo, Zh" uniqKey="Guo Z">ZH Guo</name></author><author><name sortKey="Li, Dz" uniqKey="Li D">DZ Li</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Zhang, Yj" uniqKey="Zhang Y">YJ Zhang</name></author><author><name sortKey="Ma, Pf" uniqKey="Ma P">PF Ma</name></author><author><name sortKey="Li, Dz" uniqKey="Li D">DZ Li</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Burke, Sv" uniqKey="Burke S">SV Burke</name></author><author><name sortKey="Grennan, Cp" uniqKey="Grennan C">CP Grennan</name></author><author><name sortKey="Duvall, Mr" uniqKey="Duvall M">MR Duvall</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Gao, J" uniqKey="Gao J">J Gao</name></author><author><name sortKey="Li, K" uniqKey="Li K">K Li</name></author><author><name sortKey="Gao, Lz" uniqKey="Gao L">LZ Gao</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Wysocki, Wp" uniqKey="Wysocki W">WP Wysocki</name></author><author><name sortKey="Clark, Lg" uniqKey="Clark L">LG Clark</name></author><author><name sortKey="Attigala, L" uniqKey="Attigala L">L Attigala</name></author><author><name sortKey="Ruiz Sanchez, E" uniqKey="Ruiz Sanchez E">E Ruiz-Sanchez</name></author><author><name sortKey="Duvall, Mr" uniqKey="Duvall M">MR Duvall</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Ma, Pf" uniqKey="Ma P">PF Ma</name></author><author><name sortKey="Zhang, Yx" uniqKey="Zhang Y">YX Zhang</name></author><author><name sortKey="Zeng, Cx" uniqKey="Zeng C">CX Zeng</name></author><author><name sortKey="Guo, Zh" uniqKey="Guo Z">ZH Guo</name></author><author><name sortKey="Li, Dz" uniqKey="Li D">DZ Li</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Smith, Dr" uniqKey="Smith D">DR Smith</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Timmis, Jn" uniqKey="Timmis J">JN Timmis</name></author><author><name sortKey="Ayliffe, Ma" uniqKey="Ayliffe M">MA Ayliffe</name></author><author><name sortKey="Huang, Cy" uniqKey="Huang C">CY Huang</name></author><author><name sortKey="Martin, W" uniqKey="Martin W">W Martin</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Li, H" uniqKey="Li H">H Li</name></author><author><name sortKey="Chiu, Cc" uniqKey="Chiu C">CC Chiu</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Barrett, Cf" uniqKey="Barrett C">CF Barrett</name></author><author><name sortKey="Freudenstein, Jv" uniqKey="Freudenstein J">JV Freudenstein</name></author><author><name sortKey="Li, J" uniqKey="Li J">J Li</name></author><author><name sortKey="Mayfield Jones, Dr" uniqKey="Mayfield Jones D">DR Mayfield-Jones</name></author><author><name sortKey="Perez, L" uniqKey="Perez L">L Perez</name></author><author><name sortKey="Pires, Jc" uniqKey="Pires J">JC Pires</name></author><author><name sortKey="Santos, C" uniqKey="Santos C">C Santos</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Tiller, N" uniqKey="Tiller N">N Tiller</name></author><author><name sortKey="Bock, R" uniqKey="Bock R">R Bock</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Hazkani Covo, E" uniqKey="Hazkani Covo E">E Hazkani-Covo</name></author><author><name sortKey="Zeller, Rm" uniqKey="Zeller R">RM Zeller</name></author><author><name sortKey="Martin, W" uniqKey="Martin W">W Martin</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Smith, Dr" uniqKey="Smith D">DR Smith</name></author><author><name sortKey="Crosby, K" uniqKey="Crosby K">K Crosby</name></author><author><name sortKey="Lee, Rw" uniqKey="Lee R">RW Lee</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Cummings, Hs" uniqKey="Cummings H">HS Cummings</name></author><author><name sortKey="Hershey, Jwb" uniqKey="Hershey J">JWB Hershey</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Millen, Rs" uniqKey="Millen R">RS Millen</name></author><author><name sortKey="Olmstead, Rg" uniqKey="Olmstead R">RG Olmstead</name></author><author><name sortKey="Adams, Kl" uniqKey="Adams K">KL Adams</name></author><author><name sortKey="Palmer, Jd" uniqKey="Palmer J">JD Palmer</name></author><author><name sortKey="Lao, Nt" uniqKey="Lao N">NT Lao</name></author><author><name sortKey="Heggie, L" uniqKey="Heggie L">L Heggie</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Gantt, Js" uniqKey="Gantt J">JS Gantt</name></author><author><name sortKey="Baldauf, Sl" uniqKey="Baldauf S">SL Baldauf</name></author><author><name sortKey="Calie, Pj" uniqKey="Calie P">PJ Calie</name></author><author><name sortKey="Weeden, Nf" uniqKey="Weeden N">NF Weeden</name></author><author><name sortKey="Palmer, Jd" uniqKey="Palmer J">JD Palmer</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Park, S" uniqKey="Park S">S Park</name></author><author><name sortKey="Jansen, Rk" uniqKey="Jansen R">RK Jansen</name></author><author><name sortKey="Park, S" uniqKey="Park S">S Park</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Ueda, M" uniqKey="Ueda M">M Ueda</name></author><author><name sortKey="Fujimoto, M" uniqKey="Fujimoto M">M Fujimoto</name></author><author><name sortKey="Arimura, S" uniqKey="Arimura S">S Arimura</name></author><author><name sortKey="Murata, J" uniqKey="Murata J">J Murata</name></author><author><name sortKey="Tsutsumi, N" uniqKey="Tsutsumi N">N Tsutsumi</name></author><author><name sortKey="Kadowaki, K" uniqKey="Kadowaki K">K Kadowaki</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Cusack, Bp" uniqKey="Cusack B">BP Cusack</name></author><author><name sortKey="Wolfe, Kh" uniqKey="Wolfe K">KH Wolfe</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Ueda, M" uniqKey="Ueda M">M Ueda</name></author><author><name sortKey="Kuniyoshi, T" uniqKey="Kuniyoshi T">T Kuniyoshi</name></author><author><name sortKey="Yamamoto, H" uniqKey="Yamamoto H">H Yamamoto</name></author><author><name sortKey="Sugimoto, K" uniqKey="Sugimoto K">K Sugimoto</name></author><author><name sortKey="Ishizaki, K" uniqKey="Ishizaki K">K Ishizaki</name></author><author><name sortKey="Kohchi, T" uniqKey="Kohchi T">T Kohchi</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Munekage, Y" uniqKey="Munekage Y">Y Munekage</name></author><author><name sortKey="Hashimoto, M" uniqKey="Hashimoto M">M Hashimoto</name></author><author><name sortKey="Miyake, C" uniqKey="Miyake C">C Miyake</name></author><author><name sortKey="Tomizawa, K I" uniqKey="Tomizawa K">K-I Tomizawa</name></author><author><name sortKey="Endo, T" uniqKey="Endo T">T Endo</name></author><author><name sortKey="Tasaka, M" uniqKey="Tasaka M">M Tasaka</name></author><author><name sortKey="Shikanai, T" uniqKey="Shikanai T">T Shikanai</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Peltier, G" uniqKey="Peltier G">G Peltier</name></author><author><name sortKey="Cournac, L" uniqKey="Cournac L">L Cournac</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Wakasugi, T" uniqKey="Wakasugi T">T Wakasugi</name></author><author><name sortKey="Tsudzuki, J" uniqKey="Tsudzuki J">J Tsudzuki</name></author><author><name sortKey="Ito, S" uniqKey="Ito S">S Ito</name></author><author><name sortKey="Nakashima, K" uniqKey="Nakashima K">K Nakashima</name></author><author><name sortKey="Tsudzuki, T" uniqKey="Tsudzuki T">T Tsudzuki</name></author><author><name sortKey="Sugiura, M" uniqKey="Sugiura M">M Sugiura</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Sanderson, Mj" uniqKey="Sanderson M">MJ Sanderson</name></author><author><name sortKey="Copetti, D" uniqKey="Copetti D">D Copetti</name></author><author><name sortKey="Burquez, A" uniqKey="Burquez A">A Búrquez</name></author><author><name sortKey="Bustamante, E" uniqKey="Bustamante E">E Bustamante</name></author><author><name sortKey="Charboneau, Jl" uniqKey="Charboneau J">JL Charboneau</name></author><author><name sortKey="Eguiarte, Le" uniqKey="Eguiarte L">LE Eguiarte</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Mccoy, Sr" uniqKey="Mccoy S">SR McCoy</name></author><author><name sortKey="Kuehl, Jv" uniqKey="Kuehl J">JV Kuehl</name></author><author><name sortKey="Boore, Jl" uniqKey="Boore J">JL Boore</name></author><author><name sortKey="Raubeson, La" uniqKey="Raubeson L">LA Raubeson</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Braukmann, Twa" uniqKey="Braukmann T">TWA Braukmann</name></author><author><name sortKey="Kuzmina, M" uniqKey="Kuzmina M">M Kuzmina</name></author><author><name sortKey="Stefanovi, S" uniqKey="Stefanovi S">S Stefanović</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Blazier, J" uniqKey="Blazier J">J Blazier</name></author><author><name sortKey="Guisinger, Mm" uniqKey="Guisinger M">MM Guisinger</name></author><author><name sortKey="Jansen, Rk" uniqKey="Jansen R">RK Jansen</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Weng, M L" uniqKey="Weng M">M-L Weng</name></author><author><name sortKey="Blazier, Jc" uniqKey="Blazier J">JC Blazier</name></author><author><name sortKey="Govindu, M" uniqKey="Govindu M">M Govindu</name></author><author><name sortKey="Jansen, Rk" uniqKey="Jansen R">RK Jansen</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Ranade, Ss" uniqKey="Ranade S">SS Ranade</name></author><author><name sortKey="Garcia Gil, Mr" uniqKey="Garcia Gil M">MR García-Gil</name></author><author><name sortKey="Rossell, Ja" uniqKey="Rossell J">JA Rosselló</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Ruhlman, Ta" uniqKey="Ruhlman T">TA Ruhlman</name></author><author><name sortKey="Chang, Wj" uniqKey="Chang W">WJ Chang</name></author><author><name sortKey="Chen, Jj" uniqKey="Chen J">JJ Chen</name></author><author><name sortKey="Huang, Yt" uniqKey="Huang Y">YT Huang</name></author><author><name sortKey="Chan, Mt" uniqKey="Chan M">MT Chan</name></author><author><name sortKey="Zhang, J" uniqKey="Zhang J">J Zhang</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Takabayashi, A" uniqKey="Takabayashi A">A Takabayashi</name></author><author><name sortKey="Endo, T" uniqKey="Endo T">T Endo</name></author><author><name sortKey="Shikanai, T" uniqKey="Shikanai T">T Shikanai</name></author><author><name sortKey="Sato, F" uniqKey="Sato F">F Sato</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Burrows, Pa" uniqKey="Burrows P">PA Burrows</name></author><author><name sortKey="Sazanov, La" uniqKey="Sazanov L">LA Sazanov</name></author><author><name sortKey="Svab, Z" uniqKey="Svab Z">Z Svab</name></author><author><name sortKey="Maliga, P" uniqKey="Maliga P">P Maliga</name></author><author><name sortKey="Nixon, Pj" uniqKey="Nixon P">PJ Nixon</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Kofer, W" uniqKey="Kofer W">W Kofer</name></author><author><name sortKey="Koop, H U" uniqKey="Koop H">H-U Koop</name></author><author><name sortKey="Wanner, G" uniqKey="Wanner G">G Wanner</name></author><author><name sortKey="Steinmuller, K" uniqKey="Steinmuller K">K Steinmüller</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Shikanai, T" uniqKey="Shikanai T">T Shikanai</name></author><author><name sortKey="Endo, T" uniqKey="Endo T">T Endo</name></author><author><name sortKey="Hashimoto, T" uniqKey="Hashimoto T">T Hashimoto</name></author><author><name sortKey="Yamada, Y" uniqKey="Yamada Y">Y Yamada</name></author><author><name sortKey="Asada, K" uniqKey="Asada K">K Asada</name></author><author><name sortKey="Yokota, A" uniqKey="Yokota A">A Yokota</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Jin, S" uniqKey="Jin S">S Jin</name></author><author><name sortKey="Daniell, H" uniqKey="Daniell H">H Daniell</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Daniell, H" uniqKey="Daniell H">H Daniell</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Dheeraj, V" uniqKey="Dheeraj V">V Dheeraj</name></author><author><name sortKey="Daniell, H" uniqKey="Daniell H">H Daniell</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Dunne, A" uniqKey="Dunne A">A Dunne</name></author><author><name sortKey="Maple R Dem, J" uniqKey="Maple R Dem J">J Maple‐Grødem</name></author><author><name sortKey="Gargano, D" uniqKey="Gargano D">D Gargano</name></author><author><name sortKey="Haslam, Rp" uniqKey="Haslam R">RP Haslam</name></author><author><name sortKey="Napier, Ja" uniqKey="Napier J">JA Napier</name></author><author><name sortKey="Chua, Nh" uniqKey="Chua N">NH Chua</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Kavanagh, Ta" uniqKey="Kavanagh T">TA Kavanagh</name></author><author><name sortKey="Thanh, Nd" uniqKey="Thanh N">ND Thanh</name></author><author><name sortKey="Lao, Nt" uniqKey="Lao N">NT Lao</name></author><author><name sortKey="Mcgrath, N" uniqKey="Mcgrath N">N McGrath</name></author><author><name sortKey="Peter, So" uniqKey="Peter S">SO Peter</name></author><author><name sortKey="Horvath, Em" uniqKey="Horvath E">EM Horváth</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Guda, C" uniqKey="Guda C">C Guda</name></author><author><name sortKey="Lee, Sb" uniqKey="Lee S">SB Lee</name></author><author><name sortKey="Daniell, H" uniqKey="Daniell H">H Daniell</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Ruhlman, T" uniqKey="Ruhlman T">T Ruhlman</name></author><author><name sortKey="Verma, D" uniqKey="Verma D">D Verma</name></author><author><name sortKey="Samson, N" uniqKey="Samson N">N Samson</name></author><author><name sortKey="Daniell, H" uniqKey="Daniell H">H Daniell</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Daniell, H" uniqKey="Daniell H">H Daniell</name></author><author><name sortKey="Datta, R" uniqKey="Datta R">R Datta</name></author><author><name sortKey="Varma, S" uniqKey="Varma S">S Varma</name></author><author><name sortKey="Gray, S" uniqKey="Gray S">S Gray</name></author><author><name sortKey="Lee, Sb" uniqKey="Lee S">SB Lee</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Krichevsky, A" uniqKey="Krichevsky A">A Krichevsky</name></author><author><name sortKey="Meyers, B" uniqKey="Meyers B">B Meyers</name></author><author><name sortKey="Vainstein, A" uniqKey="Vainstein A">A Vainstein</name></author><author><name sortKey="Maliga, P" uniqKey="Maliga P">P Maliga</name></author><author><name sortKey="Citovsky, V" uniqKey="Citovsky V">V Citovsky</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Daniell, H" uniqKey="Daniell H">H Daniell</name></author><author><name sortKey="Vivekananda, J" uniqKey="Vivekananda J">J Vivekananda</name></author><author><name sortKey="Nielsen, B" uniqKey="Nielsen B">B Nielsen</name></author><author><name sortKey="Ye, G" uniqKey="Ye G">G Ye</name></author><author><name sortKey="Tewari, K" uniqKey="Tewari K">K Tewari</name></author><author><name sortKey="Sanford, J" uniqKey="Sanford J">J Sanford</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Klein, Rr" uniqKey="Klein R">RR Klein</name></author><author><name sortKey="Mullet, Je" uniqKey="Mullet J">JE Mullet</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Wurbs, D" uniqKey="Wurbs D">D Wurbs</name></author><author><name sortKey="Ruf, S" uniqKey="Ruf S">S Ruf</name></author><author><name sortKey="Bock, R" uniqKey="Bock R">R Bock</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Mcbride, Ke" uniqKey="Mcbride K">KE McBride</name></author><author><name sortKey="Schaaf, Dj" uniqKey="Schaaf D">DJ Schaaf</name></author><author><name sortKey="Daley, M" uniqKey="Daley M">M Daley</name></author><author><name sortKey="Stalker, Dm" uniqKey="Stalker D">DM Stalker</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Kumar, S" uniqKey="Kumar S">S Kumar</name></author><author><name sortKey="Dhingra, A" uniqKey="Dhingra A">A Dhingra</name></author><author><name sortKey="Daniell, H" uniqKey="Daniell H">H Daniell</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Dhingra, A" uniqKey="Dhingra A">A Dhingra</name></author><author><name sortKey="Portis, Ar" uniqKey="Portis A">AR Portis</name></author><author><name sortKey="Daniell, H" uniqKey="Daniell H">H Daniell</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="De Cosa, B" uniqKey="De Cosa B">B De Cosa</name></author><author><name sortKey="Moar, W" uniqKey="Moar W">W Moar</name></author><author><name sortKey="Lee, Sb" uniqKey="Lee S">SB Lee</name></author><author><name sortKey="Miller, M" uniqKey="Miller M">M Miller</name></author><author><name sortKey="Daniell, H" uniqKey="Daniell H">H Daniell</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Ruf, S" uniqKey="Ruf S">S Ruf</name></author><author><name sortKey="Hermann, M" uniqKey="Hermann M">M Hermann</name></author><author><name sortKey="Berger, Ij" uniqKey="Berger I">IJ Berger</name></author><author><name sortKey="Carrer, H" uniqKey="Carrer H">H Carrer</name></author><author><name sortKey="Bock, R" uniqKey="Bock R">R Bock</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Zhou, F" uniqKey="Zhou F">F Zhou</name></author><author><name sortKey="Badillo Corona, Ja" uniqKey="Badillo Corona J">JA Badillo-Corona</name></author><author><name sortKey="Karcher, D" uniqKey="Karcher D">D Karcher</name></author><author><name sortKey="Gonzalez Rabade, N" uniqKey="Gonzalez Rabade N">N Gonzalez-Rabade</name></author><author><name sortKey="Piepenburg, K" uniqKey="Piepenburg K">K Piepenburg</name></author><author><name sortKey="Borchers, Am" uniqKey="Borchers A">AM Borchers</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Lee, Sb" uniqKey="Lee S">SB Lee</name></author><author><name sortKey="Li, B" uniqKey="Li B">B Li</name></author><author><name sortKey="Jin, S" uniqKey="Jin S">S Jin</name></author><author><name sortKey="Daniell, H" uniqKey="Daniell H">H Daniell</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Jin, S" uniqKey="Jin S">S Jin</name></author><author><name sortKey="Kanagaraj, A" uniqKey="Kanagaraj A">A Kanagaraj</name></author><author><name sortKey="Verma, D" uniqKey="Verma D">D Verma</name></author><author><name sortKey="Lange, T" uniqKey="Lange T">T Lange</name></author><author><name sortKey="Daniell, H" uniqKey="Daniell H">H Daniell</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Jin, S" uniqKey="Jin S">S Jin</name></author><author><name sortKey="Zhang, X" uniqKey="Zhang X">X Zhang</name></author><author><name sortKey="Daniell, H" uniqKey="Daniell H">H Daniell</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Liu, Cw" uniqKey="Liu C">CW Liu</name></author><author><name sortKey="Lin, Cc" uniqKey="Lin C">CC Lin</name></author><author><name sortKey="Chen, Jj" uniqKey="Chen J">JJ Chen</name></author><author><name sortKey="Tseng, Mj" uniqKey="Tseng M">MJ Tseng</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Dufourmantel, N" uniqKey="Dufourmantel N">N Dufourmantel</name></author><author><name sortKey="Pelissier, B" uniqKey="Pelissier B">B Pelissier</name></author><author><name sortKey="Garcon, F" uniqKey="Garcon F">F Garcon</name></author><author><name sortKey="Peltier, G" uniqKey="Peltier G">G Peltier</name></author><author><name sortKey="Ferullo, Jm" uniqKey="Ferullo J">JM Ferullo</name></author><author><name sortKey="Tissot, G" uniqKey="Tissot G">G Tissot</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Dufourmantel, N" uniqKey="Dufourmantel N">N Dufourmantel</name></author><author><name sortKey="Tissot, G" uniqKey="Tissot G">G Tissot</name></author><author><name sortKey="Goutorbe, F" uniqKey="Goutorbe F">F Goutorbe</name></author><author><name sortKey="Garcon, F" uniqKey="Garcon F">F Garcon</name></author><author><name sortKey="Muhr, C" uniqKey="Muhr C">C Muhr</name></author><author><name sortKey="Jansens, S" uniqKey="Jansens S">S Jansens</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Singh, Ak" uniqKey="Singh A">AK Singh</name></author><author><name sortKey="Verma, Ss" uniqKey="Verma S">SS Verma</name></author><author><name sortKey="Bansal, Kc" uniqKey="Bansal K">KC Bansal</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Jin, S" uniqKey="Jin S">S Jin</name></author><author><name sortKey="Singh, Nd" uniqKey="Singh N">ND Singh</name></author><author><name sortKey="Li, L" uniqKey="Li L">L Li</name></author><author><name sortKey="Zhang, X" uniqKey="Zhang X">X Zhang</name></author><author><name sortKey="Daniell, H" uniqKey="Daniell H">H Daniell</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Zhang, J" uniqKey="Zhang J">J Zhang</name></author><author><name sortKey="Khan, Sa" uniqKey="Khan S">SA Khan</name></author><author><name sortKey="Hasse, C" uniqKey="Hasse C">C Hasse</name></author><author><name sortKey="Ruf, S" uniqKey="Ruf S">S Ruf</name></author><author><name sortKey="Heckel, Dg" uniqKey="Heckel D">DG Heckel</name></author><author><name sortKey="Bock, R" uniqKey="Bock R">R Bock</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Viitanen, Pv" uniqKey="Viitanen P">PV Viitanen</name></author><author><name sortKey="Devine, Al" uniqKey="Devine A">AL Devine</name></author><author><name sortKey="Khan, Ms" uniqKey="Khan M">MS Khan</name></author><author><name sortKey="Deuel, Dl" uniqKey="Deuel D">DL Deuel</name></author><author><name sortKey="Van Dyk, De" uniqKey="Van Dyk D">DE Van Dyk</name></author><author><name sortKey="Daniell, H" uniqKey="Daniell H">H Daniell</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Verma, D" uniqKey="Verma D">D Verma</name></author><author><name sortKey="Kanagaraj, A" uniqKey="Kanagaraj A">A Kanagaraj</name></author><author><name sortKey="Jin, Sx" uniqKey="Jin S">SX Jin</name></author><author><name sortKey="Singh, Nd" uniqKey="Singh N">ND Singh</name></author><author><name sortKey="Kolattukudy, Pe" uniqKey="Kolattukudy P">PE Kolattukudy</name></author><author><name sortKey="Daniell, H" uniqKey="Daniell H">H Daniell</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Schneider, C" uniqKey="Schneider C">C Schneider</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Shintani, D" uniqKey="Shintani D">D Shintani</name></author><author><name sortKey="Dellapenna, D" uniqKey="Dellapenna D">D DellaPenna</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Jin, S" uniqKey="Jin S">S Jin</name></author><author><name sortKey="Daniell, H" uniqKey="Daniell H">H Daniell</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Apel, W" uniqKey="Apel W">W Apel</name></author><author><name sortKey="Bock, R" uniqKey="Bock R">R Bock</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Grabowski, H" uniqKey="Grabowski H">H Grabowski</name></author><author><name sortKey="Cockburn, I" uniqKey="Cockburn I">I Cockburn</name></author><author><name sortKey="Long, G" uniqKey="Long G">G Long</name></author></analytic></biblStruct><biblStruct></biblStruct><biblStruct><analytic><author><name sortKey="Holtz, Br" uniqKey="Holtz B">BR Holtz</name></author><author><name sortKey="Berquist, Br" uniqKey="Berquist B">BR Berquist</name></author><author><name sortKey="Bennett, Ld" uniqKey="Bennett L">LD Bennett</name></author><author><name sortKey="Kommineni, Vj" uniqKey="Kommineni V">VJ Kommineni</name></author><author><name sortKey="Munigunti, Rk" uniqKey="Munigunti R">RK Munigunti</name></author><author><name sortKey="White, El" uniqKey="White E">EL White</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Kwon, Kc" uniqKey="Kwon K">KC Kwon</name></author><author><name sortKey="Daniell, H" uniqKey="Daniell H">H Daniell</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="El Kaoutari, A" uniqKey="El Kaoutari A">A El Kaoutari</name></author><author><name sortKey="Armougom, F" uniqKey="Armougom F">F Armougom</name></author><author><name sortKey="Gordon, Ji" uniqKey="Gordon J">JI Gordon</name></author><author><name sortKey="Raoult, D" uniqKey="Raoult D">D Raoult</name></author><author><name sortKey="Henrissat, B" uniqKey="Henrissat B">B Henrissat</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Kwon, Kc" uniqKey="Kwon K">KC Kwon</name></author><author><name sortKey="Nityanandam, R" uniqKey="Nityanandam R">R Nityanandam</name></author><author><name sortKey="New, Js" uniqKey="New J">JS New</name></author><author><name sortKey="Daniell, H" uniqKey="Daniell H">H Daniell</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Shenoy, V" uniqKey="Shenoy V">V Shenoy</name></author><author><name sortKey="Kwon, Kc" uniqKey="Kwon K">KC Kwon</name></author><author><name sortKey="Rathinasabapathy, A" uniqKey="Rathinasabapathy A">A Rathinasabapathy</name></author><author><name sortKey="Lin, Sn" uniqKey="Lin S">SN Lin</name></author><author><name sortKey="Jin, Gy" uniqKey="Jin G">GY Jin</name></author><author><name sortKey="Song, Cj" uniqKey="Song C">CJ Song</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Kohli, N" uniqKey="Kohli N">N Kohli</name></author><author><name sortKey="Westerveld, Dr" uniqKey="Westerveld D">DR Westerveld</name></author><author><name sortKey="Ayache, Ac" uniqKey="Ayache A">AC Ayache</name></author><author><name sortKey="Verma, A" uniqKey="Verma A">A Verma</name></author><author><name sortKey="Shil, P" uniqKey="Shil P">P Shil</name></author><author><name sortKey="Prasad, T" uniqKey="Prasad T">T Prasad</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Chan, Ht" uniqKey="Chan H">HT Chan</name></author><author><name sortKey="Daniell, H" uniqKey="Daniell H">H Daniell</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Davoodi Semiromi, A" uniqKey="Davoodi Semiromi A">A Davoodi-Semiromi</name></author><author><name sortKey="Schreiber, M" uniqKey="Schreiber M">M Schreiber</name></author><author><name sortKey="Nalapalli, S" uniqKey="Nalapalli S">S Nalapalli</name></author><author><name sortKey="Verma, D" uniqKey="Verma D">D Verma</name></author><author><name sortKey="Singh, Nd" uniqKey="Singh N">ND Singh</name></author><author><name sortKey="Banks, Rk" uniqKey="Banks R">RK Banks</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Lakshmi, Ps" uniqKey="Lakshmi P">PS Lakshmi</name></author><author><name sortKey="Verma, D" uniqKey="Verma D">D Verma</name></author><author><name sortKey="Yang, X" uniqKey="Yang X">X Yang</name></author><author><name sortKey="Lloyd, B" uniqKey="Lloyd B">B Lloyd</name></author><author><name sortKey="Daniell, H" uniqKey="Daniell H">H Daniell</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Hagelberg, E" uniqKey="Hagelberg E">E Hagelberg</name></author><author><name sortKey="Hofreiter, M" uniqKey="Hofreiter M">M Hofreiter</name></author><author><name sortKey="Keyser, C" uniqKey="Keyser C">C Keyser</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Golenberg, Em" uniqKey="Golenberg E">EM Golenberg</name></author><author><name sortKey="Giannasi, De" uniqKey="Giannasi D">DE Giannasi</name></author><author><name sortKey="Clegg, Mt" uniqKey="Clegg M">MT Clegg</name></author><author><name sortKey="Smiley, Cj" uniqKey="Smiley C">CJ Smiley</name></author><author><name sortKey="Durbin, M" uniqKey="Durbin M">M Durbin</name></author><author><name sortKey="Henderson, D" uniqKey="Henderson D">D Henderson</name></author><author><name sortKey="Zurawski, G" uniqKey="Zurawski G">G Zurawski</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Rossell, Ja" uniqKey="Rossell J">JA Rosselló</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Zhu, A" uniqKey="Zhu A">A Zhu</name></author><author><name sortKey="Guo, W" uniqKey="Guo W">W Guo</name></author><author><name sortKey="Gupta, S" uniqKey="Gupta S">S Gupta</name></author><author><name sortKey="Fan, W" uniqKey="Fan W">W Fan</name></author><author><name sortKey="Mower, Jp" uniqKey="Mower J">JP Mower</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Von Kohn, C" uniqKey="Von Kohn C">C von Kohn</name></author><author><name sortKey="Kielkowska, A" uniqKey="Kielkowska A">A Kielkowska</name></author><author><name sortKey="Havey, Mj" uniqKey="Havey M">MJ Havey</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Nashima, K" uniqKey="Nashima K">K Nashima</name></author><author><name sortKey="Terakami, S" uniqKey="Terakami S">S Terakami</name></author><author><name sortKey="Nishitani, C" uniqKey="Nishitani C">C Nishitani</name></author><author><name sortKey="Kunihisa, M" uniqKey="Kunihisa M">M Kunihisa</name></author><author><name sortKey="Shoda, M" uniqKey="Shoda M">M Shoda</name></author><author><name sortKey="Takeuchi, M" uniqKey="Takeuchi M">M Takeuchi</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Downie, Sr" uniqKey="Downie S">SR Downie</name></author><author><name sortKey="Jansen, Rk" uniqKey="Jansen R">RK Jansen</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Liu, Y" uniqKey="Liu Y">Y Liu</name></author><author><name sortKey="Huo, N" uniqKey="Huo N">N Huo</name></author><author><name sortKey="Dong, L" uniqKey="Dong L">L Dong</name></author><author><name sortKey="Wang, Y" uniqKey="Wang Y">Y Wang</name></author><author><name sortKey="Zhang, S" uniqKey="Zhang S">S Zhang</name></author><author><name sortKey="Young, Ha" uniqKey="Young H">HA Young</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Schmitz Linneweber, C" uniqKey="Schmitz Linneweber C">C Schmitz-Linneweber</name></author><author><name sortKey="Regel, R" uniqKey="Regel R">R Regel</name></author><author><name sortKey="Du, Tg" uniqKey="Du T">TG Du</name></author><author><name sortKey="Hupfer, H" uniqKey="Hupfer H">H Hupfer</name></author><author><name sortKey="Herrmann, Rg" uniqKey="Herrmann R">RG Herrmann</name></author><author><name sortKey="Maier, Rm" uniqKey="Maier R">RM Maier</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Hu, Z Y" uniqKey="Hu Z">Z-Y Hu</name></author><author><name sortKey="Hua, W" uniqKey="Hua W">W Hua</name></author><author><name sortKey="Huang, S M" uniqKey="Huang S">S-M Huang</name></author><author><name sortKey="Wang, H Z" uniqKey="Wang H">H-Z Wang</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Yang, Jb" uniqKey="Yang J">JB Yang</name></author><author><name sortKey="Li, Dz" uniqKey="Li D">DZ Li</name></author><author><name sortKey="Li, Ht" uniqKey="Li H">HT Li</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Oh, H" uniqKey="Oh H">H Oh</name></author><author><name sortKey="Seo, B" uniqKey="Seo B">B Seo</name></author><author><name sortKey="Lee, S" uniqKey="Lee S">S Lee</name></author><author><name sortKey="Ahn, D H" uniqKey="Ahn D">D-H Ahn</name></author><author><name sortKey="Jo, E" uniqKey="Jo E">E Jo</name></author><author><name sortKey="Park, J K" uniqKey="Park J">J-K Park</name></author><author><name sortKey="Min, G S" uniqKey="Min G">G-S Min</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Jo, Yd" uniqKey="Jo Y">YD Jo</name></author><author><name sortKey="Park, J" uniqKey="Park J">J Park</name></author><author><name sortKey="Kim, J" uniqKey="Kim J">J Kim</name></author><author><name sortKey="Song, W" uniqKey="Song W">W Song</name></author><author><name sortKey="Hur, Cg" uniqKey="Hur C">CG Hur</name></author><author><name sortKey="Lee, Yh" uniqKey="Lee Y">YH Lee</name></author><author><name sortKey="Kang, Bc" uniqKey="Kang B">BC Kang</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Ming, R" uniqKey="Ming R">R Ming</name></author><author><name sortKey="Hou, S" uniqKey="Hou S">S Hou</name></author><author><name sortKey="Feng, Y" uniqKey="Feng Y">Y Feng</name></author><author><name sortKey="Yu, Q" uniqKey="Yu Q">Q Yu</name></author><author><name sortKey="Dionne Laporte, A" uniqKey="Dionne Laporte A">A Dionne-Laporte</name></author><author><name sortKey="Saw, Jh" uniqKey="Saw J">JH Saw</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Ku, C" uniqKey="Ku C">C Ku</name></author><author><name sortKey="Chung, Wc" uniqKey="Chung W">WC Chung</name></author><author><name sortKey="Chen, Ll" uniqKey="Chen L">LL Chen</name></author><author><name sortKey="Kuo, Ch" uniqKey="Kuo C">CH Kuo</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Mariac, C" uniqKey="Mariac C">C Mariac</name></author><author><name sortKey="Scarcelli, N" uniqKey="Scarcelli N">N Scarcelli</name></author><author><name sortKey="Pouzadou, J" uniqKey="Pouzadou J">J Pouzadou</name></author><author><name sortKey="Barnaud, A" uniqKey="Barnaud A">A Barnaud</name></author><author><name sortKey="Billot, C" uniqKey="Billot C">C Billot</name></author><author><name sortKey="Faye, A" uniqKey="Faye A">A Faye</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Ahmed, I" uniqKey="Ahmed I">I Ahmed</name></author><author><name sortKey="Biggs, Pj" uniqKey="Biggs P">PJ Biggs</name></author><author><name sortKey="Matthews, Pj" uniqKey="Matthews P">PJ Matthews</name></author><author><name sortKey="Collins, Lj" uniqKey="Collins L">LJ Collins</name></author><author><name sortKey="Hendy, Md" uniqKey="Hendy M">MD Hendy</name></author><author><name sortKey="Lockhart, Pj" uniqKey="Lockhart P">PJ Lockhart</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Plader, W" uniqKey="Plader W">W Plader</name></author><author><name sortKey="Yukawa, Y" uniqKey="Yukawa Y">Y Yukawa</name></author><author><name sortKey="Sugiura, M" uniqKey="Sugiura M">M Sugiura</name></author><author><name sortKey="Malepszy, S" uniqKey="Malepszy S">S Malepszy</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Barrett, Cf" uniqKey="Barrett C">CF Barrett</name></author><author><name sortKey="Specht, Cd" uniqKey="Specht C">CD Specht</name></author><author><name sortKey="Leebens Mack, J" uniqKey="Leebens Mack J">J Leebens-Mack</name></author><author><name sortKey="Stevenson, Dw" uniqKey="Stevenson D">DW Stevenson</name></author><author><name sortKey="Zomlefer, Wb" uniqKey="Zomlefer W">WB Zomlefer</name></author><author><name sortKey="Davis, Ji" uniqKey="Davis J">JI Davis</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Wang, B" uniqKey="Wang B">B Wang</name></author><author><name sortKey="Han, L" uniqKey="Han L">L Han</name></author><author><name sortKey="Chen, C" uniqKey="Chen C">C Chen</name></author><author><name sortKey="Wang, Z" uniqKey="Wang Z">Z Wang</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Ye, Cy" uniqKey="Ye C">CY Ye</name></author><author><name sortKey="Lin, Z" uniqKey="Lin Z">Z Lin</name></author><author><name sortKey="Li, G" uniqKey="Li G">G Li</name></author><author><name sortKey="Wang, Yy" uniqKey="Wang Y">YY Wang</name></author><author><name sortKey="Qiu, J" uniqKey="Qiu J">J Qiu</name></author><author><name sortKey="Fu, F" uniqKey="Fu F">F Fu</name></author><author><name sortKey="Zhang, H" uniqKey="Zhang H">H Zhang</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Wu, Cs" uniqKey="Wu C">CS Wu</name></author><author><name sortKey="Lai, Yt" uniqKey="Lai Y">YT Lai</name></author><author><name sortKey="Lin, Cp" uniqKey="Lin C">CP Lin</name></author><author><name sortKey="Wang, Yn" uniqKey="Wang Y">YN Wang</name></author><author><name sortKey="Chaw, Sm" uniqKey="Chaw S">SM Chaw</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Logacheva, Md" uniqKey="Logacheva M">MD Logacheva</name></author><author><name sortKey="Samigullin, Th" uniqKey="Samigullin T">TH Samigullin</name></author><author><name sortKey="Dhingra, A" uniqKey="Dhingra A">A Dhingra</name></author><author><name sortKey="Penin, Aa" uniqKey="Penin A">AA Penin</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Cahoon, Ab" uniqKey="Cahoon A">AB Cahoon</name></author><author><name sortKey="Sharpe, Rm" uniqKey="Sharpe R">RM Sharpe</name></author><author><name sortKey="Mysayphonh, C" uniqKey="Mysayphonh C">C Mysayphonh</name></author><author><name sortKey="Thompson, Ej" uniqKey="Thompson E">EJ Thompson</name></author><author><name sortKey="Ward, Ad" uniqKey="Ward A">AD Ward</name></author><author><name sortKey="Lin, A" uniqKey="Lin A">A Lin</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Shulaev, V" uniqKey="Shulaev V">V Shulaev</name></author><author><name sortKey="Sargent, Dj" uniqKey="Sargent D">DJ Sargent</name></author><author><name sortKey="Crowhurst, Rn" uniqKey="Crowhurst R">RN Crowhurst</name></author><author><name sortKey="Mockler, Tc" uniqKey="Mockler T">TC Mockler</name></author><author><name sortKey="Folkerts, O" uniqKey="Folkerts O">O Folkerts</name></author><author><name sortKey="Delcher, Al" uniqKey="Delcher A">AL Delcher</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Dempewolf, H" uniqKey="Dempewolf H">H Dempewolf</name></author><author><name sortKey="Kane, Nc" uniqKey="Kane N">NC Kane</name></author><author><name sortKey="Ostevik, Kl" uniqKey="Ostevik K">KL Ostevik</name></author><author><name sortKey="Geleta, M" uniqKey="Geleta M">M Geleta</name></author><author><name sortKey="Barker, Ms" uniqKey="Barker M">MS Barker</name></author><author><name sortKey="Lai, Z" uniqKey="Lai Z">Z Lai</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Timme, Re" uniqKey="Timme R">RE Timme</name></author><author><name sortKey="Kuehl, Jv" uniqKey="Kuehl J">JV Kuehl</name></author><author><name sortKey="Boore, Jl" uniqKey="Boore J">JL Boore</name></author><author><name sortKey="Jansen, Rk" uniqKey="Jansen R">RK Jansen</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Barrett, Cf" uniqKey="Barrett C">CF Barrett</name></author><author><name sortKey="Davis, Ji" uniqKey="Davis J">JI Davis</name></author><author><name sortKey="Leebens Ack, J" uniqKey="Leebens Ack J">J Leebens‐Mack</name></author><author><name sortKey="Conran, Jg" uniqKey="Conran J">JG Conran</name></author><author><name sortKey="Stevenson, Dw" uniqKey="Stevenson D">DW Stevenson</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Sanchez Puerta, Mv" uniqKey="Sanchez Puerta M">MV Sanchez-Puerta</name></author><author><name sortKey="Abbona, Cc" uniqKey="Abbona C">CC Abbona</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Yan, L" uniqKey="Yan L">L Yan</name></author><author><name sortKey="Lai, X" uniqKey="Lai X">X Lai</name></author><author><name sortKey="Li, X" uniqKey="Li X">X Li</name></author><author><name sortKey="Wei, C" uniqKey="Wei C">C Wei</name></author><author><name sortKey="Tan, X" uniqKey="Tan X">X Tan</name></author><author><name sortKey="Zhang, Y" uniqKey="Zhang Y">Y Zhang</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Mcneal, Jr" uniqKey="Mcneal J">JR McNeal</name></author><author><name sortKey="Kuehl, Jv" uniqKey="Kuehl J">JV Kuehl</name></author><author><name sortKey="Boore, Jl" uniqKey="Boore J">JL Boore</name></author><author><name sortKey="De Pamphilis, Cw" uniqKey="De Pamphilis C">CW de Pamphilis</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Kanamoto, H" uniqKey="Kanamoto H">H Kanamoto</name></author><author><name sortKey="Yamashita, A" uniqKey="Yamashita A">A Yamashita</name></author><author><name sortKey="Asao, H" uniqKey="Asao H">H Asao</name></author><author><name sortKey="Okumura, S" uniqKey="Okumura S">S Okumura</name></author><author><name sortKey="Takase, H" uniqKey="Takase H">H Takase</name></author><author><name sortKey="Hattori, M" uniqKey="Hattori M">M Hattori</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Mennes, Cb" uniqKey="Mennes C">CB Mennes</name></author><author><name sortKey="Lam, Vk" uniqKey="Lam V">VK Lam</name></author><author><name sortKey="Rudall, Pj" uniqKey="Rudall P">PJ Rudall</name></author><author><name sortKey="Lyon, Sp" uniqKey="Lyon S">SP Lyon</name></author><author><name sortKey="Graham, Sw" uniqKey="Graham S">SW Graham</name></author><author><name sortKey="Smets, Ef" uniqKey="Smets E">EF Smets</name></author><author><name sortKey="Merckx, Vs" uniqKey="Merckx V">VS Merckx</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Hand, Ml" uniqKey="Hand M">ML Hand</name></author><author><name sortKey="Spangenberg, Gc" uniqKey="Spangenberg G">GC Spangenberg</name></author><author><name sortKey="Forster, Jw" uniqKey="Forster J">JW Forster</name></author><author><name sortKey="Cogan, No" uniqKey="Cogan N">NO Cogan</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Kato, T" uniqKey="Kato T">T Kato</name></author><author><name sortKey="Kaneko, T" uniqKey="Kaneko T">T Kaneko</name></author><author><name sortKey="Sato, S" uniqKey="Sato S">S Sato</name></author><author><name sortKey="Nakamura, Y" uniqKey="Nakamura Y">Y Nakamura</name></author><author><name sortKey="Tabata, S" uniqKey="Tabata S">S Tabata</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Raubeson, La" uniqKey="Raubeson L">LA Raubeson</name></author><author><name sortKey="Peery, R" uniqKey="Peery R">R Peery</name></author><author><name sortKey="Chumley, Tw" uniqKey="Chumley T">TW Chumley</name></author><author><name sortKey="Dziubek, C" uniqKey="Dziubek C">C Dziubek</name></author><author><name sortKey="Fourcade, Hm" uniqKey="Fourcade H">HM Fourcade</name></author><author><name sortKey="Boore, Jl" uniqKey="Boore J">JL Boore</name></author><author><name sortKey="Jansen, Rk" uniqKey="Jansen R">RK Jansen</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Hiratsuka, J" uniqKey="Hiratsuka J">J Hiratsuka</name></author><author><name sortKey="Shimada, H" uniqKey="Shimada H">H Shimada</name></author><author><name sortKey="Whittier, R" uniqKey="Whittier R">R Whittier</name></author><author><name sortKey="Ishibashi, T" uniqKey="Ishibashi T">T Ishibashi</name></author><author><name sortKey="Sakamoto, M" uniqKey="Sakamoto M">M Sakamoto</name></author><author><name sortKey="Mori, M" uniqKey="Mori M">M Mori</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Kim, Kj" uniqKey="Kim K">KJ Kim</name></author><author><name sortKey="Lee, Hl" uniqKey="Lee H">HL Lee</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Young, Ha" uniqKey="Young H">HA Young</name></author><author><name sortKey="Lanzatella, Cl" uniqKey="Lanzatella C">CL Lanzatella</name></author><author><name sortKey="Sarath, G" uniqKey="Sarath G">G Sarath</name></author><author><name sortKey="Tobias, Cm" uniqKey="Tobias C">CM Tobias</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Kumar, S" uniqKey="Kumar S">S Kumar</name></author><author><name sortKey="Hahn, Fm" uniqKey="Hahn F">FM Hahn</name></author><author><name sortKey="Mcmahan, Cm" uniqKey="Mcmahan C">CM McMahan</name></author><author><name sortKey="Cornish, K" uniqKey="Cornish K">K Cornish</name></author><author><name sortKey="Whalen, Mc" uniqKey="Whalen M">MC Whalen</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Chumley, Tw" uniqKey="Chumley T">TW Chumley</name></author><author><name sortKey="Palmer, Jd" uniqKey="Palmer J">JD Palmer</name></author><author><name sortKey="Mower, Jp" uniqKey="Mower J">JP Mower</name></author><author><name sortKey="Fourcade, Hm" uniqKey="Fourcade H">HM Fourcade</name></author><author><name sortKey="Calie, Pj" uniqKey="Calie P">PJ Calie</name></author><author><name sortKey="Boore, Jl" uniqKey="Boore J">JL Boore</name></author><author><name sortKey="Jansen, Rk" uniqKey="Jansen R">RK Jansen</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Jeong, Ym" uniqKey="Jeong Y">YM Jeong</name></author><author><name sortKey="Chung, Wh" uniqKey="Chung W">WH Chung</name></author><author><name sortKey="Mun, Jh" uniqKey="Mun J">JH Mun</name></author><author><name sortKey="Kim, N" uniqKey="Kim N">N Kim</name></author><author><name sortKey="Yu, Hj" uniqKey="Yu H">HJ Yu</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Rivarola, M" uniqKey="Rivarola M">M Rivarola</name></author><author><name sortKey="Foster, Jt" uniqKey="Foster J">JT Foster</name></author><author><name sortKey="Chan, Ap" uniqKey="Chan A">AP Chan</name></author><author><name sortKey="Williams, Al" uniqKey="Williams A">AL Williams</name></author><author><name sortKey="Rice, Dw" uniqKey="Rice D">DW Rice</name></author><author><name sortKey="Liu, X" uniqKey="Liu X">X Liu</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Calsa Junior, T" uniqKey="Calsa Junior T">T Calsa Junior</name></author><author><name sortKey="Carraro, Dm" uniqKey="Carraro D">DM Carraro</name></author><author><name sortKey="Benatti, Mr" uniqKey="Benatti M">MR Benatti</name></author><author><name sortKey="Barbosa, Ac" uniqKey="Barbosa A">AC Barbosa</name></author><author><name sortKey="Kitajima, Jp" uniqKey="Kitajima J">JP Kitajima</name></author><author><name sortKey="Carrer, H" uniqKey="Carrer H">H Carrer</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Qian, J" uniqKey="Qian J">J Qian</name></author><author><name sortKey="Song, J" uniqKey="Song J">J Song</name></author><author><name sortKey="Gao, H" uniqKey="Gao H">H Gao</name></author><author><name sortKey="Zhu, Y" uniqKey="Zhu Y">Y Zhu</name></author><author><name sortKey="Xu, J" uniqKey="Xu J">J Xu</name></author><author><name sortKey="Pang, X" uniqKey="Pang X">X Pang</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Yi, Dk" uniqKey="Yi D">DK Yi</name></author><author><name sortKey="Kim, Kj" uniqKey="Kim K">KJ Kim</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Chung, Hj" uniqKey="Chung H">HJ Chung</name></author><author><name sortKey="Jung, Jd" uniqKey="Jung J">JD Jung</name></author><author><name sortKey="Park, Hw" uniqKey="Park H">HW Park</name></author><author><name sortKey="Kim, Jh" uniqKey="Kim J">JH Kim</name></author><author><name sortKey="Cha, Hw" uniqKey="Cha H">HW Cha</name></author><author><name sortKey="Min, Sr" uniqKey="Min S">SR Min</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Schmitz Linneweber, C" uniqKey="Schmitz Linneweber C">C Schmitz-Linneweber</name></author><author><name sortKey="Maier, Rm" uniqKey="Maier R">RM Maier</name></author><author><name sortKey="Alcaraz, Jp" uniqKey="Alcaraz J">JP Alcaraz</name></author><author><name sortKey="Cottet, A" uniqKey="Cottet A">A Cottet</name></author><author><name sortKey="Herrmann, Rg" uniqKey="Herrmann R">RG Herrmann</name></author><author><name sortKey="Mache, R" uniqKey="Mache R">R Mache</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Yi, Dk" uniqKey="Yi D">DK Yi</name></author><author><name sortKey="Yang, Jc" uniqKey="Yang J">JC Yang</name></author><author><name sortKey="So, S" uniqKey="So S">S So</name></author><author><name sortKey="Joo, M" uniqKey="Joo M">M Joo</name></author><author><name sortKey="Kim, Dk" uniqKey="Kim D">DK Kim</name></author><author><name sortKey="Shin, Ch" uniqKey="Shin C">CH Shin</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Yao, X" uniqKey="Yao X">X Yao</name></author><author><name sortKey="Tang, P" uniqKey="Tang P">P Tang</name></author><author><name sortKey="Li, Z" uniqKey="Li Z">Z Li</name></author><author><name sortKey="Li, D" uniqKey="Li D">D Li</name></author><author><name sortKey="Liu, Y" uniqKey="Liu Y">Y Liu</name></author><author><name sortKey="Huang, H" uniqKey="Huang H">H Huang</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Hsu, Cy" uniqKey="Hsu C">CY Hsu</name></author><author><name sortKey="Wu, Cs" uniqKey="Wu C">CS Wu</name></author><author><name sortKey="Chaw, Sm" uniqKey="Chaw S">SM Chaw</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Ruhsam, M" uniqKey="Ruhsam M">M Ruhsam</name></author><author><name sortKey="Rai, Hs" uniqKey="Rai H">HS Rai</name></author><author><name sortKey="Mathews, S" uniqKey="Mathews S">S Mathews</name></author><author><name sortKey="Ross, Tg" uniqKey="Ross T">TG Ross</name></author><author><name sortKey="Graham, Sw" uniqKey="Graham S">SW Graham</name></author><author><name sortKey="Raubeson, La" uniqKey="Raubeson L">LA Raubeson</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Ma, J" uniqKey="Ma J">J Ma</name></author><author><name sortKey="Yang, B" uniqKey="Yang B">B Yang</name></author><author><name sortKey="Zhu, W" uniqKey="Zhu W">W Zhu</name></author><author><name sortKey="Sun, L" uniqKey="Sun L">L Sun</name></author><author><name sortKey="Tian, J" uniqKey="Tian J">J Tian</name></author><author><name sortKey="Wang, X" uniqKey="Wang X">X Wang</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Hansen, Dr" uniqKey="Hansen D">DR Hansen</name></author><author><name sortKey="Dastidar, Sg" uniqKey="Dastidar S">SG Dastidar</name></author><author><name sortKey="Cai, Z" uniqKey="Cai Z">Z Cai</name></author><author><name sortKey="Penaflor, C" uniqKey="Penaflor C">C Penaflor</name></author><author><name sortKey="Kuehl, Jv" uniqKey="Kuehl J">JV Kuehl</name></author><author><name sortKey="Boore, Jl" uniqKey="Boore J">JL Boore</name></author><author><name sortKey="Jansen, Rk" uniqKey="Jansen R">RK Jansen</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Wu, Cs" uniqKey="Wu C">CS Wu</name></author><author><name sortKey="Chaw, Sm" uniqKey="Chaw S">SM Chaw</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Shi, C" uniqKey="Shi C">C Shi</name></author><author><name sortKey="Liu, Y" uniqKey="Liu Y">Y Liu</name></author><author><name sortKey="Huang, H" uniqKey="Huang H">H Huang</name></author><author><name sortKey="Xia, Eh" uniqKey="Xia E">EH Xia</name></author><author><name sortKey="Zhang, Hb" uniqKey="Zhang H">HB Zhang</name></author><author><name sortKey="Gao, Lz" uniqKey="Gao L">LZ Gao</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Huang, H" uniqKey="Huang H">H Huang</name></author><author><name sortKey="Shi, C" uniqKey="Shi C">C Shi</name></author><author><name sortKey="Liu, Y" uniqKey="Liu Y">Y Liu</name></author><author><name sortKey="Mao, Sy" uniqKey="Mao S">SY Mao</name></author><author><name sortKey="Gao, Lz" uniqKey="Gao L">LZ Gao</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Lin, Cp" uniqKey="Lin C">CP Lin</name></author><author><name sortKey="Huang, Jp" uniqKey="Huang J">JP Huang</name></author><author><name sortKey="Wu, Cs" uniqKey="Wu C">CS Wu</name></author><author><name sortKey="Hsu, Cy" uniqKey="Hsu C">CY Hsu</name></author><author><name sortKey="Chaw, Sm" uniqKey="Chaw S">SM Chaw</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Wu, Cs" uniqKey="Wu C">CS Wu</name></author><author><name sortKey="Wang, Yn" uniqKey="Wang Y">YN Wang</name></author><author><name sortKey="Hsu, Cy" uniqKey="Hsu C">CY Hsu</name></author><author><name sortKey="Lin, Cp" uniqKey="Lin C">CP Lin</name></author><author><name sortKey="Chaw, Sm" uniqKey="Chaw S">SM Chaw</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Male, Pj" uniqKey="Male P">PJ Male</name></author><author><name sortKey="Bardon, L" uniqKey="Bardon L">L Bardon</name></author><author><name sortKey="Besnard, G" uniqKey="Besnard G">G Besnard</name></author><author><name sortKey="Coissac, E" uniqKey="Coissac E">E Coissac</name></author><author><name sortKey="Delsuc, F" uniqKey="Delsuc F">F Delsuc</name></author><author><name sortKey="Engel, J" uniqKey="Engel J">J Engel</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Huang, Yy" uniqKey="Huang Y">YY Huang</name></author><author><name sortKey="Matzke, Aj" uniqKey="Matzke A">AJ Matzke</name></author><author><name sortKey="Matzke, M" uniqKey="Matzke M">M Matzke</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Bayly, Mj" uniqKey="Bayly M">MJ Bayly</name></author><author><name sortKey="Rigault, P" uniqKey="Rigault P">P Rigault</name></author><author><name sortKey="Spokevicius, A" uniqKey="Spokevicius A">A Spokevicius</name></author><author><name sortKey="Ladiges, Py" uniqKey="Ladiges P">PY Ladiges</name></author><author><name sortKey="Ades, Pk" uniqKey="Ades P">PK Ades</name></author><author><name sortKey="Anderson, C" uniqKey="Anderson C">C Anderson</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Hirao, T" uniqKey="Hirao T">T Hirao</name></author><author><name sortKey="Watanabe, A" uniqKey="Watanabe A">A Watanabe</name></author><author><name sortKey="Kurita, M" uniqKey="Kurita M">M Kurita</name></author><author><name sortKey="Kondo, T" uniqKey="Kondo T">T Kondo</name></author><author><name sortKey="Takata, K" uniqKey="Takata K">K Takata</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Uthaipaisanwong, P" uniqKey="Uthaipaisanwong P">P Uthaipaisanwong</name></author><author><name sortKey="Chanprasert, J" uniqKey="Chanprasert J">J Chanprasert</name></author><author><name sortKey="Shearman, Jr" uniqKey="Shearman J">JR Shearman</name></author><author><name sortKey="Sangsrakru, D" uniqKey="Sangsrakru D">D Sangsrakru</name></author><author><name sortKey="Yoocha, T" uniqKey="Yoocha T">T Yoocha</name></author><author><name sortKey="Jomchai, N" uniqKey="Jomchai N">N Jomchai</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Steane, D" uniqKey="Steane D">D Steane</name></author><author><name sortKey="Jones, R" uniqKey="Jones R">R Jones</name></author><author><name sortKey="Vaillancourt, R" uniqKey="Vaillancourt R">R Vaillancourt</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Tangphatsornruang, S" uniqKey="Tangphatsornruang S">S Tangphatsornruang</name></author><author><name sortKey="Uthaipaisanwong, P" uniqKey="Uthaipaisanwong P">P Uthaipaisanwong</name></author><author><name sortKey="Sangsrakru, D" uniqKey="Sangsrakru D">D Sangsrakru</name></author><author><name sortKey="Chanprasert, J" uniqKey="Chanprasert J">J Chanprasert</name></author><author><name sortKey="Yoocha, T" uniqKey="Yoocha T">T Yoocha</name></author><author><name sortKey="Jomchai, N" uniqKey="Jomchai N">N Jomchai</name></author><author><name sortKey="Tragoonrung, S" uniqKey="Tragoonrung S">S Tragoonrung</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Lee, Hl" uniqKey="Lee H">HL Lee</name></author><author><name sortKey="Jansen, Rk" uniqKey="Jansen R">RK Jansen</name></author><author><name sortKey="Chumley, Tw" uniqKey="Chumley T">TW Chumley</name></author><author><name sortKey="Kim, Kj" uniqKey="Kim K">KJ Kim</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Asif, Mh" uniqKey="Asif M">MH Asif</name></author><author><name sortKey="Mantri, Ss" uniqKey="Mantri S">SS Mantri</name></author><author><name sortKey="Sharma, A" uniqKey="Sharma A">A Sharma</name></author><author><name sortKey="Srivastava, A" uniqKey="Srivastava A">A Srivastava</name></author><author><name sortKey="Trivedi, I" uniqKey="Trivedi I">I Trivedi</name></author><author><name sortKey="Gupta, P" uniqKey="Gupta P">P Gupta</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Guo, W" uniqKey="Guo W">W Guo</name></author><author><name sortKey="Grewe, F" uniqKey="Grewe F">F Grewe</name></author><author><name sortKey="Cobo Clark, A" uniqKey="Cobo Clark A">A Cobo-Clark</name></author><author><name sortKey="Fan, W" uniqKey="Fan W">W Fan</name></author><author><name sortKey="Duan, Z" uniqKey="Duan Z">Z Duan</name></author><author><name sortKey="Adams, Rp" uniqKey="Adams R">RP Adams</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Cai, Z" uniqKey="Cai Z">Z Cai</name></author><author><name sortKey="Penaflor, C" uniqKey="Penaflor C">C Penaflor</name></author><author><name sortKey="Kuehl, Jv" uniqKey="Kuehl J">JV Kuehl</name></author><author><name sortKey="Leebens Mack, J" uniqKey="Leebens Mack J">J Leebens-Mack</name></author><author><name sortKey="Carlson, Je" uniqKey="Carlson J">JE Carlson</name></author><author><name sortKey="De Pamphilis, Cw" uniqKey="De Pamphilis C">CW de Pamphilis</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Chen, J" uniqKey="Chen J">J Chen</name></author><author><name sortKey="Hao, Z" uniqKey="Hao Z">Z Hao</name></author><author><name sortKey="Xu, H" uniqKey="Xu H">H Xu</name></author><author><name sortKey="Yang, L" uniqKey="Yang L">L Yang</name></author><author><name sortKey="Liu, G" uniqKey="Liu G">G Liu</name></author><author><name sortKey="Sheng, Y" uniqKey="Sheng Y">Y Sheng</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Ravi, V" uniqKey="Ravi V">V Ravi</name></author><author><name sortKey="Khurana, Jp" uniqKey="Khurana J">JP Khurana</name></author><author><name sortKey="Tyagi, Ak" uniqKey="Tyagi A">AK Tyagi</name></author><author><name sortKey="Khurana, P" uniqKey="Khurana P">P Khurana</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Straub, Sc" uniqKey="Straub S">SC Straub</name></author><author><name sortKey="Moore, Mj" uniqKey="Moore M">MJ Moore</name></author><author><name sortKey="Soltis, Ps" uniqKey="Soltis P">PS Soltis</name></author><author><name sortKey="Soltis, De" uniqKey="Soltis D">DE Soltis</name></author><author><name sortKey="Liston, A" uniqKey="Liston A">A Liston</name></author><author><name sortKey="Livshultz, T" uniqKey="Livshultz T">T Livshultz</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Besnard, G" uniqKey="Besnard G">G Besnard</name></author><author><name sortKey="Hernandez, P" uniqKey="Hernandez P">P Hernández</name></author><author><name sortKey="Khadari, B" uniqKey="Khadari B">B Khadari</name></author><author><name sortKey="Dorado, G" uniqKey="Dorado G">G Dorado</name></author><author><name sortKey="Savolainen, V" uniqKey="Savolainen V">V Savolainen</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Yang, M" uniqKey="Yang M">M Yang</name></author><author><name sortKey="Zhang, X" uniqKey="Zhang X">X Zhang</name></author><author><name sortKey="Liu, G" uniqKey="Liu G">G Liu</name></author><author><name sortKey="Yin, Y" uniqKey="Yin Y">Y Yin</name></author><author><name sortKey="Chen, K" uniqKey="Chen K">K Chen</name></author><author><name sortKey="Yun, Q" uniqKey="Yun Q">Q Yun</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Fang, Mf" uniqKey="Fang M">MF Fang</name></author><author><name sortKey="Wang, Yj" uniqKey="Wang Y">YJ Wang</name></author><author><name sortKey="Zu, Ym" uniqKey="Zu Y">YM Zu</name></author><author><name sortKey="Dong, Wl" uniqKey="Dong W">WL Dong</name></author><author><name sortKey="Wang, Rn" uniqKey="Wang R">RN Wang</name></author><author><name sortKey="Deng, Tt" uniqKey="Deng T">TT Deng</name></author><author><name sortKey="Li, Zh" uniqKey="Li Z">ZH Li</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Vieira Ldo, N" uniqKey="Vieira Ldo N">N Vieira Ldo</name></author><author><name sortKey="Faoro, H" uniqKey="Faoro H">H Faoro</name></author><author><name sortKey="Rogalski, M" uniqKey="Rogalski M">M Rogalski</name></author><author><name sortKey="Fraga, Hp" uniqKey="Fraga H">HP Fraga</name></author><author><name sortKey="Cardoso, Rl" uniqKey="Cardoso R">RL Cardoso</name></author><author><name sortKey="De Souza, Em" uniqKey="De Souza E">EM de Souza</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Okumura, S" uniqKey="Okumura S">S Okumura</name></author><author><name sortKey="Sawada, M" uniqKey="Sawada M">M Sawada</name></author><author><name sortKey="Park, Yw" uniqKey="Park Y">YW Park</name></author><author><name sortKey="Hayashi, T" uniqKey="Hayashi T">T Hayashi</name></author><author><name sortKey="Shimamura, M" uniqKey="Shimamura M">M Shimamura</name></author><author><name sortKey="Takase, H" uniqKey="Takase H">H Takase</name></author><author><name sortKey="Tomizawa, K" uniqKey="Tomizawa K">K Tomizawa</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Wang, S" uniqKey="Wang S">S Wang</name></author><author><name sortKey="Shi, C" uniqKey="Shi C">C Shi</name></author><author><name sortKey="Gao, Lz" uniqKey="Gao L">LZ Gao</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Terakami, S" uniqKey="Terakami S">S Terakami</name></author><author><name sortKey="Matsumura, Y" uniqKey="Matsumura Y">Y Matsumura</name></author><author><name sortKey="Kurita, K" uniqKey="Kurita K">K Kurita</name></author><author><name sortKey="Kanamori, H" uniqKey="Kanamori H">H Kanamori</name></author><author><name sortKey="Katayose, Y" uniqKey="Katayose Y">Y Katayose</name></author><author><name sortKey="Yamamoto, T" uniqKey="Yamamoto T">T Yamamoto</name></author><author><name sortKey="Katayama, H" uniqKey="Katayama H">H Katayama</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Alexander, Lw" uniqKey="Alexander L">LW Alexander</name></author><author><name sortKey="Woeste, Ke" uniqKey="Woeste K">KE Woeste</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Yang, B" uniqKey="Yang B">B Yang</name></author><author><name sortKey="Li, M" uniqKey="Li M">M Li</name></author><author><name sortKey="Ma, J" uniqKey="Ma J">J Ma</name></author><author><name sortKey="Fu, Z" uniqKey="Fu Z">Z Fu</name></author><author><name sortKey="Xu, X" uniqKey="Xu X">X Xu</name></author><author><name sortKey="Chen, Q" uniqKey="Chen Q">Q Chen</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Fajardo, D" uniqKey="Fajardo D">D Fajardo</name></author><author><name sortKey="Senalik, D" uniqKey="Senalik D">D Senalik</name></author><author><name sortKey="Ames, M" uniqKey="Ames M">M Ames</name></author><author><name sortKey="Zhu, H" uniqKey="Zhu H">H Zhu</name></author><author><name sortKey="Steffan, Sa" uniqKey="Steffan S">SA Steffan</name></author><author><name sortKey="Harbut, R" uniqKey="Harbut R">R Harbut</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Yap, Jy" uniqKey="Yap J">JY Yap</name></author><author><name sortKey="Rohner, T" uniqKey="Rohner T">T Rohner</name></author><author><name sortKey="Greenfield, A" uniqKey="Greenfield A">A Greenfield</name></author><author><name sortKey="Van Der Merwe, M" uniqKey="Van Der Merwe M">M Van Der Merwe</name></author><author><name sortKey="Mcpherson, H" uniqKey="Mcpherson H">H McPherson</name></author><author><name sortKey="Glenn, W" uniqKey="Glenn W">W Glenn</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Shaw, J" uniqKey="Shaw J">J Shaw</name></author><author><name sortKey="Lickey, Eb" uniqKey="Lickey E">EB Lickey</name></author><author><name sortKey="Beck, Jt" uniqKey="Beck J">JT Beck</name></author><author><name sortKey="Farmer, Sb" uniqKey="Farmer S">SB Farmer</name></author><author><name sortKey="Liu, W" uniqKey="Liu W">W Liu</name></author><author><name sortKey="Miller, J" uniqKey="Miller J">J Miller</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Ruhlman, Ta" uniqKey="Ruhlman T">TA Ruhlman</name></author><author><name sortKey="Rajasekaran, K" uniqKey="Rajasekaran K">K Rajasekaran</name></author><author><name sortKey="Cary, Jw" uniqKey="Cary J">JW Cary</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Chakrabarti, Sk" uniqKey="Chakrabarti S">SK Chakrabarti</name></author><author><name sortKey="Lutz, Ka" uniqKey="Lutz K">KA Lutz</name></author><author><name sortKey="Lertwiriyawong, B" uniqKey="Lertwiriyawong B">B Lertwiriyawong</name></author><author><name sortKey="Svab, Z" uniqKey="Svab Z">Z Svab</name></author><author><name sortKey="Maliga, P" uniqKey="Maliga P">P Maliga</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Degray, G" uniqKey="Degray G">G DeGray</name></author><author><name sortKey="Rajasekaran, K" uniqKey="Rajasekaran K">K Rajasekaran</name></author><author><name sortKey="Smith, F" uniqKey="Smith F">F Smith</name></author><author><name sortKey="Sanford, J" uniqKey="Sanford J">J Sanford</name></author><author><name sortKey="Daniell, H" uniqKey="Daniell H">H Daniell</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Chen, Pj" uniqKey="Chen P">PJ Chen</name></author><author><name sortKey="Senthilkumar, R" uniqKey="Senthilkumar R">R Senthilkumar</name></author><author><name sortKey="Jane, Wn" uniqKey="Jane W">WN Jane</name></author><author><name sortKey="He, Y" uniqKey="He Y">Y He</name></author><author><name sortKey="Tian, Z" uniqKey="Tian Z">Z Tian</name></author><author><name sortKey="Yeh, Kw" uniqKey="Yeh K">KW Yeh</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Wang, Yp" uniqKey="Wang Y">YP Wang</name></author><author><name sortKey="Wei, Zy" uniqKey="Wei Z">ZY Wei</name></author><author><name sortKey="Zhang, Yy" uniqKey="Zhang Y">YY Zhang</name></author><author><name sortKey="Lin, Cj" uniqKey="Lin C">CJ Lin</name></author><author><name sortKey="Zhong, Xf" uniqKey="Zhong X">XF Zhong</name></author><author><name sortKey="Wang, Yl" uniqKey="Wang Y">YL Wang</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Mcbride, Ke" uniqKey="Mcbride K">KE McBride</name></author><author><name sortKey="Svab, Z" uniqKey="Svab Z">Z Svab</name></author><author><name sortKey="Schaaf, Dj" uniqKey="Schaaf D">DJ Schaaf</name></author><author><name sortKey="Hogan, Ps" uniqKey="Hogan P">PS Hogan</name></author><author><name sortKey="Stalker, Dm" uniqKey="Stalker D">DM Stalker</name></author><author><name sortKey="Maliga, P" uniqKey="Maliga P">P Maliga</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Kota, M" uniqKey="Kota M">M Kota</name></author><author><name sortKey="Daniell, H" uniqKey="Daniell H">H Daniell</name></author><author><name sortKey="Varma, S" uniqKey="Varma S">S Varma</name></author><author><name sortKey="Garczynski, Sf" uniqKey="Garczynski S">SF Garczynski</name></author><author><name sortKey="Gould, F" uniqKey="Gould F">F Gould</name></author><author><name sortKey="Moar, Wj" uniqKey="Moar W">WJ Moar</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Lee, Sb" uniqKey="Lee S">SB Lee</name></author><author><name sortKey="Kwon, Hb" uniqKey="Kwon H">HB Kwon</name></author><author><name sortKey="Kwon, Sj" uniqKey="Kwon S">SJ Kwon</name></author><author><name sortKey="Park, Sc" uniqKey="Park S">SC Park</name></author><author><name sortKey="Jeong, Mj" uniqKey="Jeong M">MJ Jeong</name></author><author><name sortKey="Han, Se" uniqKey="Han S">SE Han</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Ruiz, On" uniqKey="Ruiz O">ON Ruiz</name></author><author><name sortKey="Hussein, Hs" uniqKey="Hussein H">HS Hussein</name></author><author><name sortKey="Terry, N" uniqKey="Terry N">N Terry</name></author><author><name sortKey="Daniell, H" uniqKey="Daniell H">H Daniell</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Ruiz, On" uniqKey="Ruiz O">ON Ruiz</name></author><author><name sortKey="Alvarez, D" uniqKey="Alvarez D">D Alvarez</name></author><author><name sortKey="Torres, C" uniqKey="Torres C">C Torres</name></author><author><name sortKey="Roman, L" uniqKey="Roman L">L Roman</name></author><author><name sortKey="Daniell, H" uniqKey="Daniell H">H Daniell</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Lutz, Ka" uniqKey="Lutz K">KA Lutz</name></author><author><name sortKey="Knapp, Je" uniqKey="Knapp J">JE Knapp</name></author><author><name sortKey="Maliga, P" uniqKey="Maliga P">P Maliga</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Ye, Gn" uniqKey="Ye G">GN Ye</name></author><author><name sortKey="Hajdukiewicz, Pt" uniqKey="Hajdukiewicz P">PT Hajdukiewicz</name></author><author><name sortKey="Broyles, D" uniqKey="Broyles D">D Broyles</name></author><author><name sortKey="Rodriguez, D" uniqKey="Rodriguez D">D Rodriguez</name></author><author><name sortKey="Xu, Cw" uniqKey="Xu C">CW Xu</name></author><author><name sortKey="Nehra, N" uniqKey="Nehra N">N Nehra</name></author><author><name sortKey="Staub, Jm" uniqKey="Staub J">JM Staub</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Shimizu, M" uniqKey="Shimizu M">M Shimizu</name></author><author><name sortKey="Goto, M" uniqKey="Goto M">M Goto</name></author><author><name sortKey="Hanai, M" uniqKey="Hanai M">M Hanai</name></author><author><name sortKey="Shimizu, T" uniqKey="Shimizu T">T Shimizu</name></author><author><name sortKey="Izawa, N" uniqKey="Izawa N">N Izawa</name></author><author><name sortKey="Kanamoto, H" uniqKey="Kanamoto H">H Kanamoto</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Iamtham, S" uniqKey="Iamtham S">S Iamtham</name></author><author><name sortKey="Day, A" uniqKey="Day A">A Day</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Dufourmantel, N" uniqKey="Dufourmantel N">N Dufourmantel</name></author><author><name sortKey="Dubald, M" uniqKey="Dubald M">M Dubald</name></author><author><name sortKey="Matringe, M" uniqKey="Matringe M">M Matringe</name></author><author><name sortKey="Canard, H" uniqKey="Canard H">H Canard</name></author><author><name sortKey="Garcon, F" uniqKey="Garcon F">F Garcon</name></author><author><name sortKey="Job, C" uniqKey="Job C">C Job</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Fouad, Wm" uniqKey="Fouad W">WM Fouad</name></author><author><name sortKey="Altpeter, F" uniqKey="Altpeter F">F Altpeter</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Lu, Y" uniqKey="Lu Y">Y Lu</name></author><author><name sortKey="Rijzaani, H" uniqKey="Rijzaani H">H Rijzaani</name></author><author><name sortKey="Karcher, D" uniqKey="Karcher D">D Karcher</name></author><author><name sortKey="Ruf, S" uniqKey="Ruf S">S Ruf</name></author><author><name sortKey="Bock, R" uniqKey="Bock R">R Bock</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Ruiz, On" uniqKey="Ruiz O">ON Ruiz</name></author><author><name sortKey="Daniell, H" uniqKey="Daniell H">H Daniell</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Yabuta, Y" uniqKey="Yabuta Y">Y Yabuta</name></author><author><name sortKey="Tanaka, H" uniqKey="Tanaka H">H Tanaka</name></author><author><name sortKey="Yoshimura, S" uniqKey="Yoshimura S">S Yoshimura</name></author><author><name sortKey="Suzuki, A" uniqKey="Suzuki A">A Suzuki</name></author><author><name sortKey="Tamoi, M" uniqKey="Tamoi M">M Tamoi</name></author><author><name sortKey="Maruta, T" uniqKey="Maruta T">T Maruta</name></author><author><name sortKey="Shigeoka, S" uniqKey="Shigeoka S">S Shigeoka</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Harada, H" uniqKey="Harada H">H Harada</name></author><author><name sortKey="Maoka, T" uniqKey="Maoka T">T Maoka</name></author><author><name sortKey="Osawa, A" uniqKey="Osawa A">A Osawa</name></author><author><name sortKey="Hattan, J" uniqKey="Hattan J">J Hattan</name></author><author><name sortKey="Kanamoto, H" uniqKey="Kanamoto H">H Kanamoto</name></author><author><name sortKey="Shindo, K" uniqKey="Shindo K">K Shindo</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Pengelly, Jj" uniqKey="Pengelly J">JJ Pengelly</name></author><author><name sortKey="Forster, B" uniqKey="Forster B">B Forster</name></author><author><name sortKey="Von Caemmerer, S" uniqKey="Von Caemmerer S">S von Caemmerer</name></author><author><name sortKey="Badger, Mr" uniqKey="Badger M">MR Badger</name></author><author><name sortKey="Price, Gd" uniqKey="Price G">GD Price</name></author><author><name sortKey="Whitney, Sm" uniqKey="Whitney S">SM Whitney</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Sanz Barrio, R" uniqKey="Sanz Barrio R">R Sanz-Barrio</name></author><author><name sortKey="Corral Martinez, P" uniqKey="Corral Martinez P">P Corral-Martinez</name></author><author><name sortKey="Ancin, M" uniqKey="Ancin M">M Ancin</name></author><author><name sortKey="Segui Simarro, Jm" uniqKey="Segui Simarro J">JM Segui-Simarro</name></author><author><name sortKey="Farran, I" uniqKey="Farran I">I Farran</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Elghabi, Z" uniqKey="Elghabi Z">Z Elghabi</name></author><author><name sortKey="Karcher, D" uniqKey="Karcher D">D Karcher</name></author><author><name sortKey="Zhou, F" uniqKey="Zhou F">F Zhou</name></author><author><name sortKey="Ruf, S" uniqKey="Ruf S">S Ruf</name></author><author><name sortKey="Bock, R" uniqKey="Bock R">R Bock</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Agrawal, P" uniqKey="Agrawal P">P Agrawal</name></author><author><name sortKey="Verma, D" uniqKey="Verma D">D Verma</name></author><author><name sortKey="Daniell, H" uniqKey="Daniell H">H Daniell</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Verma, D" uniqKey="Verma D">D Verma</name></author><author><name sortKey="Jin, S" uniqKey="Jin S">S Jin</name></author><author><name sortKey="Kanagaraj, A" uniqKey="Kanagaraj A">A Kanagaraj</name></author><author><name sortKey="Singh, Nd" uniqKey="Singh N">ND Singh</name></author><author><name sortKey="Daniel, J" uniqKey="Daniel J">J Daniel</name></author><author><name sortKey="Kolattukudy, Pe" uniqKey="Kolattukudy P">PE Kolattukudy</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Saxena, B" uniqKey="Saxena B">B Saxena</name></author><author><name sortKey="Subramaniyan, M" uniqKey="Subramaniyan M">M Subramaniyan</name></author><author><name sortKey="Malhotra, K" uniqKey="Malhotra K">K Malhotra</name></author><author><name sortKey="Bhavesh, Ns" uniqKey="Bhavesh N">NS Bhavesh</name></author><author><name sortKey="Potlakayala, Sd" uniqKey="Potlakayala S">SD Potlakayala</name></author><author><name sortKey="Kumar, S" uniqKey="Kumar S">S Kumar</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Yu, Lx" uniqKey="Yu L">LX Yu</name></author><author><name sortKey="Gray, Bn" uniqKey="Gray B">BN Gray</name></author><author><name sortKey="Rutzke, Cj" uniqKey="Rutzke C">CJ Rutzke</name></author><author><name sortKey="Walker, Lp" uniqKey="Walker L">LP Walker</name></author><author><name sortKey="Wilson, Db" uniqKey="Wilson D">DB Wilson</name></author><author><name sortKey="Hanson, Mr" uniqKey="Hanson M">MR Hanson</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Petersen, K" uniqKey="Petersen K">K Petersen</name></author><author><name sortKey="Bock, R" uniqKey="Bock R">R Bock</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Arai, Y" uniqKey="Arai Y">Y Arai</name></author><author><name sortKey="Shikanai, T" uniqKey="Shikanai T">T Shikanai</name></author><author><name sortKey="Doi, Y" uniqKey="Doi Y">Y Doi</name></author><author><name sortKey="Yoshida, S" uniqKey="Yoshida S">S Yoshida</name></author><author><name sortKey="Yamaguchi, I" uniqKey="Yamaguchi I">I Yamaguchi</name></author><author><name sortKey="Nakashita, H" uniqKey="Nakashita H">H Nakashita</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Hasunuma, T" uniqKey="Hasunuma T">T Hasunuma</name></author><author><name sortKey="Miyazawa, Si" uniqKey="Miyazawa S">SI Miyazawa</name></author><author><name sortKey="Yoshimura, S" uniqKey="Yoshimura S">S Yoshimura</name></author><author><name sortKey="Shinzaki, Y" uniqKey="Shinzaki Y">Y Shinzaki</name></author><author><name sortKey="Tomizawa, Ki" uniqKey="Tomizawa K">KI Tomizawa</name></author><author><name sortKey="Shindo, K" uniqKey="Shindo K">K Shindo</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Nakahira, Y" uniqKey="Nakahira Y">Y Nakahira</name></author><author><name sortKey="Ishikawa, K" uniqKey="Ishikawa K">K Ishikawa</name></author><author><name sortKey="Tanaka, K" uniqKey="Tanaka K">K Tanaka</name></author><author><name sortKey="Tozawa, Y" uniqKey="Tozawa Y">Y Tozawa</name></author><author><name sortKey="Shiina, T" uniqKey="Shiina T">T Shiina</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Sherman, A" uniqKey="Sherman A">A Sherman</name></author><author><name sortKey="Su, J" uniqKey="Su J">J Su</name></author><author><name sortKey="Lin, S" uniqKey="Lin S">S Lin</name></author><author><name sortKey="Wang, X" uniqKey="Wang X">X Wang</name></author><author><name sortKey="Herzog, Rw" uniqKey="Herzog R">RW Herzog</name></author><author><name sortKey="Daniell, H" uniqKey="Daniell H">H Daniell</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Sanz Barrio, R" uniqKey="Sanz Barrio R">R Sanz-Barrio</name></author><author><name sortKey="Fernandez San Millan, A" uniqKey="Fernandez San Millan A">A Fernandez-San Millan</name></author><author><name sortKey="Corral Martinez, P" uniqKey="Corral Martinez P">P Corral-Martinez</name></author><author><name sortKey="Segui Simarro, Jm" uniqKey="Segui Simarro J">JM Segui-Simarro</name></author><author><name sortKey="Farran, I" uniqKey="Farran I">I Farran</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Farran, I" uniqKey="Farran I">I Farran</name></author><author><name sortKey="Mccarthy Suarez, I" uniqKey="Mccarthy Suarez I">I McCarthy-Suarez</name></author><author><name sortKey="Rio Manterola, F" uniqKey="Rio Manterola F">F Rio-Manterola</name></author><author><name sortKey="Mansilla, C" uniqKey="Mansilla C">C Mansilla</name></author><author><name sortKey="Lasarte, Jj" uniqKey="Lasarte J">JJ Lasarte</name></author><author><name sortKey="Mingo Castel, Am" uniqKey="Mingo Castel A">AM Mingo-Castel</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Boyhan, D" uniqKey="Boyhan D">D Boyhan</name></author><author><name sortKey="Daniell, H" uniqKey="Daniell H">H Daniell</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Fernandez San Millan, A" uniqKey="Fernandez San Millan A">A Fernandez-San Millan</name></author><author><name sortKey="Mingo Castel, A" uniqKey="Mingo Castel A">A Mingo-Castel</name></author><author><name sortKey="Miller, M" uniqKey="Miller M">M Miller</name></author><author><name sortKey="Daniell, H" uniqKey="Daniell H">H Daniell</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Daniell, H" uniqKey="Daniell H">H Daniell</name></author><author><name sortKey="Ruiz, G" uniqKey="Ruiz G">G Ruiz</name></author><author><name sortKey="Denes, B" uniqKey="Denes B">B Denes</name></author><author><name sortKey="Sandberg, L" uniqKey="Sandberg L">L Sandberg</name></author><author><name sortKey="Langridge, W" uniqKey="Langridge W">W Langridge</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Wang, X" uniqKey="Wang X">X Wang</name></author><author><name sortKey="Su, J" uniqKey="Su J">J Su</name></author><author><name sortKey="Sherman, A" uniqKey="Sherman A">A Sherman</name></author><author><name sortKey="Rogers, Gl" uniqKey="Rogers G">GL Rogers</name></author><author><name sortKey="Liao, G" uniqKey="Liao G">G Liao</name></author><author><name sortKey="Hoffman, Be" uniqKey="Hoffman B">BE Hoffman</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Su, J" uniqKey="Su J">J Su</name></author><author><name sortKey="Sherman, A" uniqKey="Sherman A">A Sherman</name></author><author><name sortKey="Doerfler, Pa" uniqKey="Doerfler P">PA Doerfler</name></author><author><name sortKey="Byrne, Bj" uniqKey="Byrne B">BJ Byrne</name></author><author><name sortKey="Herzog, Rw" uniqKey="Herzog R">RW Herzog</name></author><author><name sortKey="Daniell, H" uniqKey="Daniell H">H Daniell</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Youm, Jw" uniqKey="Youm J">JW Youm</name></author><author><name sortKey="Jeon, Jh" uniqKey="Jeon J">JH Jeon</name></author><author><name sortKey="Kim, H" uniqKey="Kim H">H Kim</name></author><author><name sortKey="Min, Sr" uniqKey="Min S">SR Min</name></author><author><name sortKey="Kim, Ms" uniqKey="Kim M">MS Kim</name></author><author><name sortKey="Joung, H" uniqKey="Joung H">H Joung</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Arlen, Pa" uniqKey="Arlen P">PA Arlen</name></author><author><name sortKey="Falconer, R" uniqKey="Falconer R">R Falconer</name></author><author><name sortKey="Cherukumilli, S" uniqKey="Cherukumilli S">S Cherukumilli</name></author><author><name sortKey="Cole, A" uniqKey="Cole A">A Cole</name></author><author><name sortKey="Cole, Am" uniqKey="Cole A">AM Cole</name></author><author><name sortKey="Oishi, Kk" uniqKey="Oishi K">KK Oishi</name></author><author><name sortKey="Daniell, H" uniqKey="Daniell H">H Daniell</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Ruhlman, T" uniqKey="Ruhlman T">T Ruhlman</name></author><author><name sortKey="Ahangari, R" uniqKey="Ahangari R">R Ahangari</name></author><author><name sortKey="Devine, A" uniqKey="Devine A">A Devine</name></author><author><name sortKey="Samsam, M" uniqKey="Samsam M">M Samsam</name></author><author><name sortKey="Daniell, H" uniqKey="Daniell H">H Daniell</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Leelavathi, S" uniqKey="Leelavathi S">S Leelavathi</name></author><author><name sortKey="Reddy, Vs" uniqKey="Reddy V">VS Reddy</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Lim, S" uniqKey="Lim S">S Lim</name></author><author><name sortKey="Ashida, H" uniqKey="Ashida H">H Ashida</name></author><author><name sortKey="Watanabe, R" uniqKey="Watanabe R">R Watanabe</name></author><author><name sortKey="Inai, K" uniqKey="Inai K">K Inai</name></author><author><name sortKey="Kim, Ys" uniqKey="Kim Y">YS Kim</name></author><author><name sortKey="Mukougawa, K" uniqKey="Mukougawa K">K Mukougawa</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Nadai, M" uniqKey="Nadai M">M Nadai</name></author><author><name sortKey="Bally, J" uniqKey="Bally J">J Bally</name></author><author><name sortKey="Vitel, M" uniqKey="Vitel M">M Vitel</name></author><author><name sortKey="Job, C" uniqKey="Job C">C Job</name></author><author><name sortKey="Tissot, G" uniqKey="Tissot G">G Tissot</name></author><author><name sortKey="Botterman, J" uniqKey="Botterman J">J Botterman</name></author><author><name sortKey="Dubald, M" uniqKey="Dubald M">M Dubald</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Gisby, Mf" uniqKey="Gisby M">MF Gisby</name></author><author><name sortKey="Mellors, P" uniqKey="Mellors P">P Mellors</name></author><author><name sortKey="Madesis, P" uniqKey="Madesis P">P Madesis</name></author><author><name sortKey="Ellin, M" uniqKey="Ellin M">M Ellin</name></author><author><name sortKey="Laverty, H" uniqKey="Laverty H">H Laverty</name></author><author><name sortKey="O Kane, S" uniqKey="O Kane S">S O'Kane</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Farran, I" uniqKey="Farran I">I Farran</name></author><author><name sortKey="Rio Manterola, F" uniqKey="Rio Manterola F">F Rio-Manterola</name></author><author><name sortKey="Iniguez, M" uniqKey="Iniguez M">M Iniguez</name></author><author><name sortKey="Garate, S" uniqKey="Garate S">S Garate</name></author><author><name sortKey="Prieto, J" uniqKey="Prieto J">J Prieto</name></author><author><name sortKey="Mingo Castel, Am" uniqKey="Mingo Castel A">AM Mingo-Castel</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Staub, Jm" uniqKey="Staub J">JM Staub</name></author><author><name sortKey="Garcia, B" uniqKey="Garcia B">B Garcia</name></author><author><name sortKey="Graves, J" uniqKey="Graves J">J Graves</name></author><author><name sortKey="Hajdukiewicz, Pt" uniqKey="Hajdukiewicz P">PT Hajdukiewicz</name></author><author><name sortKey="Hunter, P" uniqKey="Hunter P">P Hunter</name></author><author><name sortKey="Nehra, N" uniqKey="Nehra N">N Nehra</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Oey, M" uniqKey="Oey M">M Oey</name></author><author><name sortKey="Lohse, M" uniqKey="Lohse M">M Lohse</name></author><author><name sortKey="Scharff, Lb" uniqKey="Scharff L">LB Scharff</name></author><author><name sortKey="Kreikemeyer, B" uniqKey="Kreikemeyer B">B Kreikemeyer</name></author><author><name sortKey="Bock, R" uniqKey="Bock R">R Bock</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Koya, V" uniqKey="Koya V">V Koya</name></author><author><name sortKey="Moayeri, M" uniqKey="Moayeri M">M Moayeri</name></author><author><name sortKey="Leppla, Sh" uniqKey="Leppla S">SH Leppla</name></author><author><name sortKey="Daniell, H" uniqKey="Daniell H">H Daniell</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Watson, J" uniqKey="Watson J">J Watson</name></author><author><name sortKey="Koya, V" uniqKey="Koya V">V Koya</name></author><author><name sortKey="Leppla, Sh" uniqKey="Leppla S">SH Leppla</name></author><author><name sortKey="Daniell, H" uniqKey="Daniell H">H Daniell</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Millan, Afs" uniqKey="Millan A">AFS Millan</name></author><author><name sortKey="Ortigosa, Sm" uniqKey="Ortigosa S">SM Ortigosa</name></author><author><name sortKey="Hervas Stubbs, S" uniqKey="Hervas Stubbs S">S Hervas-Stubbs</name></author><author><name sortKey="Corral Martinez, P" uniqKey="Corral Martinez P">P Corral-Martinez</name></author><author><name sortKey="Segui Simarro, Jm" uniqKey="Segui Simarro J">JM Segui-Simarro</name></author><author><name sortKey="Gaetan, J" uniqKey="Gaetan J">J Gaetan</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Yacono, Md" uniqKey="Yacono M">MD Yacono</name></author><author><name sortKey="Farran, I" uniqKey="Farran I">I Farran</name></author><author><name sortKey="Becher, Ml" uniqKey="Becher M">ML Becher</name></author><author><name sortKey="Sander, V" uniqKey="Sander V">V Sander</name></author><author><name sortKey="Sanchez, Vr" uniqKey="Sanchez V">VR Sanchez</name></author><author><name sortKey="Martin, V" uniqKey="Martin V">V Martin</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Kolotilin, I" uniqKey="Kolotilin I">I Kolotilin</name></author><author><name sortKey="Kaldis, A" uniqKey="Kaldis A">A Kaldis</name></author><author><name sortKey="Devriendt, B" uniqKey="Devriendt B">B Devriendt</name></author><author><name sortKey="Joensuu, J" uniqKey="Joensuu J">J Joensuu</name></author><author><name sortKey="Cox, E" uniqKey="Cox E">E Cox</name></author><author><name sortKey="Menassa, R" uniqKey="Menassa R">R Menassa</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Arlen, Pa" uniqKey="Arlen P">PA Arlen</name></author><author><name sortKey="Singleton, M" uniqKey="Singleton M">M Singleton</name></author><author><name sortKey="Adamovicz, Jj" uniqKey="Adamovicz J">JJ Adamovicz</name></author><author><name sortKey="Ding, Y" uniqKey="Ding Y">Y Ding</name></author><author><name sortKey="Davoodi Semiromi, A" uniqKey="Davoodi Semiromi A">A Davoodi-Semiromi</name></author><author><name sortKey="Daniell, H" uniqKey="Daniell H">H Daniell</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Molina, A" uniqKey="Molina A">A Molina</name></author><author><name sortKey="Hervas Stubbs, S" uniqKey="Hervas Stubbs S">S Hervas-Stubbs</name></author><author><name sortKey="Daniell, H" uniqKey="Daniell H">H Daniell</name></author><author><name sortKey="Mingo Castel, Am" uniqKey="Mingo Castel A">AM Mingo-Castel</name></author><author><name sortKey="Veramendi, J" uniqKey="Veramendi J">J Veramendi</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Lentz, Em" uniqKey="Lentz E">EM Lentz</name></author><author><name sortKey="Mozgovoj, Mv" uniqKey="Mozgovoj M">MV Mozgovoj</name></author><author><name sortKey="Bellido, D" uniqKey="Bellido D">D Bellido</name></author><author><name sortKey="Santos, Mjd" uniqKey="Santos M">MJD Santos</name></author><author><name sortKey="Wigdorovitz, A" uniqKey="Wigdorovitz A">A Wigdorovitz</name></author><author><name sortKey="Bravo Almonacid, Ff" uniqKey="Bravo Almonacid F">FF Bravo-Almonacid</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Daniell, H" uniqKey="Daniell H">H Daniell</name></author><author><name sortKey="Lee, Sb" uniqKey="Lee S">SB Lee</name></author><author><name sortKey="Panchal, T" uniqKey="Panchal T">T Panchal</name></author><author><name sortKey="Wiebe, Po" uniqKey="Wiebe P">PO Wiebe</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Kang, Tj" uniqKey="Kang T">TJ Kang</name></author><author><name sortKey="Loc, Nh" uniqKey="Loc N">NH Loc</name></author><author><name sortKey="Jang, Mo" uniqKey="Jang M">MO Jang</name></author><author><name sortKey="Jang, Ys" uniqKey="Jang Y">YS Jang</name></author><author><name sortKey="Kim, Ys" uniqKey="Kim Y">YS Kim</name></author><author><name sortKey="Seo, Je" uniqKey="Seo J">JE Seo</name></author><author><name sortKey="Yang, Ms" uniqKey="Yang M">MS Yang</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Chebolu, S" uniqKey="Chebolu S">S Chebolu</name></author><author><name sortKey="Daniell, H" uniqKey="Daniell H">H Daniell</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Glenz, K" uniqKey="Glenz K">K Glenz</name></author><author><name sortKey="Bouchon, B" uniqKey="Bouchon B">B Bouchon</name></author><author><name sortKey="Stehle, T" uniqKey="Stehle T">T Stehle</name></author><author><name sortKey="Wallich, R" uniqKey="Wallich R">R Wallich</name></author><author><name sortKey="Simon, Mm" uniqKey="Simon M">MM Simon</name></author><author><name sortKey="Warzecha, H" uniqKey="Warzecha H">H Warzecha</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Rosales Mendoza, S" uniqKey="Rosales Mendoza S">S Rosales-Mendoza</name></author><author><name sortKey="Alpuche Solis, Ag" uniqKey="Alpuche Solis A">AG Alpuche-Solis</name></author><author><name sortKey="Soria Guerra, Re" uniqKey="Soria Guerra R">RE Soria-Guerra</name></author><author><name sortKey="Moreno Fierros, L" uniqKey="Moreno Fierros L">L Moreno-Fierros</name></author><author><name sortKey="Martinez Gonzalez, L" uniqKey="Martinez Gonzalez L">L Martinez-Gonzalez</name></author><author><name sortKey="Herrera Diaz, A" uniqKey="Herrera Diaz A">A Herrera-Diaz</name></author><author><name sortKey="Korban, Ss" uniqKey="Korban S">SS Korban</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Soria Guerra, Re" uniqKey="Soria Guerra R">RE Soria-Guerra</name></author><author><name sortKey="Alpuche Solis, Ag" uniqKey="Alpuche Solis A">AG Alpuche-Solis</name></author><author><name sortKey="Rosales Mendoza, S" uniqKey="Rosales Mendoza S">S Rosales-Mendoza</name></author><author><name sortKey="Moreno Fierros, L" uniqKey="Moreno Fierros L">L Moreno-Fierros</name></author><author><name sortKey="Bendik, Em" uniqKey="Bendik E">EM Bendik</name></author><author><name sortKey="Martinez Gonzalez, L" uniqKey="Martinez Gonzalez L">L Martinez-Gonzalez</name></author><author><name sortKey="Korban, Ss" uniqKey="Korban S">SS Korban</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Rubio Infante, N" uniqKey="Rubio Infante N">N Rubio-Infante</name></author><author><name sortKey="Govea Alonso, Do" uniqKey="Govea Alonso D">DO Govea-Alonso</name></author><author><name sortKey="Alpuche Solis, Ag" uniqKey="Alpuche Solis A">AG Alpuche-Solis</name></author><author><name sortKey="Garcia Hernandez, Al" uniqKey="Garcia Hernandez A">AL Garcia-Hernandez</name></author><author><name sortKey="Soria Guerra, Re" uniqKey="Soria Guerra R">RE Soria-Guerra</name></author><author><name sortKey="Paz Maldonado, Lmt" uniqKey="Paz Maldonado L">LMT Paz-Maldonado</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Waheed, Mt" uniqKey="Waheed M">MT Waheed</name></author><author><name sortKey="Thones, N" uniqKey="Thones N">N Thones</name></author><author><name sortKey="Muller, M" uniqKey="Muller M">M Muller</name></author><author><name sortKey="Hassan, Sw" uniqKey="Hassan S">SW Hassan</name></author><author><name sortKey="Gottschamel, J" uniqKey="Gottschamel J">J Gottschamel</name></author><author><name sortKey="Lossl, E" uniqKey="Lossl E">E Lossl</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Gonzalez Rabade, N" uniqKey="Gonzalez Rabade N">N Gonzalez-Rabade</name></author><author><name sortKey="Mcgowan, Eg" uniqKey="Mcgowan E">EG McGowan</name></author><author><name sortKey="Zhou, F" uniqKey="Zhou F">F Zhou</name></author><author><name sortKey="Mccabe, Ms" uniqKey="Mccabe M">MS McCabe</name></author><author><name sortKey="Bock, R" uniqKey="Bock R">R Bock</name></author><author><name sortKey="Dix, Pj" uniqKey="Dix P">PJ Dix</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Zhou, Yx" uniqKey="Zhou Y">YX Zhou</name></author><author><name sortKey="Lee, Myt" uniqKey="Lee M">MYT Lee</name></author><author><name sortKey="Ng, Jmh" uniqKey="Ng J">JMH Ng</name></author><author><name sortKey="Chye, Ml" uniqKey="Chye M">ML Chye</name></author><author><name sortKey="Yip, Wk" uniqKey="Yip W">WK Yip</name></author><author><name sortKey="Zee, Sy" uniqKey="Zee S">SY Zee</name></author><author><name sortKey="Lam, E" uniqKey="Lam E">E Lam</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Shao, Hb" uniqKey="Shao H">HB Shao</name></author><author><name sortKey="He, Dm" uniqKey="He D">DM He</name></author><author><name sortKey="Qian, Kx" uniqKey="Qian K">KX Qian</name></author><author><name sortKey="Shen, Gf" uniqKey="Shen G">GF Shen</name></author><author><name sortKey="Su, Zl" uniqKey="Su Z">ZL Su</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Tregoning, Js" uniqKey="Tregoning J">JS Tregoning</name></author><author><name sortKey="Nixon, P" uniqKey="Nixon P">P Nixon</name></author><author><name sortKey="Kuroda, H" uniqKey="Kuroda H">H Kuroda</name></author><author><name sortKey="Svab, Z" uniqKey="Svab Z">Z Svab</name></author><author><name sortKey="Clare, S" uniqKey="Clare S">S Clare</name></author><author><name sortKey="Bowe, F" uniqKey="Bowe F">F Bowe</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Morgenfeld, M" uniqKey="Morgenfeld M">M Morgenfeld</name></author><author><name sortKey="Lentz, E" uniqKey="Lentz E">E Lentz</name></author><author><name sortKey="Segretin, Me" uniqKey="Segretin M">ME Segretin</name></author><author><name sortKey="Alfano, Ef" uniqKey="Alfano E">EF Alfano</name></author><author><name sortKey="Bravo Almonacid, F" uniqKey="Bravo Almonacid F">F Bravo-Almonacid</name></author></analytic></biblStruct></listBibl></div1></back></TEI><pmc article-type="review-article"><pmc-dir>properties open_access</pmc-dir>
<front><journal-meta><journal-id journal-id-type="nlm-ta">Genome Biol</journal-id><journal-id journal-id-type="iso-abbrev">Genome Biol</journal-id><journal-title-group><journal-title>Genome Biology</journal-title></journal-title-group><issn pub-type="ppub">1474-7596</issn><issn pub-type="epub">1474-760X</issn><publisher><publisher-name>BioMed Central</publisher-name><publisher-loc>London</publisher-loc></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">27339192</article-id><article-id pub-id-type="pmc">4918201</article-id><article-id pub-id-type="publisher-id">1004</article-id><article-id pub-id-type="doi">10.1186/s13059-016-1004-2</article-id><article-categories><subj-group subj-group-type="heading"><subject>Review</subject></subj-group></article-categories><title-group><article-title>Chloroplast genomes: diversity, evolution, and applications in genetic engineering</article-title></title-group><contrib-group><contrib contrib-type="author" corresp="yes"><name><surname>Daniell</surname><given-names>Henry</given-names></name><address><email>hdaniell@upenn.edu</email></address><xref ref-type="aff" rid="Aff1"></xref></contrib><contrib contrib-type="author"><name><surname>Lin</surname><given-names>Choun-Sea</given-names></name><xref ref-type="aff" rid="Aff2"></xref></contrib><contrib contrib-type="author"><name><surname>Yu</surname><given-names>Ming</given-names></name><xref ref-type="aff" rid="Aff1"></xref></contrib><contrib contrib-type="author"><name><surname>Chang</surname><given-names>Wan-Jung</given-names></name><xref ref-type="aff" rid="Aff2"></xref></contrib><aff id="Aff1"><label></label>Department of Biochemistry, School of Dental Medicine, University of Pennsylvania, South 40th St, Philadelphia, PA 19104-6030 USA</aff><aff id="Aff2"><label></label>Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan</aff></contrib-group><pub-date pub-type="epub"><day>23</day><month>6</month><year>2016</year></pub-date><pub-date pub-type="pmc-release"><day>23</day><month>6</month><year>2016</year></pub-date><pub-date pub-type="collection"><year>2016</year></pub-date><volume>17</volume><elocation-id>134</elocation-id><permissions><copyright-statement>© The Author(s). 2016</copyright-statement><license license-type="OpenAccess"><license-p><bold>Open Access</bold>This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (<ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/licenses/by/4.0/">http://creativecommons.org/licenses/by/4.0/</ext-link>), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (<ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/publicdomain/zero/1.0/">http://creativecommons.org/publicdomain/zero/1.0/</ext-link>) applies to the data made available in this article, unless otherwise stated.</license-p></license></permissions><abstract id="Abs1"><p>Chloroplasts play a crucial role in sustaining life on earth. The availability of over 800 sequenced chloroplast genomes from a variety of land plants has enhanced our understanding of chloroplast biology, intracellular gene transfer, conservation, diversity, and the genetic basis by which chloroplast transgenes can be engineered to enhance plant agronomic traits or to produce high-value agricultural or biomedical products. In this review, we discuss the impact of chloroplast genome sequences on understanding the origins of economically important cultivated species and changes that have taken place during domestication. We also discuss the potential biotechnological applications of chloroplast genomes.</p><sec><title>Electronic supplementary material</title><p>The online version of this article (doi:10.1186/s13059-016-1004-2) contains supplementary material, which is available to authorized users.</p></sec></abstract><funding-group><award-group><funding-source><institution-wrap><institution-id institution-id-type="FundRef">http://dx.doi.org/10.13039/100000050</institution-id><institution>National Heart, Lung, and Blood Institute</institution></institution-wrap></funding-source><award-id>107904</award-id><principal-award-recipient><name><surname>Daniell</surname><given-names>Henry</given-names></name></principal-award-recipient></award-group><award-group><funding-source><institution>National Institutes of Health (US)</institution></funding-source><award-id>HL 109442</award-id><principal-award-recipient><name><surname>Daniell</surname><given-names>Henry</given-names></name></principal-award-recipient></award-group></funding-group><custom-meta-group><custom-meta><meta-name>issue-copyright-statement</meta-name><meta-value>© The Author(s) 2016</meta-value></custom-meta></custom-meta-group></article-meta></front><body><sec id="Sec1" sec-type="introduction"><title>Introduction</title><p>Chloroplasts are active metabolic centers that sustain life on earth by converting solar energy to carbohydrates through the process of photosynthesis and oxygen release. Although photosynthesis is often recognized as the key function of plastids, they also play vital roles in other aspects of plant physiology and development, including the synthesis of amino acids, nucleotides, fatty acids, phytohormones, vitamins and a plethora of metabolites, and the assimilation of sulfur and nitrogen. Metabolites that are synthesized in chloroplasts are important for plant interactions with their environment (responses to heat, drought, salt, light, and so on) and their defense against invading pathogens. So, chloroplasts serve as metabolic centers in cellular reactions to signals and respond via retrograde signaling [<xref ref-type="bibr" rid="CR1">1</xref>, <xref ref-type="bibr" rid="CR2">2</xref>]. The chloroplast genome encodes many key proteins that are involved in photosynthesis and other metabolic processes.</p><p>The advent of high-throughput sequencing technologies has facilitated rapid progress in the field of chloroplast genetics and genomics. Since the first chloroplast genome, from tobacco (<italic>Nicotiana tabacum</italic>), was sequenced in 1986 [<xref ref-type="bibr" rid="CR3">3</xref>], over 800 complete chloroplast genome sequences have been made available in the National Center for Biotechnology Information (NCBI) organelle genome database, including 300 from crop and tree genomes. Insights gained from complete chloroplast genome sequences have enhanced our understanding of plant biology and diversity; chloroplast genomes have made significant contributions to phylogenetic studies of several plant families and to resolving evolutionary relationships within phylogenetic clades. In addition, chloroplast genome sequences have revealed considerable variation within and between plant species in terms of both sequence and structural variation. This information has been especially valuable for our understanding of the climatic adaptation of economically important crops, facilitating the breeding of closely related species and the identification and conservation of valuable traits [<xref ref-type="bibr" rid="CR4">4</xref>, <xref ref-type="bibr" rid="CR5">5</xref>]. Improved understanding of variation among chloroplast genomes has also allowed the identification of specific examples of chloroplast gene transfer to plant nuclear or mitochondrial genomes, which has shed new light on the relationship between these three genomes in plants.</p><p>In addition to improving our understanding of plant biology and evolution, chloroplast genomics research has important translational applications, such as conferring protection against biotic or abiotic stress and the development of vaccines and biopharmaceuticals in edible crop plants. Indeed, the first commercial-scale production of a human blood protein in a Current Good Manufacturing Processes (cGMP) facility was published recently [<xref ref-type="bibr" rid="CR6">6</xref>]. The lack of conservation of intergenic spacer regions, even among chloroplast genomes of closely related plant species, and the species specificity of regulatory sequences have facilitated the development of highly efficient transformation vectors for the integration and expression of foreign genes in chloroplasts. Because the published literature is rarely cross-referenced, this review highlights the impact of chloroplast genomes on various biotechnology applications. In addition to our enhanced understanding of chloroplast biology, we discuss in depth the roles of chloroplast genome sequences in improving our understanding of intracellular gene transfer, conservation, diversity, and the genetic basis by which chloroplast transgenes are engineered to enhance plant agronomic traits or to produce high-value agricultural or biomedical products. In addition, we discuss the impact of chloroplast genome sequences on increasing our understanding of the origins of economically important cultivated species and changes that occurred during domestication.</p></sec><sec id="Sec2"><title>Advances in chloroplast genome sequencing technology</title><p>One of the important factors in the rapid advancement of the chloroplast genomics field is improvement in sequencing technologies. In studies conducted before the availability of high-throughput methods, isolated chloroplasts were used for the amplification of the entire chloroplast genome by rolling circle amplification [<xref ref-type="bibr" rid="CR7">7</xref>–<xref ref-type="bibr" rid="CR12">12</xref>]. An alternative strategy is to screen bacterial artificial chromosome (BAC) or fosmid libraries using chloroplast genome sequences as probes [<xref ref-type="bibr" rid="CR13">13</xref>–<xref ref-type="bibr" rid="CR20">20</xref>]; however, these methods are subject to many challenges, including difficulty in constructing good-quality BAC or fosmid libraries, large numbers of PCR reactions, and the possibility of contamination from other organellar DNA [<xref ref-type="bibr" rid="CR21">21</xref>–<xref ref-type="bibr" rid="CR32">32</xref>]. The PCR approach is also difficult to apply to species that have no relatives whose chloroplast genomes have been sequenced or those with highly rearranged chloroplast genomes.</p><p>The development of next-generation sequencing (NGS) methods provided scientists with faster and cheaper methods to sequence chloroplast genomes. Moore and colleagues [<xref ref-type="bibr" rid="CR33">33</xref>] first reported using NGS to determine chloroplast genome sequences, in <italic>Nandina</italic> and <italic>Platanus</italic>. Although multiple NGS platforms are available for chloroplast genome sequencing [<xref ref-type="bibr" rid="CR34">34</xref>], Illumina is currently the major NGS platform used for chloroplast genomes [<xref ref-type="bibr" rid="CR21">21</xref>, <xref ref-type="bibr" rid="CR32">32</xref>, <xref ref-type="bibr" rid="CR35">35</xref>, <xref ref-type="bibr" rid="CR36">36</xref>] because it allows the use of rolling circle amplification products [<xref ref-type="bibr" rid="CR35">35</xref>, <xref ref-type="bibr" rid="CR37">37</xref>]. Investigators can then use bioinformatics platforms to perform de novo assembly without the need for reference genome sequences; from these assemblies it is possible to identify consensus chloroplast genome sequences [<xref ref-type="bibr" rid="CR32">32</xref>]. A third-generation sequencer, the PacBio system which uses single molecule real-time (SMRT) sequencing, is now widely used in chloroplast genome sequencing [<xref ref-type="bibr" rid="CR38">38</xref>–<xref ref-type="bibr" rid="CR43">43</xref>]. Its advantage is long read lengths [<xref ref-type="bibr" rid="CR44">44</xref>], which facilitate de novo genome assembly, particularly in the four chloroplast junctions between the inverted repeat (IR) and single-copy regions.</p><p>The low accuracy (~85 % of the raw data) of the long reads produced by the PacBio platform [<xref ref-type="bibr" rid="CR45">45</xref>] can be corrected by combining the latest chemistry with a hierarchical genome assembly process algorithm; accuracy rates as high as 99.999 % can be achieved after such post-error corrections [<xref ref-type="bibr" rid="CR46">46</xref>]. Accuracy can also be increased using Illumina short reads [<xref ref-type="bibr" rid="CR42">42</xref>]. In a study of <italic>Potentilla micrantha</italic>, sequencing with the Illumina platform produced seven contigs covering only 90.59 % of the chloroplast genome; by contrast, using the PacBio platform with error correction, the entire genome was successfully assembled in a single contig [<xref ref-type="bibr" rid="CR39">39</xref>].</p></sec><sec id="Sec3"><title>Chloroplast genome structure</title><p>The chloroplast genomes of land plants have highly conserved structures and organization of content; they comprise a single circular molecule with a quadripartite structure that includes two copies of an IR region that separate large and small single-copy (LSC and SSC) regions (Fig. <xref rid="Fig1" ref-type="fig">1a, b</xref>). The chloroplast genome includes 120–130 genes, primarily participating in photosynthesis, transcription, and translation. Recent studies have identified considerable diversity within non-coding intergenic spacer regions, which often include important regulatory sequences [<xref ref-type="bibr" rid="CR13">13</xref>]. Despite the overall conservation in structure, chloroplast genome size varies between species, ranging from 107 kb (<italic>Cathaya argyrophylla</italic>) to 218 kb (<italic>Pelargonium</italic>), and is independent of nuclear genome size (Table <xref rid="Tab1" ref-type="table">1</xref>). Certain lineages of land-plant chloroplast genomes also show significant structural rearrangements, with evidence of the loss of IR regions or entire gene families. Furthermore, there is also evidence for the existence of linear chloroplast genomes, as illustrated in Fig. <xref rid="Fig1" ref-type="fig">1b</xref>. The percentage of each form within the cell varies in different reports [<xref ref-type="bibr" rid="CR47">47</xref>, <xref ref-type="bibr" rid="CR48">48</xref>].<fig id="Fig1"><label>Fig. 1</label><caption><p>Map of the soybean (<italic>Glycine max</italic>) chloroplast genome. This genome was used to engineer biotic stress tolerance against insects and herbicides. The quadripartite structure includes two copies of an IR region (<italic>IRA</italic> and <italic>IRB</italic>) that separate large single-copy (<italic>LSC</italic>) and small single-copy (<italic>SSC</italic>) regions [<xref ref-type="bibr" rid="CR18">18</xref>]. <bold>a</bold> Circular form. The GC content graph (<italic>gray circle</italic> inside) marks the 50 % threshold of GC content. <bold>b</bold> Linear form. Different <italic>colors</italic> indicate genes in different functional groups. <italic>IR</italic> inverted repeat, <italic>LSU</italic> large subunit, <italic>SSU</italic> small subunit</p></caption><graphic xlink:href="13059_2016_1004_Fig1_HTML" id="MO1"></graphic></fig><table-wrap id="Tab1"><label>Table 1</label><caption><p>Alphabetical list of crop and tree species that have complete annotated chloroplast genome sequences</p></caption><table frame="hsides" rules="groups"><thead><tr><th>Species</th><th>Common name</th><th>Accession</th><th>Genome size (bp)</th><th>Uses</th><th>Reference(s)</th></tr></thead><tbody><tr><td>Crops</td><td></td><td></td><td></td><td></td><td></td></tr><tr><td><italic>Acorus gramineus</italic></td><td>Sweet flag</td><td>NC_026299</td><td>152849</td><td>Ornamental</td><td>[<xref ref-type="bibr" rid="CR169">169</xref>]</td></tr><tr><td><italic>Agrostis stolonifera</italic></td><td>Creeping bent grass</td><td>NC_008591</td><td>136584</td><td>Forage</td><td>[<xref ref-type="bibr" rid="CR8">8</xref>]</td></tr><tr><td><italic>Allium cepa</italic></td><td>Onion</td><td>NC_024813</td><td>153538</td><td>Vegetable</td><td>[<xref ref-type="bibr" rid="CR170">170</xref>]</td></tr><tr><td><italic>Ananas comosus</italic></td><td>Pineapple</td><td>NC_026220</td><td>159636</td><td>Fruit</td><td>[<xref ref-type="bibr" rid="CR171">171</xref>]</td></tr><tr><td><italic>Anthriscus cerefolium</italic></td><td>Chervil</td><td>NC_015113</td><td>154719</td><td>Medicinal</td><td>[<xref ref-type="bibr" rid="CR172">172</xref>]</td></tr><tr><td><italic>Artemisia frigida</italic></td><td>Fringed sagewort</td><td>NC_020607</td><td>151076</td><td>Medicinal</td><td>[<xref ref-type="bibr" rid="CR173">173</xref>]</td></tr><tr><td><italic>Atropa belladonna</italic></td><td>Belladonna</td><td>NC_004561</td><td>156687</td><td>Medicinal</td><td>[<xref ref-type="bibr" rid="CR174">174</xref>]</td></tr><tr><td><italic>Brassica napus</italic> (2)*</td><td>Canola</td><td>NC_016734</td><td>152860</td><td>Oil</td><td>[<xref ref-type="bibr" rid="CR175">175</xref>]</td></tr><tr><td><italic>Calanthe triplicata</italic></td><td>Black orchid</td><td>NC_024544</td><td>158759</td><td>Flower</td><td>[<xref ref-type="bibr" rid="CR176">176</xref>]</td></tr><tr><td><italic>Cannabis sativa</italic> (2)</td><td>Marijuana</td><td>NC_027223</td><td>153854</td><td>Fiber</td><td>[<xref ref-type="bibr" rid="CR177">177</xref>]</td></tr><tr><td><italic>Capsicum annuum</italic> (2)</td><td>Pepper</td><td>NC_018552</td><td>156781</td><td>Vegetable</td><td>[<xref ref-type="bibr" rid="CR178">178</xref>]</td></tr><tr><td><italic>Carica papaya</italic></td><td>Papaya</td><td>NC_010323</td><td>160100</td><td>Fruit</td><td>[<xref ref-type="bibr" rid="CR179">179</xref>]</td></tr><tr><td><italic>Catharanthus roseus</italic></td><td>Madagascar periwinkle</td><td>NC_021423</td><td>154950</td><td>Flower</td><td>[<xref ref-type="bibr" rid="CR180">180</xref>]</td></tr><tr><td><italic>Cenchrus americanus</italic></td><td>Pearl millet</td><td>NC_024171</td><td>140718</td><td>Cereals</td><td>[<xref ref-type="bibr" rid="CR181">181</xref>]</td></tr><tr><td><italic>Cicer arietinum</italic></td><td>Chickpea</td><td>NC_011163</td><td>125319</td><td>Vegetable</td><td>[<xref ref-type="bibr" rid="CR7">7</xref>]</td></tr><tr><td><italic>Coix lacryma-jobi</italic></td><td>Job's tears</td><td>NC_013273</td><td>140745</td><td>Cereals</td><td>[<xref ref-type="bibr" rid="CR29">29</xref>]</td></tr><tr><td><italic>Colocasia esculenta</italic></td><td>Taro</td><td>NC_016753</td><td>162424</td><td>Vegetable</td><td>[<xref ref-type="bibr" rid="CR182">182</xref>]</td></tr><tr><td><italic>Cucumis sativus</italic> (3)</td><td>Cucumber</td><td>NC_007144</td><td>155293</td><td>Vegetable</td><td>[<xref ref-type="bibr" rid="CR183">183</xref>]</td></tr><tr><td><italic>Curcuma roscoeana</italic></td><td>Jewel of Burma</td><td>NC_022928</td><td>159512</td><td>Medicinal</td><td>[<xref ref-type="bibr" rid="CR184">184</xref>]</td></tr><tr><td><italic>Cymbidium tortisepalum</italic> (5)</td><td>Cymbidium orchid</td><td>NC_021431</td><td>155627</td><td>Flower</td><td>[<xref ref-type="bibr" rid="CR55">55</xref>]</td></tr><tr><td><italic>Cypripedium formosanum</italic> (3)</td><td>Formosa's lady's slipper</td><td>NC_026772</td><td>178131</td><td>Flower</td><td>[<xref ref-type="bibr" rid="CR32">32</xref>]</td></tr><tr><td><italic>Daucus carota</italic></td><td>Carrot</td><td>NC_008325</td><td>155911</td><td>Vegetable</td><td>[<xref ref-type="bibr" rid="CR9">9</xref>]</td></tr><tr><td><italic>Dendrobium catenatum</italic></td><td>Dendrobium orchid</td><td>NC_024019</td><td>152221</td><td>Flower</td><td>[<xref ref-type="bibr" rid="CR56">56</xref>]</td></tr><tr><td><italic>Dieffenbachia seguine</italic></td><td>Dumbcane</td><td>NC_027272</td><td>163699</td><td>Ornamental</td><td>[<xref ref-type="bibr" rid="CR185">185</xref>]</td></tr><tr><td><italic>Digitaria exilis</italic></td><td>White fonio</td><td>NC_024176</td><td>140908</td><td>Cereals</td><td>[<xref ref-type="bibr" rid="CR181">181</xref>]</td></tr><tr><td><italic>Echinochloa oryzicola</italic></td><td>Late barnyard grass</td><td>NC_024643</td><td>139891</td><td>Cereals</td><td>[<xref ref-type="bibr" rid="CR186">186</xref>]</td></tr><tr><td><italic>Ephedra equisetina</italic></td><td>Ma Huang</td><td>NC_011954</td><td>109518</td><td>Medicinal</td><td>[<xref ref-type="bibr" rid="CR187">187</xref>]</td></tr><tr><td><italic>Erycina pusilla</italic></td><td>Mini orchid</td><td>NC_018114</td><td>143164</td><td>Flower</td><td>[<xref ref-type="bibr" rid="CR36">36</xref>]</td></tr><tr><td><italic>Fagopyrum esculentum</italic> (2)</td><td>Common buckwheat</td><td>NC_010776</td><td>159599</td><td>Cereals</td><td>[<xref ref-type="bibr" rid="CR188">188</xref>]</td></tr><tr><td><italic>Festuca arundinacea</italic> (4)</td><td>Kentucky fescue</td><td>NC_011713</td><td>136048</td><td>Forage</td><td>[<xref ref-type="bibr" rid="CR189">189</xref>]</td></tr><tr><td><italic>Fragaria vesca</italic> (6)</td><td>Wild strawberry</td><td>NC_015206</td><td>155691</td><td>Fruit</td><td>[<xref ref-type="bibr" rid="CR190">190</xref>]</td></tr><tr><td><italic>Glycine max</italic> (9)</td><td>Soybean</td><td>NC_007942</td><td>152218</td><td>Oil</td><td>[<xref ref-type="bibr" rid="CR18">18</xref>]</td></tr><tr><td><italic>Glycyrrhiza glabra</italic></td><td>Common liquorice</td><td>NC_024038</td><td>127943</td><td>Medicinal</td><td>[<xref ref-type="bibr" rid="CR74">74</xref>]</td></tr><tr><td><italic>Gossypium barbadense</italic> (22)</td><td>Sea island cotton</td><td>NC_008641</td><td>160317</td><td>Fiber</td><td>[<xref ref-type="bibr" rid="CR69">69</xref>]</td></tr><tr><td><italic>Guizotia abyssinica</italic></td><td>Ramtilla</td><td>NC_010601</td><td>151762</td><td>Bird seed</td><td>[<xref ref-type="bibr" rid="CR191">191</xref>]</td></tr><tr><td><italic>Helianthus annuus</italic> (9)</td><td>Common sunflower</td><td>NC_007977</td><td>151104</td><td>Oil</td><td>[<xref ref-type="bibr" rid="CR192">192</xref>]</td></tr><tr><td><italic>Heliconia collinsiana</italic></td><td>Platanillo</td><td>NC_020362</td><td>161907</td><td>Ornamental</td><td>[<xref ref-type="bibr" rid="CR193">193</xref>]</td></tr><tr><td><italic>Hordeum vulgare</italic></td><td>Barley</td><td>NC_008590</td><td>136462</td><td>Cereals</td><td>[<xref ref-type="bibr" rid="CR8">8</xref>]</td></tr><tr><td><italic>Hyoscyamus niger</italic></td><td>Henbane</td><td>NC_024261</td><td>155720</td><td>Medicinal</td><td>[<xref ref-type="bibr" rid="CR194">194</xref>]</td></tr><tr><td><italic>Ipomoea batatas</italic></td><td>Sweet potato</td><td>NC_026703</td><td>161303</td><td>Vegetable</td><td>[<xref ref-type="bibr" rid="CR195">195</xref>]</td></tr><tr><td><italic>Ipomoea purpurea</italic></td><td>Common morning glory</td><td>NC_009808</td><td>162046</td><td>Ornamental</td><td>[<xref ref-type="bibr" rid="CR196">196</xref>]</td></tr><tr><td><italic>Lactuca sativa</italic></td><td>Lettuce</td><td>NC_007578</td><td>152765</td><td>Vegetable</td><td>[<xref ref-type="bibr" rid="CR197">197</xref>]</td></tr><tr><td><italic>Lilium superbum</italic></td><td>Turk's-cap lily</td><td>NC_026787</td><td>152069</td><td>Flower</td><td>[<xref ref-type="bibr" rid="CR198">198</xref>]</td></tr><tr><td><italic>Lolium multiflorum</italic> (2)</td><td>Ryegrass</td><td>NC_019651</td><td>135175</td><td>Lawn</td><td>[<xref ref-type="bibr" rid="CR199">199</xref>]</td></tr><tr><td><italic>Lotus japonicus</italic></td><td>Birdsfoot trefoil</td><td>NC_002694</td><td>150519</td><td>Forage</td><td>[<xref ref-type="bibr" rid="CR200">200</xref>]</td></tr><tr><td><italic>Manihot esculenta</italic></td><td>Cassava</td><td>EU117376</td><td>161453</td><td>Starch crop</td><td>[<xref ref-type="bibr" rid="CR20">20</xref>]</td></tr><tr><td><italic>Masdevallia picturata</italic> (2)</td><td>Masdevallia orchid</td><td>NC_026777</td><td>157423</td><td>Flower</td><td>[<xref ref-type="bibr" rid="CR32">32</xref>]</td></tr><tr><td><italic>Musa textilis</italic></td><td>Banana</td><td>NC_022926</td><td>161347</td><td>Fruit</td><td>[<xref ref-type="bibr" rid="CR184">184</xref>]</td></tr><tr><td><italic>Nicotiana tabacum</italic> (4)</td><td>Tobacco</td><td>Z00044</td><td>155943</td><td>Tobacco</td><td>[<xref ref-type="bibr" rid="CR3">3</xref>]</td></tr><tr><td><italic>Nuphar advena</italic></td><td>Spatterdock</td><td>NC_008788</td><td>160866</td><td>Medicinal</td><td>[<xref ref-type="bibr" rid="CR201">201</xref>]</td></tr><tr><td><italic>Nymphaea alba</italic> (2)</td><td>White water-lily</td><td>NC_006050</td><td>159930</td><td>Flower</td><td>[<xref ref-type="bibr" rid="CR24">24</xref>]</td></tr><tr><td><italic>Oncidium</italic> hybrid</td><td>Oncidium</td><td>NC_014056</td><td>146484</td><td>Flower</td><td>[<xref ref-type="bibr" rid="CR54">54</xref>]</td></tr><tr><td><italic>Oryza sativa</italic> (6)</td><td>Rice</td><td>X15901</td><td>134525</td><td>Cereals</td><td>[<xref ref-type="bibr" rid="CR202">202</xref>]</td></tr><tr><td><italic>Panax ginseng</italic> (2)</td><td>Ginseng</td><td>NC_006290</td><td>156318</td><td>Medicinal</td><td>[<xref ref-type="bibr" rid="CR203">203</xref>]</td></tr><tr><td><italic>Panicum virgatum</italic></td><td>Switchgrass</td><td>NC_015990</td><td>139619</td><td>Biofuel</td><td>[<xref ref-type="bibr" rid="CR204">204</xref>]</td></tr><tr><td><italic>Paphiopedilum armeniacum</italic> (2)</td><td>Slipper orchid</td><td>NC_026779</td><td>162682</td><td>Flower</td><td>[<xref ref-type="bibr" rid="CR32">32</xref>]</td></tr><tr><td><italic>Parthenium argentatum</italic></td><td>Guayule</td><td>NC_013553</td><td>152803</td><td>Biofuel</td><td>[<xref ref-type="bibr" rid="CR205">205</xref>]</td></tr><tr><td><italic>Pelargonium</italic> (2)</td><td>Geranium</td><td>NC_008454</td><td>217942</td><td>Flower</td><td>[<xref ref-type="bibr" rid="CR206">206</xref>]</td></tr><tr><td><italic>Phalaenopsis</italic> hybrid (3)</td><td>Phalaenopsis orchid</td><td>NC_007499</td><td>148964</td><td>Flower</td><td>[<xref ref-type="bibr" rid="CR51">51</xref>]</td></tr><tr><td><italic>Phaseolus vulgaris</italic></td><td>Kidney bean</td><td>NC_009259</td><td>150285</td><td>Bean</td><td>[<xref ref-type="bibr" rid="CR78">78</xref>]</td></tr><tr><td><italic>Pisum sativum</italic></td><td>Pea</td><td>NC_014057</td><td>122169</td><td>Vegetable</td><td>[<xref ref-type="bibr" rid="CR76">76</xref>]</td></tr><tr><td><italic>Raphanus sativus</italic></td><td>Radish</td><td>NC_024469</td><td>153368</td><td>Vegetable</td><td>[<xref ref-type="bibr" rid="CR207">207</xref>]</td></tr><tr><td><italic>Ravenala madagascariensis</italic></td><td>Traveller's tree</td><td>NC_022927</td><td>166170</td><td>Ornamental</td><td>[<xref ref-type="bibr" rid="CR184">184</xref>]</td></tr><tr><td><italic>Ricinus communis</italic></td><td>Castor bean</td><td>NC_016736</td><td>163161</td><td>Oil</td><td>[<xref ref-type="bibr" rid="CR208">208</xref>]</td></tr><tr><td><italic>Saccharum</italic> hybrid (2)</td><td>Sugarcane</td><td>NC_005878</td><td>141182</td><td>Sugar</td><td>[<xref ref-type="bibr" rid="CR209">209</xref>]</td></tr><tr><td><italic>Salvia miltiorrhiza</italic></td><td>Redroot sage</td><td>NC_020431</td><td>151328</td><td>Medicinal</td><td>[<xref ref-type="bibr" rid="CR210">210</xref>]</td></tr><tr><td><italic>Secale cereale</italic></td><td>Rye</td><td>NC_021761</td><td>114843</td><td>Cereals</td><td>[<xref ref-type="bibr" rid="CR64">64</xref>]</td></tr><tr><td><italic>Sesamum indicum</italic></td><td>Sesame</td><td>NC_016433</td><td>153324</td><td>Oil</td><td>[<xref ref-type="bibr" rid="CR211">211</xref>]</td></tr><tr><td><italic>Solanum lycopersicum</italic> (11)</td><td>Tomato</td><td>NC_007898</td><td>155461</td><td>Vegetable</td><td>[<xref ref-type="bibr" rid="CR13">13</xref>]</td></tr><tr><td><italic>Solanum tuberosum</italic></td><td>Potato</td><td>DQ231562</td><td>155312</td><td>Starch crop</td><td>[<xref ref-type="bibr" rid="CR212">212</xref>]</td></tr><tr><td><italic>Sorghum bicolor</italic> (2)</td><td>Sorghum</td><td>NC_008602</td><td>140754</td><td>Cereals</td><td>[<xref ref-type="bibr" rid="CR8">8</xref>]</td></tr><tr><td><italic>Spinacia oleracea</italic></td><td>Spinach</td><td>NC_002202</td><td>150725</td><td>Vegetable</td><td>[<xref ref-type="bibr" rid="CR213">213</xref>]</td></tr><tr><td><italic>Trifolium grandiflorum</italic> (8)</td><td>Large-flower hop clover</td><td>NC_024034</td><td>125628</td><td>Forage</td><td>[<xref ref-type="bibr" rid="CR74">74</xref>]</td></tr><tr><td><italic>Triticum aestivum</italic> (6)</td><td>Bread wheat</td><td>NC_002762</td><td>134545</td><td>Cereals</td><td>[<xref ref-type="bibr" rid="CR63">63</xref>]</td></tr><tr><td><italic>Vanilla planifolia</italic></td><td>Vanilla</td><td>NC_026778</td><td>148011</td><td>Fruit</td><td>[<xref ref-type="bibr" rid="CR32">32</xref>]</td></tr><tr><td><italic>Vigna radiata</italic> (3)</td><td>Mung bean</td><td>NC_013843</td><td>151271</td><td>Bean</td><td>[<xref ref-type="bibr" rid="CR79">79</xref>]</td></tr><tr><td><italic>Zea mays</italic></td><td>Maize</td><td>NC_001666</td><td>140384</td><td>Cereals</td><td>[<xref ref-type="bibr" rid="CR62">62</xref>]</td></tr><tr><td><italic>Zingiber spectabile</italic></td><td>True ginger</td><td>NC_020363</td><td>155890</td><td>Ornamental</td><td>[<xref ref-type="bibr" rid="CR193">193</xref>]</td></tr><tr><td>Trees and perennial plants</td><td></td><td></td><td></td><td></td><td></td></tr><tr><td><italic>Abies koreana</italic></td><td>Fir</td><td>NC_026892</td><td>121373</td><td>Wood</td><td>[<xref ref-type="bibr" rid="CR214">214</xref>]</td></tr><tr><td><italic>Actinidia chinensis</italic> (2)</td><td>Kiwifriut</td><td>NC_026690</td><td>156346</td><td>Fruit</td><td>[<xref ref-type="bibr" rid="CR215">215</xref>]</td></tr><tr><td><italic>Amentotaxus formosana</italic></td><td>Taiwan catkin yew</td><td>NC_024945</td><td>136430</td><td>Timber</td><td>[<xref ref-type="bibr" rid="CR216">216</xref>]</td></tr><tr><td><italic>Araucaria heterophylla</italic></td><td>Norfolk island araucaria</td><td>NC_026450</td><td>146723</td><td>Timber</td><td>[<xref ref-type="bibr" rid="CR217">217</xref>]</td></tr><tr><td><italic>Bambusa multiplex</italic> (4)</td><td>Golden goddess bamboo</td><td>NC_024668</td><td>139394</td><td>Ornamental</td><td>[<xref ref-type="bibr" rid="CR91">91</xref>]</td></tr><tr><td><italic>Bambusa oldhamii</italic></td><td>Green bamboo</td><td>NC_012927</td><td>139350</td><td>Vegetable</td><td>[<xref ref-type="bibr" rid="CR28">28</xref>]</td></tr><tr><td><italic>Berberis bealei</italic></td><td>Beale's mahonia</td><td>NC_022457</td><td>164792</td><td>Ornamental</td><td>[<xref ref-type="bibr" rid="CR218">218</xref>]</td></tr><tr><td><italic>Bismarckia nobilis</italic></td><td>Bismarck palm</td><td>NC_020366</td><td>158210</td><td>Ornamental</td><td>[<xref ref-type="bibr" rid="CR193">193</xref>]</td></tr><tr><td><italic>Buxus microphylla</italic></td><td>Japanese box</td><td>NC_009599</td><td>159010</td><td>Ornamental</td><td>[<xref ref-type="bibr" rid="CR219">219</xref>]</td></tr><tr><td><italic>Calocedrus formosana</italic></td><td>Taiwan incense-cedar</td><td>NC_023121</td><td>127311</td><td>Timber</td><td>[<xref ref-type="bibr" rid="CR220">220</xref>]</td></tr><tr><td><italic>Calycanthus floridus</italic></td><td>Carolina-allspice</td><td>NC_004993</td><td>153337</td><td>Medicinal</td><td>[<xref ref-type="bibr" rid="CR23">23</xref>]</td></tr><tr><td><italic>Camellia oleifera</italic> (13)</td><td>Tea oil plant</td><td>NC_023084</td><td>156971</td><td>Oil</td><td>[<xref ref-type="bibr" rid="CR221">221</xref>]</td></tr><tr><td><italic>Camellia reticulata</italic></td><td>To-tsubaki</td><td>NC_024663</td><td>156971</td><td>Flower</td><td>[<xref ref-type="bibr" rid="CR222">222</xref>]</td></tr><tr><td><italic>Carludovica palmata</italic></td><td>Toquilla palm</td><td>NC_026786</td><td>158545</td><td>Fiber</td><td>[<xref ref-type="bibr" rid="CR198">198</xref>]</td></tr><tr><td><italic>Castanea mollissima</italic></td><td>Chestnut</td><td>NC_014674</td><td>160799</td><td>Fruit</td><td>[<xref ref-type="bibr" rid="CR14">14</xref>]</td></tr><tr><td><italic>Cathaya argyrophylla</italic></td><td>Cathaya</td><td>NC_014589</td><td>107122</td><td>Timber</td><td>[<xref ref-type="bibr" rid="CR223">223</xref>]</td></tr><tr><td><italic>Cedrus deodara</italic></td><td>Cedar</td><td>NC_014575</td><td>119299</td><td>Timber</td><td>[<xref ref-type="bibr" rid="CR223">223</xref>]</td></tr><tr><td><italic>Cephalotaxus wilsoniana</italic> (2)</td><td>Wilson plum yew</td><td>NC_016063</td><td>136196</td><td>Timber</td><td>[<xref ref-type="bibr" rid="CR224">224</xref>]</td></tr><tr><td><italic>Chrysobalanus icaco</italic></td><td>Coco plum</td><td>NC_024061</td><td>162775</td><td>Fruit</td><td>[<xref ref-type="bibr" rid="CR225">225</xref>]</td></tr><tr><td><italic>Citrus sinensis</italic> (2)</td><td>Orange</td><td>NC_008334</td><td>160129</td><td>Fruit</td><td>[<xref ref-type="bibr" rid="CR12">12</xref>]</td></tr><tr><td><italic>Cocos nucifera</italic></td><td>Coconut</td><td>NC_022417</td><td>154731</td><td>Oil</td><td>[<xref ref-type="bibr" rid="CR226">226</xref>]</td></tr><tr><td><italic>Coffea arabica</italic></td><td>Coffee</td><td>NC_008535</td><td>155189</td><td>Beverage</td><td>[<xref ref-type="bibr" rid="CR10">10</xref>]</td></tr><tr><td><italic>Corymbia gummifera</italic> (4)</td><td>Red bloodwood</td><td>NC_022407</td><td>160713</td><td>Timber</td><td>[<xref ref-type="bibr" rid="CR227">227</xref>]</td></tr><tr><td><italic>Corynocarpus laevigata</italic></td><td>Karaka nut</td><td>NC_014807</td><td>159202</td><td>Fruit</td><td>[<xref ref-type="bibr" rid="CR37">37</xref>]</td></tr><tr><td><italic>Cryptomeria japonica</italic></td><td>Sugi</td><td>NC_010548</td><td>131810</td><td>Timber</td><td>[<xref ref-type="bibr" rid="CR228">228</xref>]</td></tr><tr><td><italic>Dendrocalamus latiflorus</italic></td><td>Sweet giant bamboo</td><td>NC_013088</td><td>139394</td><td>Vegetable</td><td>[<xref ref-type="bibr" rid="CR28">28</xref>]</td></tr><tr><td><italic>Elaeis guineensis</italic></td><td>African oil palm</td><td>NC_017602</td><td>156973</td><td>Oil</td><td>[<xref ref-type="bibr" rid="CR229">229</xref>]</td></tr><tr><td><italic>Eucalyptus globulus</italic> (32)</td><td>Eucalyptus</td><td>NC_008115</td><td>160286</td><td>Timber</td><td>[<xref ref-type="bibr" rid="CR230">230</xref>]</td></tr><tr><td><italic>Hevea brasiliensis</italic></td><td>Rubber tree</td><td>NC_015308</td><td>161191</td><td>Rubber</td><td>[<xref ref-type="bibr" rid="CR231">231</xref>]</td></tr><tr><td><italic>Jasminum nudiflorum</italic></td><td>Winter jasmine</td><td>NC_008407</td><td>165121</td><td>Ornamental</td><td>[<xref ref-type="bibr" rid="CR232">232</xref>]</td></tr><tr><td><italic>Jatropha curcas</italic></td><td>Barbados nut</td><td>NC_012224</td><td>163856</td><td>Biofuel</td><td>[<xref ref-type="bibr" rid="CR233">233</xref>]</td></tr><tr><td><italic>Juniperus bermudiana</italic> (4)</td><td>Bermuda juniper</td><td>NC_024021</td><td>127659</td><td>Timber</td><td>[<xref ref-type="bibr" rid="CR234">234</xref>]</td></tr><tr><td><italic>Larix decidua</italic></td><td>European larch</td><td>NC_016058</td><td>122474</td><td>Timber</td><td>[<xref ref-type="bibr" rid="CR224">224</xref>]</td></tr><tr><td><italic>Licania sprucei</italic> (3)</td><td>Licania</td><td>NC_024065</td><td>162228</td><td>Ornamental</td><td>[<xref ref-type="bibr" rid="CR225">225</xref>]</td></tr><tr><td><italic>Liquidambar formosana</italic></td><td>Chinese sweetgum</td><td>NC_023092</td><td>160410</td><td>Timber</td><td>[<xref ref-type="bibr" rid="CR30">30</xref>]</td></tr><tr><td><italic>Liriodendron tulipifera</italic></td><td>Tulip tree</td><td>NC_008326</td><td>159886</td><td>Timber</td><td>[<xref ref-type="bibr" rid="CR235">235</xref>]</td></tr><tr><td><italic>Metasequoia glyptostroboides</italic></td><td>Dawn redwood</td><td>NC_027423</td><td>131887</td><td>Timber</td><td>[<xref ref-type="bibr" rid="CR236">236</xref>]</td></tr><tr><td><italic>Millettia pinnata</italic></td><td>Indian beech</td><td>NC_016708</td><td>152968</td><td>Ornamental</td><td>[<xref ref-type="bibr" rid="CR81">81</xref>]</td></tr><tr><td><italic>Morus indica</italic> (3)</td><td>White mulberry</td><td>NC_008359</td><td>158484</td><td>White mulberry</td><td>[<xref ref-type="bibr" rid="CR237">237</xref>]</td></tr><tr><td><italic>Nageia nagi</italic></td><td>Asian bayberry</td><td>NC_023120</td><td>133722</td><td>Timber</td><td>[<xref ref-type="bibr" rid="CR220">220</xref>]</td></tr><tr><td><italic>Nandina domestica</italic></td><td>Heavenly bamboo</td><td>NC_008336</td><td>156599</td><td>Ornamental</td><td>[<xref ref-type="bibr" rid="CR33">33</xref>]</td></tr><tr><td><italic>Nerium oleander</italic></td><td>Oleander</td><td>NC_025656</td><td>154903</td><td>Ornamental</td><td>[<xref ref-type="bibr" rid="CR238">238</xref>]</td></tr><tr><td><italic>Olea europaea</italic> (5)</td><td>Olive</td><td>NC_015604</td><td>155862</td><td>Oil</td><td>[<xref ref-type="bibr" rid="CR239">239</xref>]</td></tr><tr><td><italic>Phoenix dactylifera</italic></td><td>Date palm</td><td>NC_013991</td><td>158462</td><td>Fruit</td><td>[<xref ref-type="bibr" rid="CR240">240</xref>]</td></tr><tr><td><italic>Phyllostachys edulis</italic> (4)</td><td>Moso bamboo</td><td>NC_015817</td><td>139679</td><td>Timber</td><td>[<xref ref-type="bibr" rid="CR89">89</xref>]</td></tr><tr><td><italic>Picea sitchensis</italic> (3)</td><td>Sitka spruce</td><td>NC_011152</td><td>120176</td><td>Timber</td><td>[<xref ref-type="bibr" rid="CR35">35</xref>]</td></tr><tr><td><italic>Pinus taiwanensis</italic> (12)</td><td>Taiwan red pine</td><td>NC_027415</td><td>119741</td><td>Timber</td><td>[<xref ref-type="bibr" rid="CR241">241</xref>]</td></tr><tr><td><italic>Platanus occidentalis</italic></td><td>American sycamore</td><td>NC_008335</td><td>161791</td><td>Ornamental</td><td>[<xref ref-type="bibr" rid="CR33">33</xref>]</td></tr><tr><td><italic>Podocarpus lambertii</italic> (3)</td><td>Podocarpus</td><td>NC_023805</td><td>133734</td><td>Ornamental</td><td>[<xref ref-type="bibr" rid="CR242">242</xref>]</td></tr><tr><td><italic>Populus alba</italic></td><td>White poplar</td><td>NC_008235</td><td>156505</td><td>Timber</td><td>[<xref ref-type="bibr" rid="CR243">243</xref>]</td></tr><tr><td><italic>Prinsepia utilis</italic></td><td>Himalayan cherry</td><td>NC_021455</td><td>156328</td><td>Ornamental</td><td>[<xref ref-type="bibr" rid="CR244">244</xref>]</td></tr><tr><td><italic>Prunus persica</italic> (6)</td><td>Peach</td><td>NC_014697</td><td>157790</td><td>Fruit</td><td>[<xref ref-type="bibr" rid="CR14">14</xref>]</td></tr><tr><td><italic>Pseudophoenix vinifera</italic></td><td>Florida cherry palm</td><td>NC_020364</td><td>157829</td><td>Ornamental</td><td>[<xref ref-type="bibr" rid="CR193">193</xref>]</td></tr><tr><td><italic>Pseudotsuga sinensis</italic></td><td>Chinese douglas</td><td>NC_016064</td><td>122513</td><td>Timber</td><td>[<xref ref-type="bibr" rid="CR224">224</xref>]</td></tr><tr><td><italic>Pyrus pyrifolia</italic> (2)</td><td>Chinese pear</td><td>NC_015996</td><td>159922</td><td>Fruit</td><td>[<xref ref-type="bibr" rid="CR245">245</xref>]</td></tr><tr><td><italic>Quercus rubra</italic> (4)</td><td>Oak</td><td>NC_020152</td><td>161304</td><td>Timber</td><td>[<xref ref-type="bibr" rid="CR246">246</xref>]</td></tr><tr><td><italic>Sapindus mukorossi</italic></td><td>Soapberries</td><td>NC_025554</td><td>160481</td><td>Medicinal</td><td>[<xref ref-type="bibr" rid="CR247">247</xref>]</td></tr><tr><td><italic>Taiwania cryptomerioides</italic> (2)</td><td>Taiwania</td><td>NC_016065</td><td>132588</td><td>Timber</td><td>[<xref ref-type="bibr" rid="CR224">224</xref>]</td></tr><tr><td><italic>Theobroma cacao</italic></td><td>Cacao tree</td><td>HQ336404</td><td>160604</td><td>Beverage</td><td>[<xref ref-type="bibr" rid="CR14">14</xref>]</td></tr><tr><td><italic>Vaccinium macrocarpon</italic></td><td>Large cranberry</td><td>NC_019616</td><td>176045</td><td>Fruit</td><td>[<xref ref-type="bibr" rid="CR248">248</xref>]</td></tr><tr><td><italic>Vitis vinifera</italic></td><td>Wine grape</td><td>NC_007957</td><td>160928</td><td>Fruit</td><td>[<xref ref-type="bibr" rid="CR19">19</xref>]</td></tr><tr><td><italic>Wollemia nobilis</italic></td><td>Wollemia</td><td>NC_027235</td><td>145630</td><td>Timber</td><td>[<xref ref-type="bibr" rid="CR249">249</xref>]</td></tr></tbody></table><table-wrap-foot><p>*The number of species in the same genus as the listed species that have sequenced and annotated chloroplast genomes is shown in parentheses</p></table-wrap-foot></table-wrap></p><p>Like the genes, the introns in land-plant chloroplast genomes are generally conserved, but the loss of introns within protein-coding genes has been reported in several plant species [<xref ref-type="bibr" rid="CR49">49</xref>], including barley (<italic>Hordeum vulgare</italic>) [<xref ref-type="bibr" rid="CR8">8</xref>], bamboo (<italic>Bambusa</italic> sp.) [<xref ref-type="bibr" rid="CR28">28</xref>], cassava (<italic>Manihot esculenta</italic>) [<xref ref-type="bibr" rid="CR20">20</xref>], and chickpea (<italic>Cicer arietinum</italic>) [<xref ref-type="bibr" rid="CR7">7</xref>]. The proteins encoded by genes in which intron loss is known to occur have diverse functions; they include an ATP synthase (atpF), a Clp protease (clpP), an RNA polymerase (rpoC2), and ribosomal proteins (rpl2, rps12, and rps16) [<xref ref-type="bibr" rid="CR49">49</xref>]. The majority of reported intron losses have been observed in specific plant groups or species, although some examples of intron loss (such as that in <italic>clpP</italic>) occur in diverse plant species, including monocots (Poaceae), eudicots (Onagraceae and Oleaceae) and gymnosperms (<italic>Pinus</italic>) [<xref ref-type="bibr" rid="CR49">49</xref>].</p></sec><sec id="Sec4"><title>Diversity of chloroplast genome sequences</title><p>At higher taxonomic levels (family level), protein-coding regions and conserved sequences of the chloroplast genome can be used for phylogenetic analysis and domestication studies [<xref ref-type="bibr" rid="CR49">49</xref>]. Earlier phylogenetic analyses utilized partial chloroplast DNA sequences. The use of variable regions or multiple DNA fragments dramatically enhanced the utility of these analyses but there is insufficient information in these sequences to provide the high-resolution necessary to differentiate closely related taxa, particularly some within-species taxa whose taxonomic relationships are unclear. Complete chloroplast genome sequences are valuable for deciphering phylogenetic relationships between closely related taxa and for improving our understanding of the evolution of plant species.</p><p>In this section, we discuss several examples of comparisons of chloroplast genomes, within and between crop species, that have provided unique insight into evolutionary relationships among taxa. We also discuss the origin and geographic distribution of economically important species, as well as their adaptations to different climatic conditions and the use of genome information in their breeding and conservation.</p><p>A key application of the chloroplast genome in agriculture is the identification of commercial cultivars and the determination of their purity. DNA barcodes derived from the chloroplast genome can be used to identify varieties and in the conservation of breeding resources. Success in breeding is determined by genetic compatibility and chloroplast genomes serve as a valuable tool for identifying plants that are likely to be closely related and, therefore, genetically compatible. Understanding the genetic relationships between cultivated crops and their wild relatives informs efforts to introduce specific advantageous traits into cultivated crops. In the section below, we discuss how chloroplast genomes have been used to elucidate the evolutionary relationships and domestication history of a few major crops and how this informs breeding programs.</p><sec id="Sec5"><title>Breeding</title><p>The Orchidaceae is a large family that encompasses about 6–11 % of all angiosperms [<xref ref-type="bibr" rid="CR50">50</xref>] and is important in floriculture. Many commercially important orchid species belong to the subfamily Epidendroideae and chloroplast genomes of several species from this subfamily have been sequenced [<xref ref-type="bibr" rid="CR51">51</xref>–<xref ref-type="bibr" rid="CR58">58</xref>]. Because it is easy to perform inter-generic crossing in orchids and because the record of breeding is sometimes incomplete, it is often difficult to validate the parental origin of commercially important varieties [<xref ref-type="bibr" rid="CR54">54</xref>]. Corrected parental information is important for breeding and variety identification. In an investigation of the Oncidiinae, a subtribe within the Epidendroideae, PCR products derived from eight conserved regions in 15 commercial varieties resolved their phylogenetic relationship at the species level [<xref ref-type="bibr" rid="CR54">54</xref>] and helped to resolve putative errors in parental origin. Parental records had indicated that <italic>Odontoglossum</italic> ‘Violetta von Holm’, <italic>Odontoglossum</italic> ‘Margarete Holm’ and <italic>Odontocidium</italic> ‘Golden Gate’ are derived from the same female parent (<italic>Odontoglossum bictoniense</italic>) but phylogenetic analyses of ‘Violetta von Holm’ did not correlate with those of ‘Golden Gate’ or ‘Margarete Holm’ [<xref ref-type="bibr" rid="CR54">54</xref>]. A possible reason for inconsistencies between the chloroplast DNA-based phylogenetic tree and the parental record is chloroplast capture. Chloroplast capture is the introgression of chloroplasts from one species into another after intrageneric and intergeneric hybridization [<xref ref-type="bibr" rid="CR59">59</xref>]. Although chloroplast genomes provide useful information for phylogenetic analyses involving closely related taxa, chloroplast capture by hybridization may distort phylogenetic relationships if captured chloroplast genomes or genes included therein are used [<xref ref-type="bibr" rid="CR60">60</xref>]. The use of both nuclear and chloroplast genomes can provide more complete phylogenies [<xref ref-type="bibr" rid="CR4">4</xref>, <xref ref-type="bibr" rid="CR61">61</xref>].</p></sec><sec id="Sec6"><title>Phylogenetic studies</title><p>There are several published chloroplast genomes from cereals, including those from sorghum (<italic>Sorghum bicolor</italic>), barley [<xref ref-type="bibr" rid="CR8">8</xref>], maize (<italic>Zea mays</italic>) [<xref ref-type="bibr" rid="CR62">62</xref>], wheat (<italic>Triticum aestivum</italic>) [<xref ref-type="bibr" rid="CR63">63</xref>], rye (<italic>Secale cereale</italic>) [<xref ref-type="bibr" rid="CR64">64</xref>], and rice (<italic>Oryza sativa</italic>) [<xref ref-type="bibr" rid="CR65">65</xref>]. Rice is one of the world's most important crops and is the primary carbohydrate source for the global human population (<ext-link ext-link-type="uri" xlink:href="http://www.ers.usda.gov/topics/crops/rice.aspx">http://www.ers.usda.gov/topics/crops/rice.aspx</ext-link>). The <italic>Oryza</italic> species are classified into ten genome types, including six diploids (AA, BB, CC, EE, FF, and GG) and four allotetraploids (BBCC, CCDD, HHJJ, and HHKK). Attempts to clarify the evolutionary relationships between cultivated rice and its wild relatives remain contentious and inconclusive [<xref ref-type="bibr" rid="CR4">4</xref>]. For example, there are two wild species that have an AA genome in Australia, <italic>Oryza meridionalis</italic> (annual) and <italic>Oryza rufipogon</italic> (perennial). <italic>Oryza sativa</italic> was domesticated from Asian <italic>O. rufipogon</italic> 10,000 years ago [<xref ref-type="bibr" rid="CR65">65</xref>]. Nevertheless, analysis of complete Australian and Asian wild rice chloroplast genomes indicated that Australian <italic>O. rufipogon</italic> chloroplast genomes are more similar to those of Australian <italic>O. meridionalis</italic> than to those of Asian <italic>O. rufipogon</italic> [<xref ref-type="bibr" rid="CR65">65</xref>–<xref ref-type="bibr" rid="CR67">67</xref>]. Using 19 chloroplast genomes of <italic>Oryza</italic> AA genome species, a robust phylogenetic tree was established, which will aid in improving rice crops and in conservation strategies [<xref ref-type="bibr" rid="CR4">4</xref>, <xref ref-type="bibr" rid="CR5">5</xref>].</p><p>Cotton is the most important textile fiber crop and the first cotton (<italic>Gossypium hirsutum</italic>) chloroplast genome was published in 2006 [<xref ref-type="bibr" rid="CR11">11</xref>]. The diploid <italic>Gossypium</italic> species comprise eight genome groups (A to G and K genomes). <italic>Gossypium hirsutum</italic> (upland cotton), the most widely planted cotton species in the world, is an allotetraploid of the ancestral A and D genome species [<xref ref-type="bibr" rid="CR68">68</xref>]. Chloroplast genome sequences are available for 22 <italic>Gossypium</italic> species and these can be used to glean information about the evolution and domestication of this crop [<xref ref-type="bibr" rid="CR11">11</xref>, <xref ref-type="bibr" rid="CR68">68</xref>, <xref ref-type="bibr" rid="CR69">69</xref>] (Table <xref rid="Tab1" ref-type="table">1</xref>). Simple sequence repeat primers were used to investigate 41 species of <italic>Gossypium</italic>, including all eight genome groups and allotetraploid species [<xref ref-type="bibr" rid="CR70">70</xref>]. The results indicated that two modern A-genome species, <italic>Gossypium herbaceum</italic> and <italic>Gossypium arboretum</italic>, were not cytoplasmic donors of tetraploid (AD) species; instead, the AD genome species originated from an extinct ancestor species of the modern A genome [<xref ref-type="bibr" rid="CR68">68</xref>, <xref ref-type="bibr" rid="CR70">70</xref>].</p></sec><sec id="Sec7"><title>Domestication</title><p>Information on chloroplast genomes is useful for understanding the domestication of several crops, particularly legumes [<xref ref-type="bibr" rid="CR71">71</xref>]. The chloroplast genome structure of legumes is very interesting; it contains multiple rearrangements, including large inverted segments and loss of inverted repeats [<xref ref-type="bibr" rid="CR72">72</xref>]. An example is a 51-kb inversion that was first identified in the soybean (<italic>Glycine max</italic>) chloroplast genome sequence [<xref ref-type="bibr" rid="CR18">18</xref>] before being reported in most members of the subfamily Papilionoideae [<xref ref-type="bibr" rid="CR7">7</xref>, <xref ref-type="bibr" rid="CR73">73</xref>–<xref ref-type="bibr" rid="CR77">77</xref>]. A 78-kb reversion was subsequently confirmed in <italic>Phaseolus</italic> and <italic>Vigna</italic> chloroplast genomes [<xref ref-type="bibr" rid="CR78">78</xref>, <xref ref-type="bibr" rid="CR79">79</xref>]. More recently, 36-kb [<xref ref-type="bibr" rid="CR80">80</xref>] and 5.6-kb [<xref ref-type="bibr" rid="CR81">81</xref>] inversions inside the 51-kb inversion were identified. There are many important genes within these inverted regions but no gene is disturbed and plant survival and performance are not affected. These unique characteristics are not only very useful in phylogenetic studies [<xref ref-type="bibr" rid="CR82">82</xref>] but also provide important information for chloroplast transformation in legumes. Chloroplast structure is also important for the design of primers needed in the amplification of sequences for further domestication and phylogenetic analysis.</p><p><italic>Citrus</italic> is one of the most commercially important fruit genera. In 2006, the first <italic>Citrus</italic> chloroplast genome, that of sweet orange (<italic>Citrus × sinensis</italic>), was published [<xref ref-type="bibr" rid="CR12">12</xref>] and this served as a reference genome for subsequent publications [<xref ref-type="bibr" rid="CR83">83</xref>, <xref ref-type="bibr" rid="CR84">84</xref>]. Phylogenetic analysis of 34 chloroplast genomes of <italic>Citrus</italic> (28) and <italic>Citrus</italic>-related genera (6) indicated that citrus fruits have the same common ancestor [<xref ref-type="bibr" rid="CR84">84</xref>, <xref ref-type="bibr" rid="CR85">85</xref>]. In four genes (<italic>matK</italic>, <italic>ndhF</italic>, <italic>ycf1</italic>, and <italic>ccsA</italic>), single-nucleotide variations and insertion/deletion frequencies were clearly higher than average and showed that these genes have been positively selected. The <italic>matK</italic> gene encodes a maturase that is involved in splicing type II introns and the <italic>matK</italic> sequence is often used in phylogenetic and evolutionary studies [<xref ref-type="bibr" rid="CR84">84</xref>]. Positive selection of <italic>matK</italic> is observed not only in citrus but is common in several other plant species. In fact, more than 30 plant groups have been shown to undergo positive selection of <italic>matK</italic> genes, indicating that the gene is subject to a number of different ecological selective pressures [<xref ref-type="bibr" rid="CR86">86</xref>]. The <italic>ndhF</italic> gene encodes a subunit of the chloroplast NAD(P)H dehydrogenase (NDH) complex. Chloroplast NDH monomers are sensitive to high light stress, suggesting that the <italic>ndh</italic> genes may also be involved in stress acclimation [<xref ref-type="bibr" rid="CR87">87</xref>]. These studies indicated that <italic>matK</italic> and <italic>ndhF</italic> show positive selection in Australian species, potentially contributing to their adaptation to a hot, dry climate [<xref ref-type="bibr" rid="CR84">84</xref>, <xref ref-type="bibr" rid="CR85">85</xref>].</p><p>Bamboo is an economically and ecologically important forest plant in Asia [<xref ref-type="bibr" rid="CR88">88</xref>]. Bamboo grows quickly and new culms are regenerated from the rhizome after harvesting, making it a sustainable and ecologically and environmentally friendly crop. The first two bamboo chloroplast genomes have been published [<xref ref-type="bibr" rid="CR28">28</xref>] and many more bamboo chloroplast genomes are now available [<xref ref-type="bibr" rid="CR88">88</xref>–<xref ref-type="bibr" rid="CR93">93</xref>]. Bamboo has a long juvenility and it is difficult to obtain flowers for taxonomic studies; consequently the taxonomic relationships of bamboo have proven challenging to unravel on the basis of traditional reproductive organ morphology. Furthermore, the extremely low rate of sequence divergence meant that the taxonomic and phylogenetic relationships of temperate woody bamboos at lower taxonomic levels proved difficult to resolve [<xref ref-type="bibr" rid="CR88">88</xref>]. These relationships were eventually resolved with high-resolution phylogenetic trees using 25 bamboo chloroplast genomes [<xref ref-type="bibr" rid="CR93">93</xref>]. In addition to woody bamboos, chloroplast genomes have also been published for herbaceous bamboo [<xref ref-type="bibr" rid="CR88">88</xref>, <xref ref-type="bibr" rid="CR92">92</xref>]. An interesting phenomenon identified in herbaceous bamboo chloroplast genomes is that of gene transfer from the mitochondrial genome to the chloroplast genome. This was an unusual observation, as the chloroplast genome is thought to be nearly immune to the transfer of DNA from nuclear and mitochondrial genomes [<xref ref-type="bibr" rid="CR88">88</xref>, <xref ref-type="bibr" rid="CR92">92</xref>, <xref ref-type="bibr" rid="CR94">94</xref>]. A possible reason for this recalcitrance to DNA transfer is the lack of an efficient DNA uptake system [<xref ref-type="bibr" rid="CR94">94</xref>]. Prior to its observation in herbaceous bamboo, this phenomenon was only observed in two eudicot chloroplast genomes [<xref ref-type="bibr" rid="CR94">94</xref>] and in monocots [<xref ref-type="bibr" rid="CR88">88</xref>, <xref ref-type="bibr" rid="CR92">92</xref>].</p></sec></sec><sec id="Sec8"><title>Transfer of chloroplast genes to nuclear or mitochondrial genomes</title><p>There are three distinct genomes in plant cells: nuclear, mitochondrial, and plastid. Mitochondria are believed to have evolved from a single endosymbiotic event by the uptake of a proteobacterium, whereas chloroplasts evolved from endosymbiosis of a cyanobacterium, after which there was a massive transfer of genes from the chloroplast to the nucleus [<xref ref-type="bibr" rid="CR95">95</xref>]. There are distinct translation systems in these organelles: nuclear-encoded genes are translated in the cytosol and the protein products are then transported to the locations in which they function, including chloroplasts [<xref ref-type="bibr" rid="CR96">96</xref>], whereas chloroplast-encoded proteins are directly synthesized within the chloroplast. Multi-subunit functional protein complexes that are involved in photosynthesis or protein synthesis are also assembled within chloroplasts.</p><p>Gene content, number, and structure are conserved in the chloroplast genome sequences of most autotrophic land plants [<xref ref-type="bibr" rid="CR97">97</xref>, <xref ref-type="bibr" rid="CR98">98</xref>] but some protein-encoding genes are absent in specific species [<xref ref-type="bibr" rid="CR49">49</xref>]. The loss of genes such as <italic>infA</italic>, <italic>rpl22</italic>, and <italic>ndh</italic> from the chloroplast genome and their intracellular transfer to the nuclear or mitochondrial genomes provide valuable information for phylogenetic analyses and evolutionary studies. It is very easy to identify the chloroplast origin of genes in plant mitochondrial or nuclear genomes [<xref ref-type="bibr" rid="CR99">99</xref>, <xref ref-type="bibr" rid="CR100">100</xref>] by intracellular gene transfer [<xref ref-type="bibr" rid="CR32">32</xref>], but this could also lead to erroneous phylogenic relationships when short sequences are used instead of complete chloroplast genome sequences.</p><p>The chloroplast <italic>translation initiation factor 1</italic> (<italic>infA</italic>) is a homolog of the essential gene <italic>infA</italic> in <italic>Escherichia coli</italic> [<xref ref-type="bibr" rid="CR101">101</xref>, <xref ref-type="bibr" rid="CR102">102</xref>]. This gene initiates translation in collaboration with two nuclear-encoded initiation factors to mediate interactions between mRNA, ribosomes, and initiator tRNA-Met [<xref ref-type="bibr" rid="CR102">102</xref>]. Many parallel losses of chloroplast-encoded <italic>infA</italic> have occurred during angiosperm evolution [<xref ref-type="bibr" rid="CR102">102</xref>] (Fig. <xref rid="Fig2" ref-type="fig">2</xref>). Nuclear-encoded <italic>infA</italic> genes have been identified in <italic>Arabidopsis thaliana</italic>, soybean, tomato (<italic>Solanum lycopersicum</italic>), and ice plant (<italic>Mesembryanthemum crystallinum</italic>) [<xref ref-type="bibr" rid="CR102">102</xref>]. Protein sequences of nuclear-encoded <italic>infA</italic> in these four species contain chloroplast transit peptides. Studies using soybean and <italic>A. thaliana</italic> infA-GFP proteins have shown that nuclear-encoded <italic>infA</italic> genes are translated in the cytosol and transported into chloroplasts [<xref ref-type="bibr" rid="CR102">102</xref>]. Many more chloroplast-encoded <italic>infA</italic> deletions have been identified recently (Fig. <xref rid="Fig2" ref-type="fig">2</xref>).<fig id="Fig2"><label>Fig. 2</label><caption><p>Chloroplast genome structure and gene expression across tracheophytes. These 658 chloroplast genomes were downloaded from NCBI Organelle Resources. The <italic>X-axis</italic> indicates the taxonomy of the chloroplast genome species following the Angiosperm Phylogeny Group III system and NCBI taxonomy. The <italic>bar width</italic> represents 100 species. The <italic>Y-axis</italic> shows the chloroplast genes, which were classified by different chloroplast regions. <italic>Gray boxes</italic> indicate absence of genes. <italic>Red boxes</italic> indicate stop codons in genes. <italic>Blue boxes</italic> indicate unknown nucleotides (<italic>N</italic>) in genes. <italic>IR</italic> inverted repeat, <italic>LSC</italic> large single-copy region, <italic>SSC</italic> small single-copy region</p></caption><graphic xlink:href="13059_2016_1004_Fig2_HTML" id="MO2"></graphic></fig></p><p>There are 57 chloroplast genomes in 26 genera in which the essential gene <italic>rpl22</italic> is reported to have been deleted from the chloroplast and transferred to the nuclear genome (Fig. <xref rid="Fig2" ref-type="fig">2</xref>) [<xref ref-type="bibr" rid="CR14">14</xref>, <xref ref-type="bibr" rid="CR103">103</xref>]. Nuclear-encoded <italic>rpl22</italic> contains a transit peptide that is predicted to deliver this protein from the cytosol to chloroplasts. These peptides are diverse, suggesting that there were two independent <italic>rpl22</italic> transfers in the Fabaceae and the Fagaceae [<xref ref-type="bibr" rid="CR14">14</xref>]. Similar transfer to the nucleus has also been observed for <italic>rpl32</italic> deletion from chloroplast genomes [<xref ref-type="bibr" rid="CR104">104</xref>–<xref ref-type="bibr" rid="CR106">106</xref>].</p><p>Eleven chloroplast genes encode <italic>ndh</italic> subunits, which are involved in photosynthesis. The ndh proteins assemble into the photosystem I complex to mediate cyclic electron transport in chloroplasts [<xref ref-type="bibr" rid="CR107">107</xref>, <xref ref-type="bibr" rid="CR108">108</xref>] and facilitate chlororespiration [<xref ref-type="bibr" rid="CR109">109</xref>]. Some autotrophic plants lack functional <italic>ndh</italic> genes in their chloroplast genomes [<xref ref-type="bibr" rid="CR36">36</xref>, <xref ref-type="bibr" rid="CR51">51</xref>, <xref ref-type="bibr" rid="CR54">54</xref>, <xref ref-type="bibr" rid="CR55">55</xref>, <xref ref-type="bibr" rid="CR110">110</xref>–<xref ref-type="bibr" rid="CR115">115</xref>] (Fig. <xref rid="Fig2" ref-type="fig">2</xref>). Unlike the single gene losses described previously, the entire family of <italic>ndh</italic> genes has been deleted in these plants. Seven orchid chloroplast genomes indicated at least three independent <italic>ndh</italic> deletions [<xref ref-type="bibr" rid="CR32">32</xref>]. Some orchid <italic>ndh</italic> DNA fragments were identified in the mitochondrial genome but the complete <italic>ndh</italic> genes required to translate putative functional protein complexes are absent [<xref ref-type="bibr" rid="CR32">32</xref>]. In the nuclear genome of Norway spruce, only non-functional plastid <italic>ndh</italic> gene fragments are present [<xref ref-type="bibr" rid="CR116">116</xref>]. Normal photosynthesis is observed in these <italic>ndh</italic>-deleted species [<xref ref-type="bibr" rid="CR32">32</xref>, <xref ref-type="bibr" rid="CR117">117</xref>]. Furthermore, <italic>ndh</italic>-deleted transformants are autotrophic and produce carbohydrates through photosynthesis [<xref ref-type="bibr" rid="CR107">107</xref>, <xref ref-type="bibr" rid="CR118">118</xref>–<xref ref-type="bibr" rid="CR121">121</xref>].</p><p>Many more chloroplast-gene deletions have been observed, including deletions of <italic>accD</italic>, <italic>ycf1</italic>, <italic>ycf2</italic>, <italic>ycf4</italic>, <italic>psaI</italic>, <italic>rpoA</italic>, <italic>rpl20</italic>, <italic>rpl23</italic>, <italic>rpl33</italic>, and <italic>rps16</italic>; many unique gene deletions have been identified in only one or a few species (<italic>psbJ</italic>, <italic>rps2</italic>, <italic>rps14</italic>, and <italic>rps19</italic>) (Fig. <xref rid="Fig2" ref-type="fig">2</xref>). The functions of these genes, phenotypes of their knock-out mutants, and evidence for their transfer are summarized in Additional file <xref rid="MOESM1" ref-type="media">1</xref>. Most essential genes that have been lost from chloroplast genomes have been transferred to the nucleus to maintain the plant's photosynthetic capacity, with the exception of <italic>ycf1</italic> and <italic>ycf2</italic>.</p><p>In summary, chloroplast genome sequences are most valuable for understanding plant evolution and phylogeny. Databases of not only plant genomes but also plant transcriptomes will be useful in investigating deletion events or the transfer of chloroplast genes to other organellar genomes to complement such deletions.</p></sec><sec id="Sec9"><title>Advances in chloroplast genome engineering</title><p>In the past century, desirable agronomic traits, including yield enhancement and resistance to pathogens or abiotic stress, were achieved by breeding cultivated crops with their wild relatives. As explained above, chloroplast genome sequences are very useful in the identification of closely related, breeding-compatible plant species. With the advent of modern biotechnology, desirable traits from unrelated species can now be readily introduced into commercial cultivars. Such genetically modified crops have revolutionized agriculture in the past two decades, dramatically reducing the use of chemical pesticides and herbicides while enhancing yield. For most commercial cultivars, herbicide- or insect-resistance genes are introduced into the nuclear genome. There are, however, a few limitations for nuclear transgenic plants, including low levels of expression (<1 % total soluble protein (TSP)) and potential escape of transgenes via pollen.</p><p>Engineering the introduction of foreign genes into the chloroplast genome addresses both of these concerns. Just two copies of transgenes are typically introduced into the nuclear genome, whereas up to 10,000 transgene copies have been engineered into the chloroplast genome of each plant cell, resulting in extremely high levels of foreign gene expression (>70 % TSP) [<xref ref-type="bibr" rid="CR122">122</xref>]. Most importantly, chloroplast genomes are maternally inherited in most cultivated crops, minimizing or eliminating transgene escape via pollen [<xref ref-type="bibr" rid="CR123">123</xref>].</p><p>The basic process of chloroplast engineering is explained in Fig. <xref rid="Fig3" ref-type="fig">3a, b</xref>. Chloroplast genome engineering is accomplished by integrating foreign genes into intergenic spacer regions without disrupting the native chloroplast genes (Fig. <xref rid="Fig3" ref-type="fig">3a</xref>). Two chloroplast genes are used as flanking sequences to facilitate integration of transgene cassettes. Transgene cassettes include a selectable marker gene and gene(s) of interest, both regulated by chloroplast gene promoters and untranslated regions (UTRs; Fig. <xref rid="Fig3" ref-type="fig">3a</xref>). Chloroplast genome sequences are essential to build transgene cassettes because they provide both flanking and regulatory sequences. Transgene cassettes that are inserted into bacterial plasmids are called chloroplast vectors and they are bombarded into plant cells using gold particles and a gene gun (Fig. <xref rid="Fig3" ref-type="fig">3b</xref>). Because of the presence of chloroplast DNA in the nuclear or mitochondrial genome, transgene cassettes may integrate via homologous or non-homologous recombination events; but any transgenes that are integrated within the nuclear or mitochondrial genome will not be expressed because chloroplast regulatory sequences are not functional in other genomes. If such integration occurs, the transgenes could be easily identified by evaluation of their integration site and eliminated [<xref ref-type="bibr" rid="CR124">124</xref>].<fig id="Fig3"><label>Fig. 3</label><caption><p>Basic process of chloroplast genetic engineering, diversity in intergenic spacer regions, and impact of transgene integration (endogenous versus heterologous genome sequences). <bold>a</bold> Complexity of heterologous sequence integration into intergenic spacer regions between lettuce and tobacco. The schematic diagram represents recombination between the tobacco transplastomic genome and the lettuce transformation vector [<xref ref-type="bibr" rid="CR128">128</xref>]. <italic>Purple bars</italic> represent unique lettuce intron sequence; the <italic>green bar</italic> represents unique tobacco intron sequence; <italic>black bars</italic> are exon regions; <italic>blue regions</italic> are looped out sequence. The expression cassette comprises: promoters (<italic>P</italic>), leader sequence (<italic>L</italic>), gene of interest (<italic>GOI</italic>), terminators (<italic>T</italic>), and selectable marker gene (<italic>SMG</italic>). <italic>IG</italic> intergenic spacer region. <bold>b</bold> Basic process of chloroplast genetic engineering. Gene delivery is performed by bombardment with gold microparticles coated with chloroplast vectors, followed by three rounds of selection to achieve homoplasmy. After confirmation of transgene integration, plants are grown in the greenhouse to increase biomass. Chloroplast transgenes are maternally inherited without Mendelian segregation of introduced traits. <bold>c</bold> Comparison of 21 of the most variable intergenic spacer regions among Solanaceae chloroplast genomes. <italic>Atr Atropa</italic>, <italic>Pot</italic> potato, <italic>Tob</italic> tobacco, <italic>Tom</italic> tomato. *Tier 1, **tier 2, and ***tier 3 regions reported in the paper by Shaw et al. [<xref ref-type="bibr" rid="CR250">250</xref>]. Plotted values were converted from percentage identity to sequence divergence on a scale from 0 to 1 as shown on the <italic>Y-axis</italic>; these values demonstrate a wide range of sequence divergence in different regions. Nucleotide sequences were determined by a bridging shotgun method and genome annotation was performed using the Dual Organellar GenoMe Annotator [<xref ref-type="bibr" rid="CR13">13</xref>]. <bold>d</bold>, <bold>e</bold> Decrease in the expression of transgenes regulated by heterologous psbA promoters and untranslated regions (UTRs) engineered via tobacco chloroplast genomes. When the lettuce (<italic>La</italic>) <italic>psbA</italic> regulatory region was used in tobacco (<italic>Na</italic>) chloroplasts or vice versa, transgene expression is dramatically reduced. <bold>d</bold> Accumulation of a cholera toxin B subunit (<italic>CTB</italic>) and proinsulin (<italic>Pins</italic>) fusion protein (<italic>CP</italic>) was quantified by densitometry and <bold>e</bold> anthrax protective antigen (<italic>PA</italic>) accumulation was estimated by enzyme-linked immunosorbent assay (ELISA). Total leaf protein (<italic>TLP</italic>) or total soluble protein (<italic>TSP</italic>) data are presented as a function of light exposure and developmental stage. The order of young, mature, and old is different in <bold>d</bold> and <bold>e</bold> because of the accumulation of more CTB-Pins in older leaves and PA in mature leaves [<xref ref-type="bibr" rid="CR128">128</xref>]. Young (top five), mature (fully grown), and old (bottom three) leaves were fully expanded and were cut from plants grown in the greenhouse for 8–10 weeks</p></caption><graphic xlink:href="13059_2016_1004_Fig3_HTML" id="MO3"></graphic></fig></p><p>One of the challenges of creating chloroplast transgenic (transplastomic) plants is the elimination of all untransformed copies (>10,000 per cell) of the native chloroplast genome and replacing them with transformed genomes that contain integrated transgene cassettes. The absence of the native chloroplast genome and the presence of only the modified genomes is referred to as the homoplasmic state, which is typically achieved after two or three rounds of selection (Fig. <xref rid="Fig3" ref-type="fig">3b</xref>). The most effective selectable marker used is the <italic>aadA</italic> gene, which confers resistance to streptomycin and spectinomycin. These antibiotics bind specifically to chloroplast ribosomes and disrupt protein synthesis without interfering with any other cellular process. Efforts to transform the chloroplast genome of cereal crops have been mostly unsuccessful. This could be due to the instability of chloroplast DNA in the mature leaves of cereals [<xref ref-type="bibr" rid="CR47">47</xref>] or to a requirement for better selectable markers [<xref ref-type="bibr" rid="CR125">125</xref>].</p><p>Table <xref rid="Tab2" ref-type="table">2</xref> provides the first global, comprehensive summary of the power of chloroplast genetic engineering, utilizing valuable information generated by the sequencing of chloroplast genomes described in previous sections. This table includes the most complete list of chloroplast genomes that have been engineered for enhanced agronomic traits or the production of different bio-products, including biopolymers, industrial enzymes, biopharmaceuticals, and vaccines. Within Table <xref rid="Tab2" ref-type="table">2</xref>, transgenes are grouped according to their functions and are organized according to their site of integration. The efficiency of transgene expression is also included in Table <xref rid="Tab2" ref-type="table">2</xref>, providing important information about the regulatory sequences used to express the transgenes.<table-wrap id="Tab2"><label>Table 2</label><caption><p>Engineering the chloroplast genome for biotechnology applications</p></caption><table frame="hsides" rules="groups"><thead><tr><th>Site of integration</th><th>Transgenes</th><th>Regulatory sequences</th><th>Efficiency of expression</th><th>Engineered traits or products</th><th>Reference(s)</th></tr></thead><tbody><tr><td colspan="6">Insect or pathogen tolerance</td></tr><tr><td>trnI/trnA</td><td><italic>Bgl-1</italic></td><td>5′psbA/3′psbA</td><td>>160-fold enzyme</td><td>Resistance against whitefly and aphid</td><td>[<xref ref-type="bibr" rid="CR141">141</xref>]</td></tr><tr><td>trnI/trnA</td><td><italic>Pta</italic></td><td>5′psbA/3′psbA</td><td>7.1–9.2 % TSP</td><td>Broad-spectrum resistance against aphid, whitefly, Lepidopteran insects, bacterial and viral pathogens</td><td>[<xref ref-type="bibr" rid="CR142">142</xref>]</td></tr><tr><td>trnI/trnA</td><td><italic>PelB1</italic>, <italic>PelD2</italic></td><td>5′psbA/3′psbA</td><td>~2.42 units mg<sup>−1</sup> FW</td><td>Resistance against <italic>Erwinia</italic> soft rot</td><td>[<xref ref-type="bibr" rid="CR150">150</xref>]</td></tr><tr><td>trnI/trnA</td><td><italic>RC1011</italic>, <italic>PG12</italic></td><td>5′psbA/3′</td><td>17–38 % TSP</td><td>Resistance to <italic>Erwinia</italic> soft rot and tobacco mosaic virus</td><td>[<xref ref-type="bibr" rid="CR140">140</xref>]</td></tr><tr><td>trnI/trnA</td><td><italic>cpo</italic></td><td>Prrn/psbA/psbA</td><td>NR</td><td>Resistance to fungal pathogens in vitro (<italic>Aspergillus flavus</italic>, <italic>Fusarium verticillioides</italic>, and <italic>Verticillium dahliae</italic>) and in planta (<italic>Alternaria alternata</italic>)</td><td>[<xref ref-type="bibr" rid="CR251">251</xref>]</td></tr><tr><td>trnI/trnA</td><td><italic>Bt cry2Aa2</italic> operon</td><td>Prrn/ggagg/psbA</td><td>45.3 % TSP</td><td>100 % mortality of cotton bollworm, beet armyworm; cuboidal Bt crystals formation</td><td>[<xref ref-type="bibr" rid="CR137">137</xref>]</td></tr><tr><td>trnI/trnA</td><td><italic>Bt cry9Aa2</italic></td><td>Prrn/ggagg/rbcL</td><td>~10 % of TSP</td><td>Resistance to <italic>Phthorimaea operculella</italic></td><td>[<xref ref-type="bibr" rid="CR252">252</xref>]</td></tr><tr><td>trnI/trnA</td><td><italic>msi-99</italic></td><td>Prrn/ggagg/psbA</td><td>21–43 % TSP</td><td>Resistance to in planta challenge of <italic>Pseudomonas syringae</italic>, <italic>Aspergillus flavus</italic>, <italic>Fusarium moniliforme</italic>, <italic>Verticillium dahlia</italic>, and <italic>Colletotrichum destructivum</italic></td><td>[<xref ref-type="bibr" rid="CR253">253</xref>]</td></tr><tr><td>trnI/trnA</td><td><italic>sporamin1</italic>, <italic>CeCPI2</italic>, and <italic>chitinase2</italic></td><td>Prrn/TpsbA</td><td>0.85–1 % TSP</td><td>Resistance against <italic>Spodoptera litura</italic> and <italic>Spodoptera exigua</italic> leaf spot, as well as soft rot diseases</td><td>[<xref ref-type="bibr" rid="CR254">254</xref>]</td></tr><tr><td>trnI/trnA</td><td><italic>MSI-99</italic></td><td>Prrn/Trps16</td><td>89.75 μg g<sup>−1</sup> FW</td><td>Resistance against rice blast fungus</td><td>[<xref ref-type="bibr" rid="CR255">255</xref>]</td></tr><tr><td>trnV/rps12/7</td><td><italic>cry1A(c)</italic></td><td>Prrn/rbcL/rps16</td><td>3–5 % of TSP</td><td>Resistance to larvae of <italic>Heliothis virescens</italic>, <italic>Helicoverpa zea</italic>, and <italic>Spodoptera exigua</italic></td><td>[<xref ref-type="bibr" rid="CR256">256</xref>]</td></tr><tr><td>trnV/rps12/7</td><td><italic>cry1Ab</italic></td><td>Prrn/T7gene10/rbcL</td><td>NR</td><td>Resistance to caterpillar of <italic>Anticarsia gemmatalis</italic></td><td>[<xref ref-type="bibr" rid="CR145">145</xref>]</td></tr><tr><td>rbcL/accD</td><td><italic>cry2Aa2</italic></td><td>Prrn/ggagg/psbA</td><td>2–3 % of TSP</td><td>Resistance to <italic>Heliothis virescens</italic>, <italic>Helicoverpa zea</italic>, and <italic>Spodoptera exigua</italic></td><td>[<xref ref-type="bibr" rid="CR257">257</xref>]</td></tr><tr><td colspan="6">Abiotic stress tolerance</td></tr><tr><td>trnI/trnA</td><td><italic>tps1</italic></td><td>Prrn/ggagg/psbA</td><td>>169-fold transcript</td><td>Drought tolerance: growth in 6 % polyethylene glycol and rehydration after 24 days of drought</td><td>[<xref ref-type="bibr" rid="CR258">258</xref>]</td></tr><tr><td>trnI/trnA</td><td><italic>merA/merB</italic></td><td>Prrn/ggagg/psbA</td><td>NR</td><td>Phytoremediation: high level tolerance to the organomercurial compounds, up to 400 μM phenylmercuric acetate</td><td>[<xref ref-type="bibr" rid="CR259">259</xref>]</td></tr><tr><td>trnI/trnA</td><td><italic>badh</italic></td><td>Prrn/T7 g10/rps16</td><td>93–101 μM g<sup>−1</sup> FW</td><td>Salt tolerance: carrot plants survived up to 400 mM NaCl</td><td>[<xref ref-type="bibr" rid="CR135">135</xref>]</td></tr><tr><td>trnI/trnA</td><td><italic>γ-TMT</italic></td><td>Prrn/T7g 10/TpsbA</td><td>>7.7 % TSP</td><td>Increased salt and heavy metal tolerance, enhanced accumulation of ɑ-tocopherol in seeds</td><td>[<xref ref-type="bibr" rid="CR153">153</xref>]</td></tr><tr><td>trnI/trnA</td><td><italic>mt1</italic></td><td>Prrn/T7 g10/Trps16</td><td>NR</td><td>Phytoremediation: resistant to mercury, up to 20 μm</td><td>[<xref ref-type="bibr" rid="CR260">260</xref>]</td></tr><tr><td>trnV/rps12/7</td><td><italic>b-bar1</italic></td><td>Prrn/TrbcL</td><td>>7 % TSP</td><td>Resistance to the herbicide phosphinothricin</td><td>[<xref ref-type="bibr" rid="CR261">261</xref>]</td></tr><tr><td>trnV/rps7/12</td><td><italic>EPSPS</italic></td><td>Prrn/Trps16</td><td>>10 % TSP</td><td>Resistance to the herbicide glyphosate</td><td>[<xref ref-type="bibr" rid="CR262">262</xref>]</td></tr><tr><td>rbcL/accD</td><td><italic>EPSPS/aroA</italic></td><td>Prrn/ggagg/psbA</td><td>NR</td><td>Resistance to glyphosate (>5 mM)</td><td>[<xref ref-type="bibr" rid="CR129">129</xref>]</td></tr><tr><td>rbcL/accD</td><td><italic>mALS</italic></td><td>PpsbA/TpsbA</td><td>NR</td><td>Tolerant to pyrimidinylcarboxylate, imidazolinon, and sulfonylurea/pyrimidinylcarboxylate herbicides</td><td>[<xref ref-type="bibr" rid="CR263">263</xref>]</td></tr><tr><td>rbcL/accD</td><td><italic>Bar</italic></td><td>Prrn/rbcL/psbA</td><td>NR</td><td>Herbicide resistance: up to 25 μg ml<sup>−1</sup> glufosinate</td><td>[<xref ref-type="bibr" rid="CR264">264</xref>]</td></tr><tr><td>rbcL/rbcL</td><td><italic>Hppd</italic></td><td>psbA/psbA/3′rbcL</td><td>5 % TSP</td><td>Resistance to herbicide</td><td>[<xref ref-type="bibr" rid="CR265">265</xref>]</td></tr><tr><td>rbcL/accD</td><td><italic>panD</italic></td><td>Prrn/rbcL 3′</td><td>>4-fold β-alanine</td><td>Tolerance to high-temperature stress</td><td>[<xref ref-type="bibr" rid="CR266">266</xref>]</td></tr><tr><td>trnfM/trnG</td><td><italic>lycopene β-cyclase</italic></td><td>atpI/rps16</td><td>0.28 mg g<sup>−1</sup> DW</td><td>Herbicide resistance and triggers conversion of lycopene</td><td>[<xref ref-type="bibr" rid="CR133">133</xref>]</td></tr><tr><td>prs14/trnG</td><td><italic>HTP</italic>, <italic>TCY</italic>, <italic>TMT</italic></td><td>Prrn/T7 g10/TrbcL</td><td>NR</td><td>Increase in vitamin E in fruit; cold-stress tolerance</td><td>[<xref ref-type="bibr" rid="CR267">267</xref>]</td></tr><tr><td colspan="6">Other agronomic traits</td></tr><tr><td>trnI/trnA</td><td><italic>phaA</italic></td><td>Prrn/psbA/psbA</td><td>14.71β-ketothiolase mg<sup>−1</sup> FW</td><td>Engineered cytoplasmic male sterility</td><td>[<xref ref-type="bibr" rid="CR268">268</xref>]</td></tr><tr><td>trnI/trnA</td><td><italic>RbcS</italic></td><td>T7g10 or psbA</td><td>>150-fold RbcS transcript</td><td>Restoration of RuBisCO activity in <italic>rbcS</italic> mutants</td><td>[<xref ref-type="bibr" rid="CR136">136</xref>]</td></tr><tr><td>rbcL/accD</td><td><italic>TC</italic>, <italic>γ -TMT</italic></td><td>PpsbA/Trsp16</td><td>3 nmol h<sup>−1</sup> mg<sup>−1</sup> FW</td><td>Vitamin E accumulation in tobacco and lettuce</td><td>[<xref ref-type="bibr" rid="CR269">269</xref>]</td></tr><tr><td>rbcL/accD</td><td><italic>CrtZ</italic>, <italic>CrtW</italic></td><td>Prrn/Trps16</td><td>NR</td><td>Accumulation of astaxanthin fatty acid esters in lettuce</td><td>[<xref ref-type="bibr" rid="CR270">270</xref>]</td></tr><tr><td>trnV/orf708</td><td><italic>BicA</italic></td><td>psbA/psbA/psbA</td><td>~0.1 % TSP</td><td>CO<sub>2</sub> capture within leaf chloroplasts</td><td>[<xref ref-type="bibr" rid="CR271">271</xref>]</td></tr><tr><td>trnV/3′rps12</td><td><italic>Trx f</italic>, <italic>Trx m</italic></td><td>prrn T7G10/rps12</td><td>NR</td><td>Starch synthesis/chloroplast redox regulation</td><td>[<xref ref-type="bibr" rid="CR272">272</xref>]</td></tr><tr><td>trnfM/trnG</td><td><italic>CV-N</italic></td><td>Prrn/T7g10/TatpA</td><td>~0.3 % TSP</td><td>Increased mRNA stability and protein stability with the expression of CV-N in chloroplasts</td><td>[<xref ref-type="bibr" rid="CR273">273</xref>]</td></tr><tr><td>trnI/trnA</td><td><italic>Bgl-1</italic></td><td>5′psbA/3′psbA</td><td>44.4 units Bgl1 g<sup>−1</sup> FW</td><td>β-Glucosidase increased enzyme cocktail efficiently to release sugar from paper, citrus peel, and wood</td><td>[<xref ref-type="bibr" rid="CR141">141</xref>]</td></tr><tr><td>trnI/trnA</td><td><italic>ubiC</italic></td><td>5′psbA/3′psbA</td><td>25 % DW</td><td>250-fold higher pHBA polymer accumulation than nuclear transgenic lines</td><td>[<xref ref-type="bibr" rid="CR149">149</xref>]</td></tr><tr><td>trnI/trnA</td><td><italic>man 1</italic></td><td>5′psbA/3′psbA</td><td>25 units g<sup>−1</sup> FW</td><td>Mannanase increased enzyme cocktail released sugar from paper, citrus peel, and wood</td><td>[<xref ref-type="bibr" rid="CR274">274</xref>]</td></tr><tr><td>trnI/trnA</td><td><italic>cutinase</italic> or <italic>swoIlenin</italic></td><td>5′PsbA/3′PsbA</td><td>47.7 % reduction of MGDG and DGDG in cutinase and 68.5 % in swollenin</td><td>Swollenin enlarged and irreversibly unwound cotton fiber; cutinase showed esterase and lipase activity; used in enzyme cocktails</td><td>[<xref ref-type="bibr" rid="CR275">275</xref>]</td></tr><tr><td rowspan="8">trnI/trnA</td><td><italic>bgl1</italic></td><td rowspan="8">5′psbA/3′psbA</td><td>14 units mg<sup>−1</sup> FW</td><td rowspan="8">Enzyme cocktails produced glucose from filter paper, pine wood, or citrus peel</td><td rowspan="8">[<xref ref-type="bibr" rid="CR150">150</xref>]</td></tr><tr><td><italic>swo1</italic></td><td>NR</td></tr><tr><td><italic>xyn2</italic></td><td>421 units mg<sup>−1</sup> FW</td></tr><tr><td><italic>Acetyl sylan esterase</italic></td><td>NR</td></tr><tr><td><italic>celD</italic></td><td>493 units mg<sup>−1</sup> FW</td></tr><tr><td><italic>celO</italic></td><td>442 units mg<sup>−1</sup> FW</td></tr><tr><td><italic>Lipase</italic></td><td>NR</td></tr><tr><td><italic>Cutinase</italic></td><td>15 units mg<sup>−1</sup> FW</td></tr><tr><td>trnI/trnA</td><td><italic>PMK</italic>, <italic>MVK</italic>, <italic>MDD</italic>, <italic>AACT</italic>, <italic>HMGS</italic>, <italic>HMGRt; IPP</italic>, <italic>FPP</italic>, <italic>ADS</italic>, <italic>CYP71AV1</italic>, <italic>AACPR</italic></td><td>Prrn/PpsbA</td><td>0.1 mg g<sup>−1</sup> FW</td><td>Artemisinic acid for several isoprenoid products</td><td>[<xref ref-type="bibr" rid="CR276">276</xref>]</td></tr><tr><td>trnI/trnA</td><td><italic>Cel6A</italic>,<italic>Cel6B</italic></td><td>Prrn/rbcL/rbcL</td><td>2–4 % TSP</td><td>Hydrolyzed crystalline cellulose</td><td>[<xref ref-type="bibr" rid="CR277">277</xref>]</td></tr><tr><td>trnfM/trnG</td><td><italic>bgl1C</italic>, <italic>cel6B</italic>, <italic>cel9A</italic>, <italic>xeg74</italic></td><td>Prrn/T7g10/TrbcL</td><td>5– 40 % TSP</td><td>Cell wall-degrading enzyme activity</td><td>[<xref ref-type="bibr" rid="CR278">278</xref>]</td></tr><tr><td>rbcL/accD</td><td><italic>phbC</italic>, <italic>phbA</italic>, <italic>phbB</italic></td><td>Prrn/rbcL 3′</td><td>0.16 % DW</td><td>Polyhydroxybutyrate (PHB) accumulation in leaves</td><td>[<xref ref-type="bibr" rid="CR279">279</xref>]</td></tr><tr><td>rbcL/accD</td><td><italic>crtZ</italic>, <italic>crtW</italic></td><td>Prrn/Trps16</td><td>>0.5 % DW</td><td>Astaxanthin accumulation</td><td>[<xref ref-type="bibr" rid="CR280">280</xref>]</td></tr><tr><td>trnV/rps7</td><td><italic>EGPh</italic></td><td>psbA/psbA/Trps16</td><td>25 % TSP</td><td>Chloroplast-derived β-1,4-endoglucanase (EGPh) was recovered from dry leaves and digested carboxymethyl cellulose (CMC) substrate</td><td>[<xref ref-type="bibr" rid="CR281">281</xref>]</td></tr><tr><td>trnI/trn A</td><td><italic>EX4</italic></td><td>PpsbA/TpsbA</td><td>14.3 % TSP</td><td>CTB–EX4 showed increased insulin secretion similar to the commercial injectable EX4 in pancreatic β-cells and in mice fed with cells expressing EX4 in chloroplasts</td><td>[<xref ref-type="bibr" rid="CR160">160</xref>]</td></tr><tr><td>trnI/trn A</td><td><italic>MBP</italic></td><td>PpsbA/TpsbA</td><td>2 % TSP</td><td>Amyloid loads were reduced in ex vivo studies in human Alzheimer’s brain and in vivo in Alzheimer’s mice fed with bio-encapsulated CTB–MBP. Abeta was also reduced in retinae and loss of retinal ganglion cells was prevented</td><td>[<xref ref-type="bibr" rid="CR162">162</xref>]</td></tr><tr><td>trnI/trn A</td><td><italic>FVIII</italic></td><td>PpsbA/TpsbA</td><td>370 mg g<sup>−1</sup> FW</td><td>Feeding of the HC/C2 antigen mixture substantially suppressed T-helper cell responses and inhibitor formation against FVIII in hemophilia A mice</td><td>[<xref ref-type="bibr" rid="CR282">282</xref>]</td></tr><tr><td>trnI/trn A</td><td><italic>HSA</italic></td><td>PpsbA/TpsbA</td><td>26 % TSP</td><td>In vitro chaperone activity of Trx m and Trx f</td><td>[<xref ref-type="bibr" rid="CR283">283</xref>]</td></tr><tr><td>trnI/trn A</td><td><italic>EDA</italic></td><td>PpsbA/TpsbA</td><td>2.0 % TSP</td><td>The vaccine adjuvant EDA from fibronectin retains its proinflammatory properties when expressed in tobacco chloroplasts</td><td>[<xref ref-type="bibr" rid="CR284">284</xref>]</td></tr><tr><td>trnI/trn A</td><td><italic>Proinsulin</italic></td><td>PpsbA/TpsbA</td><td>47 % TSP in tobacco, 53 % TLP in lettuce</td><td>Oral delivery of proinsulin in plant cells lowered glucose levels comparably to injectable commercial insulin</td><td>[<xref ref-type="bibr" rid="CR285">285</xref>]</td></tr><tr><td>trnI/trn A</td><td><italic>HSA</italic></td><td>psbA/psbA/psbA</td><td>~11 % TSP</td><td>First report of human blood protein in chloroplasts; function not evaluated</td><td>[<xref ref-type="bibr" rid="CR286">286</xref>]</td></tr><tr><td>trnI/trn A</td><td><italic>IGF</italic></td><td>psbA/psbA/psbA</td><td>32.7 % TSP</td><td>Promoted growth of cultured HU-3 cells in a dose-dependent manner</td><td>[<xref ref-type="bibr" rid="CR287">287</xref>]</td></tr><tr><td>trnI/trnA</td><td><italic>FIX</italic></td><td>PpsbA/TpsbA</td><td>1 mg g<sup>−1</sup> DW (0.56 % TLP)</td><td>Oral delivery of CTB-FIX lettuce cells suppressed inhibitor formation against FIX in hemophilia B mice</td><td>[<xref ref-type="bibr" rid="CR6">6</xref>]</td></tr><tr><td>trnI/trnA</td><td><italic>FIX</italic></td><td>Ppsba/TpsbA</td><td>3.8 % TSP; 0.4 mg g<sup>−1</sup> FW</td><td>Tolerance induction via complex immune regulation, involving tolerogenic dendritic and T-cell subsets</td><td>[<xref ref-type="bibr" rid="CR288">288</xref>]</td></tr><tr><td>trnI/trnA</td><td><italic>GAA</italic></td><td>Ppsba/TpsbA</td><td>5.7 mg g<sup>−1</sup> DW</td><td>Reduced toxic antibody responses in enzyme replacement therapy in Pompe mice</td><td>[<xref ref-type="bibr" rid="CR289">289</xref>]</td></tr><tr><td>trnI/trnA</td><td><italic>ACE2</italic><break></break><italic>Ang-(1–7)</italic></td><td>PpsbA/TpsbA</td><td>CTB–ACE2: 2.14 % TLP<break></break>CTB-Ang1–7: 8.7 % TLP</td><td>Oral delivery of ACE2 and Ang (1–7) significantly improved cardiopulmonary structure and functions, decreased the elevated right ventricular systolic blood pressure and improved pulmonary blood flow in animals with induced pulmonary hypertension</td><td>[<xref ref-type="bibr" rid="CR161">161</xref>]</td></tr><tr><td>trnI/trn A</td><td><italic>BACE</italic></td><td>Prrn/TpsbA</td><td>2.0 % TSP</td><td>Immunogenic response against the BACE antigen in mice</td><td>[<xref ref-type="bibr" rid="CR290">290</xref>]</td></tr><tr><td>trnI/trn A</td><td><italic>IFNα2b</italic></td><td>Prrn/TpsbA</td><td>3 mg g<sup>−1</sup> FW</td><td>Protected cells against VSV CPE and HIV; increased MHC I antibody on splenocytes and total number of natural killer cells and protected mice from a highly metastatic lung tumor</td><td>[<xref ref-type="bibr" rid="CR291">291</xref>]</td></tr><tr><td>trnI/trn A</td><td><italic>CTB-pins</italic></td><td>Prrn/T7g10/TpsbA and rps16</td><td>16 % TSP in tobacco, 72 % TLP in lettuce</td><td>CTB-proinsulin-fed non-obese diabetic mice significantly decreased inflammation (insulitis); insulin-producing β cells in pancreatic islets were highly protected, increased in insulin production with lower blood or urine glucose levels; increased expression of immunosuppressive cytokines</td><td>[<xref ref-type="bibr" rid="CR128">128</xref>, <xref ref-type="bibr" rid="CR292">292</xref>]</td></tr><tr><td>rbcL/accD</td><td><italic>IFN-γ</italic></td><td>PpsbA/TpsbA</td><td>6 % TSP</td><td>Protection of human lung carcinoma cells against infection by encephalomyocarditis virus</td><td>[<xref ref-type="bibr" rid="CR293">293</xref>]</td></tr><tr><td>rbcL/accD</td><td><italic>hTrx</italic></td><td>PpsbA/Trps16</td><td>1 % TSP</td><td>Protected mouse from hydrogen peroxide</td><td>[<xref ref-type="bibr" rid="CR294">294</xref>]</td></tr><tr><td>rbcL/accD</td><td><italic>A1AT</italic></td><td>PpsbA/TrbcL</td><td>2 % TSP</td><td>Binds to porcine pancreatic elastase</td><td>[<xref ref-type="bibr" rid="CR295">295</xref>]</td></tr><tr><td>rbcL/accD</td><td><italic>TGFβ3</italic></td><td>Prrn/T7g10/psbC</td><td>12 % TLP</td><td>Inhibits mink lung epithelial cell proliferation</td><td>[<xref ref-type="bibr" rid="CR296">296</xref>]</td></tr><tr><td>trnV/3′rps12</td><td><italic>hCT-1</italic></td><td>Prrn/G10L/Trps16</td><td>5 % TSP</td><td>Biologically active on human hepatocarcinoma cell line</td><td>[<xref ref-type="bibr" rid="CR297">297</xref>]</td></tr><tr><td>trnV/rps7/12</td><td><italic>hST</italic></td><td>PpsbA or Prrn/G10L/Trps16</td><td>0.2–7.0 % TSP</td><td>Promotes growth of Nb2 cells in a dose-dependent manner</td><td>[<xref ref-type="bibr" rid="CR298">298</xref>]</td></tr><tr><td>trnfM/trnG</td><td><italic>pal</italic>, <italic>cpl-1</italic></td><td>Prrn/T7g10/TpsbA</td><td>~30 % TSP</td><td>Bacteriolytic activity and kills <italic>Streptococcus pneumoniae</italic>, the causative agent of pneumonia</td><td>[<xref ref-type="bibr" rid="CR299">299</xref>]</td></tr><tr><td>trnI/trn A</td><td><italic>ESAT-6</italic></td><td>5′psbA/3′psbA</td><td>~7.5 % TSP</td><td>Hemolysis of red blood cells and GM1 binding</td><td>[<xref ref-type="bibr" rid="CR165">165</xref>]</td></tr><tr><td>trnI/trn A</td><td><italic>AMA1</italic></td><td>5′psbA/3′psbA</td><td>7.3 % TSP in tobacco, 13.2 % TSP in lettuce</td><td rowspan="3">Long-term immunity against cholera challenge; inhibition of malarial parasite; protection correlated with IgA and IgG1</td><td rowspan="3">[<xref ref-type="bibr" rid="CR164">164</xref>]</td></tr><tr><td>trnI/trn A</td><td><italic>MSP1</italic></td><td>5′psbA/3′psbA</td><td>10.1 % TSP in tobacco, 6.1 % TSP in lettuce</td></tr><tr><td>trnI/trn A</td><td><italic>2 L21</italic></td><td>5′psbA/3′psbA</td><td>6.0 % TSP</td></tr><tr><td>trnI/trn A</td><td><italic>Pag</italic></td><td>5′psb/3′psbA</td><td>~29.6 % TSP</td><td>Macrophage lysis assay, systemic immune response, toxin neutralization assay, mice survived (100 %) challenge with lethal doses of anthrax toxin</td><td>[<xref ref-type="bibr" rid="CR300">300</xref>, <xref ref-type="bibr" rid="CR301">301</xref>]</td></tr><tr><td>trnI/trn A</td><td><italic>L1</italic></td><td>PpsbA/TpsbA</td><td>20–26 % TSP</td><td>Induced systemic immune response and produced neutralizing antibodies in mice</td><td>[<xref ref-type="bibr" rid="CR302">302</xref>]</td></tr><tr><td>trnI/trnA</td><td><italic>RA4</italic></td><td>PpsbA/T psbA</td><td>0.2 % TLP</td><td>Oral administration elicited both mucosal and systemic Th1/Th2 responses to reduce <italic>Toxoplasma</italic> parasite load</td><td>[<xref ref-type="bibr" rid="CR303">303</xref>]</td></tr><tr><td>trnI/trnA</td><td><italic>rFaeG</italic></td><td>PpsbA/TrbcL</td><td>>1 % DW</td><td>Transplastomic plants expressing the rFaeG protein could possibly be used for delivery of an oral vaccine against porcine F4+ ETEC infections</td><td>[<xref ref-type="bibr" rid="CR304">304</xref>]</td></tr><tr><td>trnI/trn A</td><td><italic>F1-V</italic></td><td>Prrn/TpsbA</td><td>14.8 % TSP</td><td>Orally immunized mice heavily challenged with plague (<italic>Yersinia pestis</italic>) were protected better than those given IP injections</td><td>[<xref ref-type="bibr" rid="CR305">305</xref>]</td></tr><tr><td>trnI/trn A</td><td><italic>CTB-2 L21</italic></td><td>PpsbA/TpsbA</td><td>31.1 % TSP</td><td>Immunogenic in mice following IP or oral administration</td><td>[<xref ref-type="bibr" rid="CR306">306</xref>]</td></tr><tr><td>trnI/trnA</td><td><italic>VP8*</italic></td><td>psbA/psbA/Trps16</td><td>600 μg g<sup>−1</sup> FW</td><td>Induced strong immune response and virus neutralization</td><td>[<xref ref-type="bibr" rid="CR307">307</xref>]</td></tr><tr><td>trnI/trn A</td><td><italic>CtxB</italic></td><td>Prrn/ggagg/TpsbA</td><td>4.1 % TSP</td><td>Efficient GM1 ganglioside-binding</td><td>[<xref ref-type="bibr" rid="CR308">308</xref>]</td></tr><tr><td>trnI/trn A</td><td><italic>LTB</italic></td><td>Prrn/ggagg/TpsbA</td><td>2.5 % TSP</td><td>GM1 ganglioside-binding assay</td><td>[<xref ref-type="bibr" rid="CR309">309</xref>]</td></tr><tr><td>trnI/trn A</td><td><italic>LecA</italic></td><td>Prrn/T7g10/TpsbA</td><td>7 % TSP</td><td>Systemic immune response in mice</td><td>[<xref ref-type="bibr" rid="CR310">310</xref>]</td></tr><tr><td>trnI/trn A</td><td><italic>BACE</italic></td><td>Prrn/TpsbA</td><td>2.0 % TSP</td><td>Immunogenic response against the BACE antigen in mice</td><td>[<xref ref-type="bibr" rid="CR290">290</xref>]</td></tr><tr><td>rbcL/accD</td><td><italic>OspA</italic>, <italic>OspA-T</italic></td><td>PpsbA/TpsbA</td><td>1–10 % TSP</td><td>Systemic immune response and protection against <italic>Borrelia burgdorferi</italic> (Lyme disease)</td><td>[<xref ref-type="bibr" rid="CR311">311</xref>]</td></tr><tr><td>trnN/trn R</td><td><italic>LTB</italic></td><td>Prrn/T7g10/TrbcL</td><td>2.3 % TSP</td><td>GM1 ganglioside-binding assay; oral immunization partially protected mice from cholera toxin challenge</td><td>[<xref ref-type="bibr" rid="CR312">312</xref>]</td></tr><tr><td>trnN/trnR</td><td><italic>DPT</italic></td><td>Prrn/T7g10/TrbcL</td><td>0.8 % TSP</td><td>Immunogenic in orally inoculated mice with freeze-dried chloroplast-derived multi-epitope DPT protein</td><td>[<xref ref-type="bibr" rid="CR313">313</xref>]</td></tr><tr><td>trnN/trnR</td><td><italic>C4V3</italic></td><td>Prrn/T7g10/TrbcL</td><td>~15 μg mg<sup>−1</sup> DW</td><td>Plant-derived C4V3 has elicited both systemic and mucosal antibody responses in mice, as well as CD4+ T cell proliferation responses</td><td>[<xref ref-type="bibr" rid="CR314">314</xref>]</td></tr><tr><td>trnN/trnR</td><td><italic>L1</italic></td><td>Prrn/TrbcL</td><td>>2 % of TSP</td><td>Proper folding and display of conformational epitopes for L1 in the fusion protein by antigen capture ELISA</td><td>[<xref ref-type="bibr" rid="CR315">315</xref>]</td></tr><tr><td>trnfM/trnG</td><td><italic>p24</italic></td><td>Prrn/T7g10/TrbcL</td><td>~4 % TSP</td><td>Induced strong CD4+ and CD8+ T-cell responses in mice</td><td>[<xref ref-type="bibr" rid="CR316">316</xref>]</td></tr><tr><td>trnGtrnfM</td><td><italic>HEV E2</italic></td><td>Prrn/psbA/TpsbA</td><td>1.09 ng μg<sup>−1</sup> TSP</td><td>Immune response in mice against hepatitis E virus</td><td>[<xref ref-type="bibr" rid="CR317">317</xref>]</td></tr><tr><td>trnH/trnK</td><td><italic>CSFV E2</italic></td><td>Prrn/TpsbA</td><td>1–2 % TSP</td><td>Immune response in mice against swine fever</td><td>[<xref ref-type="bibr" rid="CR318">318</xref>]</td></tr><tr><td>rrn16/rps12/7</td><td><italic>TetC</italic></td><td>Prrn/T7 g10/TrbcL<break></break>atpB/TrbcL</td><td>10–25 % TSP</td><td>Mice developed systemic immune response and survived the tetanus toxin challenge</td><td>[<xref ref-type="bibr" rid="CR319">319</xref>]</td></tr><tr><td>rrn16/trnI</td><td><italic>E7</italic></td><td>PpsbA/Trps</td><td>3–8 % TSP</td><td>Several therapeutic HPV-specific E7-based vaccine formulations have been tested in animal models and some have advanced into clinical trials</td><td>[<xref ref-type="bibr" rid="CR320">320</xref>]</td></tr></tbody></table><table-wrap-foot><p><italic>Abbreviations</italic>: <italic>Ang (1–7)</italic> Angiotensin (1–7), <italic>BACE</italic> human b-site APP cleaving enzyme, <italic>Bgl</italic> β-glucosidase, <italic>CPE</italic> carbapenemase-producing Enterobacteriaceae, <italic>CTB</italic> cholera toxin B subunit, <italic>DGDG</italic> digalactosyldiacylglycerol, <italic>DPT</italic> diphteria, pertussis, tetanus, <italic>DW</italic> dry weight, <italic>EDA</italic> extra domain A-fibronectin, <italic>ELISA</italic> enzyme-linked immunosorbent assay, <italic>ETEC</italic> enterotoxigenic <italic>Escherichia coli</italic>, <italic>EX4</italic> exendin-4, <italic>FVIII</italic> coagulation factor VIII, <italic>FW</italic> fresh weight, <italic>HPV</italic> human papilloma virus, <italic>IP</italic> intraperitoneal, <italic>MBP</italic> myelin basic protein, <italic>MGDG</italic> monogalactosyldiacylglycerol, <italic>NR</italic> not recorded, <italic>RbcS</italic> small subunit of RuBisCO, <italic>RuBisCO</italic> ribulose-1,5-bisphosphate carboxylase/oxygenase, <italic>TLP</italic> total leaf protein, <italic>TSP</italic> total soluble protein, <italic>VSV</italic> vesicular stomatitis virus</p></table-wrap-foot></table-wrap></p></sec><sec id="Sec10"><title>Impact of sequence diversity in the chloroplast genome on transgene integration</title><p>Figure <xref rid="Fig3" ref-type="fig">3a</xref> shows examples of transplastomic genomes that have been transformed with either an endogenous or a heterologous flanking sequence. Every single nucleotide change in the heterologous sequence was subsequently edited out and corrected to achieve 100 % homology to the native sequence within the intergenic spacer region (Fig. <xref rid="Fig3" ref-type="fig">3a</xref>). The repetitive editing process significantly reduces the efficiency of transgene integration when using heterologous flanking sequences. This challenge is made even more difficult by inadequate conservation of intergenic spacer regions, even within the same family. Figure <xref rid="Fig3" ref-type="fig">3c</xref> shows comparisons of 21 of the most variable intergenic spacer regions; only four of the >150 spacer regions, including the trnl/trnA spacer region, are conserved among members of the Solanaceae. Among grass chloroplast genomes, not a single intergenic spacer region is conserved [<xref ref-type="bibr" rid="CR8">8</xref>]. This necessitates construction of species-specific chloroplast vectors using endogenous flanking sequences and underscores the need to sequence the chloroplast genomes of economically important crop species.</p></sec><sec id="Sec11"><title>Ideal sites in the chloroplast genome for transgene integration</title><p>The selection of a suitable intergenic spacer region from among more than 100 sites found in each chloroplast genome is a major concern. Statements on the lack of positional effects in the transplastomic literature are common and are used to contrast chloroplast genetic engineering with nuclear transgene integration, which is often associated with profound differences in the expression of transgenes dependent on their site of integration. Evidence shows, however, that there are also positional effects within the chloroplast genome (Table <xref rid="Tab2" ref-type="table">2</xref>). IR regions are found in duplicate in most chloroplast genomes; therefore, transgenes should be inserted within the IR region instead of the SSC or LSC regions because this should double the copy number of transgenes. Integration of a transgene cassette into one copy of the IR facilitates integration into the other copy, thereby enhancing selection pressure to achieve homoplasmy through this copy correction mechanism, a characteristic feature of the chloroplast genome [<xref ref-type="bibr" rid="CR126">126</xref>–<xref ref-type="bibr" rid="CR128">128</xref>]. Therefore, the site of integration plays a crucial role in transgene expression level and in enhancing homoplasmy under selection by antibiotics. Most importantly, in all sequenced chloroplast genomes within a single plant species, the DNA sequence in one copy of the IR is identical to that in the other copy, without any exception (Table <xref rid="Tab1" ref-type="table">1</xref>).</p><p>An early controversy in the chloroplast genetic engineering field was the suitability of transcriptionally silent spacer regions, where native genes (for example, <italic>rbcL</italic>/<italic>accD</italic>) are located on opposite strands of the chloroplast genome, or transcriptionally active spacer regions, where native genes (for example, <italic>trnA</italic>/<italic>trnI</italic>) are located within operons on the same strand. After a herbicide resistance gene was introduced into the transcriptionally active spacer region for the first time [<xref ref-type="bibr" rid="CR129">129</xref>], most subsequent studies preferentially used this site of integration (Table <xref rid="Tab2" ref-type="table">2</xref>). The integration of transgenes into the transcriptionally active spacer region (trnl/trnA) has led to 25-fold higher expression of transgenes compared with the transcriptionally silent spacer region (rbcl/accD) [<xref ref-type="bibr" rid="CR130">130</xref>], possibly due to the presence of multiple promoters (heterologous and endogenous) that enhance transcription. Introns present within <italic>trnI/trnA</italic> genes (used as flanking sequences) also provide efficient processing of native or foreign transcripts. The <italic>trnA</italic> gene intron includes a chloroplast origin of replication and produces more copies of the template (chloroplast vectors) for integration of the transgene cassette [<xref ref-type="bibr" rid="CR131">131</xref>]. In fact, among 114 transgenes in different plant species in Table <xref rid="Tab2" ref-type="table">2</xref>, 71 are integrated at the <italic>trnA</italic>/<italic>trnI</italic> site of the chloroplast genome, confirming the unique advantages of this site [<xref ref-type="bibr" rid="CR127">127</xref>, <xref ref-type="bibr" rid="CR129">129</xref>, <xref ref-type="bibr" rid="CR130">130</xref>].</p></sec><sec id="Sec12"><title>Role of chloroplast genome regulatory sequences in transgene expression</title><p>In addition to the site of integration, regulatory sequences located upstream (promoter, 5′ UTR) and downstream (3′ UTR) of transgenes play a major role in determining their expression level. The <italic>psbA</italic> regulatory region, first used almost 25 years ago [<xref ref-type="bibr" rid="CR131">131</xref>], still appears to be the best option for use in an expression cassette, as the <italic>psbA</italic> gene encodes the most highly translated protein in the chloroplast [<xref ref-type="bibr" rid="CR132">132</xref>] and it can also mediate light-induced activation of translation [<xref ref-type="bibr" rid="CR128">128</xref>]. Indeed, almost all highly expressed transgenes (>70 % TSP, >25 % dry weight) utilize the <italic>psbA</italic> regulatory region; among 114 transgenes expressed via the chloroplast genome, 84 use the <italic>psbA</italic> regulatory sequence (Table <xref rid="Tab2" ref-type="table">2</xref>). Other endogenous regulatory sequences that are used include <italic>rbcL</italic> and <italic>atpA</italic>, which result in lower transgene expression levels than the <italic>psbA</italic> promoter/5′ UTR.</p><p>Using regulatory regions from photosynthetic genes has the advantage of light regulation, making them ideal for transgene expression in photosynthetic organs (leaves; Fig. <xref rid="Fig3" ref-type="fig">3d, e</xref>). However, when the lettuce <italic>psbA</italic> regulatory region was used in tobacco chloroplasts or vice versa, transgene expression was dramatically reduced (Fig. <xref rid="Fig3" ref-type="fig">3d, e</xref>) [<xref ref-type="bibr" rid="CR128">128</xref>]. Nucleotide differences within the <italic>psbA</italic> 5′ UTR between tobacco and lettuce (<italic>Lactuca sativa</italic>) resulted in changes that decreased the interaction of RNA-binding proteins and produced variation in the size of the stem, bulge, and terminal loop of the UTR [<xref ref-type="bibr" rid="CR128">128</xref>]. In addition, most regulatory proteins (including sigma factors that bind to the promoter region) are nuclear encoded and transported to chloroplasts. This underscores a caveat associated with using regulatory sequences for transgene expression: the need to make species-specific chloroplast vectors to accommodate highly specific regulatory region-binding proteins.</p><p>Heterologous regulatory sequences are necessary for transgene expression that is independent of cellular control, especially in non-photosynthetic organs such as fruits and edible roots, where chloroplast protein synthesis is poor [<xref ref-type="bibr" rid="CR133">133</xref>]. A heterologous UTR (T7 <italic>gene10</italic>) was first evaluated for expression in leaves [<xref ref-type="bibr" rid="CR127">127</xref>, <xref ref-type="bibr" rid="CR134">134</xref>] and was subsequently tested in non-green tissues. When the expression of <italic>BETAINE ALDEHYDE DEHYDROGENASE</italic> (<italic>BADH</italic>) was regulated by the T7 <italic>gene10</italic> UTR in carrot (<italic>Daucus carota</italic>) plants, 75 % of the expression level in leaves was observed in non-green edible roots, conferring the highest level of salt tolerance (400 mM NaCl) found in the published literature (Fig. <xref rid="Fig4" ref-type="fig">4i, j</xref>) [<xref ref-type="bibr" rid="CR135">135</xref>]. Although T7 <italic>gene10</italic> has been successfully used to engineer salt tolerance in non-green tissues, its expression level is not as high as that of the <italic>psbA</italic> regulatory sequence in leaves [<xref ref-type="bibr" rid="CR136">136</xref>]. The only other heterologous UTR that expressed transgenes at high levels is that from the <italic>Bacillus thuringiensis</italic> (<italic>Bt</italic>) operon [<xref ref-type="bibr" rid="CR137">137</xref>]. Use of this operon produced the highest level of insecticidal toxin protein (52 % TLP) ever reported in the published literature [<xref ref-type="bibr" rid="CR137">137</xref>]. These high levels of toxin accumulation in chloroplasts could result from the combination of high-level expression and protein stability; the Bt protein formed cuboidal crystals within chloroplasts (Fig. <xref rid="Fig4" ref-type="fig">4e</xref>) due to co-expression of a chaperone that facilitates folding. When fed, transplastomic leaves, cotton bollworm (<italic>Helicoverpa</italic> sp.) were killed with a single bite of leaf and insects that had 40,000-fold increased resistance to Bt were also killed (Fig. <xref rid="Fig4" ref-type="fig">4f, g</xref>). Nevertheless, expression of this transgene in tomato fruit is very poor [<xref ref-type="bibr" rid="CR133">133</xref>, <xref ref-type="bibr" rid="CR138">138</xref>, <xref ref-type="bibr" rid="CR139">139</xref>] and further research is needed to enhance transgene expression in fruits.<fig id="Fig4"><label>Fig. 4</label><caption><p>Engineering the chloroplast genome to confer biotic/abiotic stress tolerance or expression of high-value products. <bold>a</bold>–<bold>d</bold> Industrial production of blood clotting factor IX (FIX) bioencapsulated in lettuce plants in a hydroponic cGMP facility. <bold>a</bold> Biomass production of FIX-expressing plants. <bold>b</bold>–<bold>d</bold> Steps in capsule preparation. After harvesting and lyophilization of fresh leaves, freeze-dried FIX-accumulating leaves were powdered and prepared as capsules [<xref ref-type="bibr" rid="CR6">6</xref>]. <bold>e</bold>–<bold>g</bold> Overexpression of the Bt cry2Aa2 operon in chloroplasts leads to the formation of the Bt insecticidal crystal protein. In bioassays with the <italic>Helicoverpa zea</italic>, <bold>f</bold> eating the transplastomic leaf kills the caterpillar, while <bold>g</bold> the control leaf is consumed by the growing caterpillar [<xref ref-type="bibr" rid="CR137">137</xref>]. <bold>h</bold> Ultrastructure of the chloroplast envelope membrane of transplastomic γ-tocopherol methyltransferase (γ-TMT) tobacco plants shows the formation of multiple layers of inner envelope membranes as the result of γ-TMT overexpression [<xref ref-type="bibr" rid="CR153">153</xref>]. <bold>i</bold>, <bold>j</bold> Expression of <italic>BETAINE ALDEHYDE DEHYDROGENASE</italic> (<italic>BADH</italic>) in carrot plants. <bold>i</bold> Transgenic carrot plants thrived in soil irrigated with 400 mM sodium chloride, whereas untransformed carrot plants showed retarded growth in the presence of salt. <bold>j</bold> Carrot roots from transplastomic plants [<xref ref-type="bibr" rid="CR135">135</xref>]. <bold>k</bold> Phenotypes of tomato fruits from transplastomic tomato plants expressing lycopene β-cyclase transgenes compared with wild-type plants. Fruits were harvested at different ripening stages. Orange color of ripe fruits indicates efficient conversion of red lycopene into orange β-carotene (provitamin A) [<xref ref-type="bibr" rid="CR154">154</xref>]</p></caption><graphic xlink:href="13059_2016_1004_Fig4_HTML" id="MO4"></graphic></fig></p></sec><sec id="Sec13"><title>Engineering the chloroplast genomes for biotechnology applications</title><sec id="Sec14"><title>Conferring stress tolerance</title><p>In the past decade, chloroplast genetic engineering has focused primarily on the overexpression of target genes with the potential to enhance biotic stress tolerance, which is very important for plant protection and yield enhancement. Yield loss due to insect pests can be very serious in many countries. In addition to cotton bollworm resistance conferred by hyper-expression of Bt protein in chloroplasts [<xref ref-type="bibr" rid="CR137">137</xref>], there are many other striking recent examples of improved biotic stress tolerance. Retrocyclin-101 and Protegrin-1 protect against <italic>Erwinia</italic> soft rot and tobacco mosaic virus (TMV), which result in yield loss in several cultivated crops [<xref ref-type="bibr" rid="CR140">140</xref>]. Whitefly and aphid resistance has been accomplished by expressing β-glucosidase [<xref ref-type="bibr" rid="CR141">141</xref>], which releases insecticidal sugar esters from hormone conjugates. Multiple resistances against aphids, whiteflies, lepidopteran insects, and bacterial and viral pathogens were achieved by expressing the <italic>Pinellia ternata agglutinin</italic> (<italic>PTA</italic>) gene in the chloroplast genome [<xref ref-type="bibr" rid="CR142">142</xref>]. More than 40 transgenes have been stably integrated into and expressed within the chloroplast genome, conferring important agronomic traits, including insect resistance in edible crops cabbage (<italic>Brassica oleracea</italic>) [<xref ref-type="bibr" rid="CR143">143</xref>], soybean [<xref ref-type="bibr" rid="CR144">144</xref>, <xref ref-type="bibr" rid="CR145">145</xref>], and eggplant (<italic>Solanum melongena</italic>) [<xref ref-type="bibr" rid="CR146">146</xref>].</p><p>More recently, scientists have begun to explore new strategies to downregulate specific target genes. One such approach is to express double-stranded RNAs (dsRNAs) within the chloroplast genome and to use RNA interference (RNAi) to confer the desired agronomic traits, mainly resistance to insects that cause severe yield loss. This strategy has been demonstrated by expressing long or short dsRNAs that activate RNAi and disrupt target genes in insects, providing efficient protection against insects without the need for chemical pesticides. One such example is the suppression of three essential proteins required for insect survival—lepidopteran chitin synthase (Chi), cytochrome P450 monooxygenase (P450), and V-ATPase—using dsRNAs in the tobacco chloroplast system [<xref ref-type="bibr" rid="CR147">147</xref>]. Each dsRNA was expressed independently in chloroplasts and leaves were fed to insects. The transcription level of target genes in <italic>Helicoverpa</italic> insects decreased to almost undetectable levels in the midgut, resulting in a significant reduction in the net weight of larvae and in pupation rate [<xref ref-type="bibr" rid="CR147">147</xref>]. Transplastomic potato plants producing <italic>β-actin</italic>-targeting long dsRNA were lethal to Colorado potato beetle (<italic>Leptinotarsa decemlineata</italic>) larvae, providing yet another crop protection mechanism [<xref ref-type="bibr" rid="CR148">148</xref>].</p></sec><sec id="Sec15"><title>Synthesis of enzymes and biomaterials</title><p>In addition to improved resistance against both biotic and abiotic stress, the chloroplast genome has been engineered to produce useful enzymes, biomaterials, and biofuels, or even to enhance biomass. The first report of metabolic engineering using chloroplast genomes produced the highest level of the poly(p-hydroxybenzoic acid (pHBA) polymer (25 % dry weight) in normal healthy plants despite the diversion of a major metabolic intermediate [<xref ref-type="bibr" rid="CR149">149</xref>]. The first use of plant-derived enzyme cocktails for the production of fermentable sugars from lignocellulosic biomass was accomplished recently [<xref ref-type="bibr" rid="CR150">150</xref>]. Unlike the single biofuel enzymes previously expressed in chloroplasts, nine different genes from bacteria or fungi were expressed in <italic>E. coli</italic> or tobacco chloroplasts using a new technique that enabled the insertion of fungal genes with several introns, eliminating the need to prepare cDNA libraries. Industrial fermentation systems are currently limited by high cost and low production capacity; chloroplast-derived enzyme cocktails offer several striking advantages, including significantly reduced cost, improved stability of chloroplast-derived enzymes, and no need for enzyme purification. Interestingly, expression of β-glucosidase released hormones from conjugates, resulting in elevated phytohormone levels and increased biomass [<xref ref-type="bibr" rid="CR141">141</xref>], an unexpected outcome of enzyme expression.</p></sec><sec id="Sec16"><title>Enhancing nutrition</title><p>Seed oils, such as those from soybean, rapeseed (<italic>Brassica napus</italic>), and maize, are the major dietary source of vitamin E. They have very low α-tocopherol content but relatively high levels of γ-tocopherol. Only a few seed oils, such as sunflower (<italic>Helianthus annuus</italic>) seed oil, contain high levels of α-tocopherol, an important precursor of vitamin E [<xref ref-type="bibr" rid="CR151">151</xref>]. γ-Tocopherol is the biosynthetic precursor of α-tocopherol, suggesting that the α-tocopherol biosynthetic pathway catalyzed by γ-tocopherol methyl transferase (γ-TMT) is the rate-limiting step [<xref ref-type="bibr" rid="CR152">152</xref>]. Engineering of the <italic>γ-tmt</italic> gene into the chloroplast genome resulted in the formation of multiple layers of the inner chloroplast envelope (Fig. <xref rid="Fig4" ref-type="fig">4h</xref>) due to γ-TMT overexpression, with around tenfold higher conversion of γ-tocopherol to α-tocopherol in seeds [<xref ref-type="bibr" rid="CR153">153</xref>]. Likewise, introducing <italic>lycopene β-cyclase</italic> genes into the tomato plastid genome increased the conversion of lycopene into provitamin A (β-carotene), with obvious phenotypic changes (Fig. <xref rid="Fig4" ref-type="fig">4k</xref>) [<xref ref-type="bibr" rid="CR154">154</xref>].</p></sec><sec id="Sec17"><title>Biopharmaceuticals</title><p>At present, protein drugs are extremely expensive; for example, >90 % of the global population cannot afford insulin, a drug needed to treat the global diabetes epidemic. The high cost of protein drugs is due to their production in prohibitively expensive fermentation systems (which cost more than $450–700 million to build depending on their capacity [<xref ref-type="bibr" rid="CR155">155</xref>, <xref ref-type="bibr" rid="CR156">156</xref>]), prohibitively expensive purification from host proteins, the need for refrigerated storage and transport, and the short shelf-life of the final product. Protein drugs made by plant chloroplasts overcome most of these challenges because they do not require expensive fermentation systems and are produced in federal drug administration (FDA)-approved hydroponic greenhouses (Fig. <xref rid="Fig4" ref-type="fig">4a</xref>) [<xref ref-type="bibr" rid="CR157">157</xref>]. Lettuce leaves expressing protein drugs are lyophilized and stored indefinitely at ambient temperature without losing their efficacy (Fig. <xref rid="Fig4" ref-type="fig">4b–d</xref>) [<xref ref-type="bibr" rid="CR6">6</xref>]. The plant cell wall protects protein drugs from acids and enzymes in the stomach because human enzymes do not digest plant cell wall glycans. Human gut microbes, however, have evolved to break down every glycosidic bond in the plant cell wall and therefore release the protein drug into the gut lumen, directing its delivery to the blood or immune system [<xref ref-type="bibr" rid="CR158">158</xref>, <xref ref-type="bibr" rid="CR159">159</xref>].</p><p>Oral delivery of several human therapeutic proteins expressed in chloroplasts is highly efficacious in the treatment of several human diseases, including diabetes, cardiovascular disease, pulmonary hypertension, and Alzheimer’s disease. Most proteins were expressed in tobacco chloroplasts for initial evaluation and were subsequently expressed in lettuce chloroplasts for advancing them to the clinic. Oral delivery of exendin-4, which modulates the secretion of insulin in a glucose-dependent manner, lowered glucose in diabetic animals by stimulating the production of insulin in a manner similar to that of the injectable drug [<xref ref-type="bibr" rid="CR160">160</xref>]. Oral delivery of angiotensin-converting enzyme 2 (ACE2) and angiotensin (Ang) (1–7) significantly improved cardiopulmonary structure and function, decreased elevated right ventricular systolic blood pressure, and improved pulmonary blood flow in animals with induced pulmonary hypertension [<xref ref-type="bibr" rid="CR161">161</xref>]. Oral delivery of plant cells expressing ACE2 and Ang (1–7) also reduced endotoxin-induced uveitis (EIU) and dramatically decreased cellular infiltration and retinal vasculitis, as well as damage and folding in experimental autoimmune uveoretinitis [<xref ref-type="bibr" rid="CR158">158</xref>]. It is also possible to orally deliver protein drugs across the blood–brain barrier to the Alzheimer’s brain to remove plaques [<xref ref-type="bibr" rid="CR162">162</xref>].</p><p>The first industrial-scale production of human blood clotting factor in a cGMP facility was reported recently [<xref ref-type="bibr" rid="CR6">6</xref>] (Fig. <xref rid="Fig4" ref-type="fig">4a–d</xref>). In a 1000 ft<sup>2</sup> hydroponic cGMP facility, it is possible to produce up to 30,000 doses for a 20-kg pediatric patient. Clotting factor made in lettuce was stable for up to 2 years when lyophilized cells were stored at ambient temperature, completely eliminating the need for the cold chain. This enables the first commercial development of an oral drug and addresses the extremely expensive purification, cold storage and transportation, and short shelf-life of current protein drugs. Oral delivery of a broad dose range was effective in the prevention of antibody formation after injection of clotting factor IX (FIX), further facilitating human clinical studies.</p></sec><sec id="Sec18"><title>Vaccines against infectious diseases</title><p>The current iteration of vaccines, using attenuated bacteria or viruses, offer protection against major infectious diseases but they also present major challenges. For example, the oral polio vaccine that is used around the globe has caused severe polio resulting from mutations and recombination with other viruses [<xref ref-type="bibr" rid="CR163">163</xref>]. In addition, all current vaccines require cold storage and transportation, making distribution in developing countries a major challenge. Many of these challenges can be overcome by using chloroplasts.</p><p>One successful chloroplast-derived vaccine conferred dual immunity against cholera and malaria in animal studies [<xref ref-type="bibr" rid="CR164">164</xref>]. Cholera is a major disease causing high mortality, with the only licensed vaccine being not only expensive but also limited in its duration of protection. No vaccine is currently available for malaria. The cholera toxin-B subunit (CTB) of <italic>Vibrio cholerae</italic> was fused to the malarial vaccine antigen apical membrane antigen-1 (AMA1) and merozoite surface protein-1 (MSP1) and expressed in lettuce or tobacco chloroplasts. While no suitable models exist to test human malaria, a cholera toxin challenge using mice immunized with chloroplast-expressed CTB was highly effective and provided the longest duration of protection in the published literature [<xref ref-type="bibr" rid="CR164">164</xref>]. These early results show that chloroplasts are ideal for producing low-cost booster vaccines against several infectious diseases [<xref ref-type="bibr" rid="CR165">165</xref>] for which the global population has been primed previously (Table <xref rid="Tab2" ref-type="table">2</xref>), but lack of an oral priming strategy is still a major limitation in this field.</p></sec></sec><sec id="Sec19"><title>Moving forward</title><p>It is amazing that the chloroplast genome can express >120 foreign genes from different organisms, including bacteria, viruses, fungi, animals, and humans. The insertion of commercially useful traits, including herbicide and insect resistance, into soybean resulted in high-level expression and superior transgene containment, with no antibiotic selectable markers; but even so, these lines were not developed commercially. Nevertheless, recurring concerns about insect resistance against biopesticides have resulted in new USDA requirements on planting <italic>Bt</italic> corn [<xref ref-type="bibr" rid="CR122">122</xref>], which may eventually require utilization of the transplastomic approach to confer agronomic traits. The nuclear transgenic approach is inadequate to develop products when higher-level transgene expression is a requirement. Thus, chloroplast transformation has a unique advantage in advancing the field of molecular farming for the production of vaccines, biopharmaceuticals, or other bio-products.</p><p>Although products with high-level expression have now advanced to the clinic or are in commercial development, a better understanding of chloroplast translation is required to improve several other gene products. The availability of chloroplast genome sequences should help in the development of codon optimization programs using highly expressed chloroplast genes, but among the ~3000 cultivated crops, sequenced chloroplast genomes are available for crops from fewer than 70 genera. Major funding agencies have not supported crop chloroplast genome sequence projects because of the misconception that all chloroplast genomes are similar, as evidenced by the publication of fewer than ten crop chloroplast genome sequences between 1986 and 2004. This review illustrates the importance of sequencing more crop chloroplast genomes for various biotechnology applications. Furthermore, new selectable markers are needed to transform the chloroplast genomes of cereals, which has been elusive for the past two decades.</p><p>Chloroplast genome sequences will be valuable assets in herbal medicine. Most medicinal plants are rare species and very little information is available to confirm their identity. DNA barcodes derived from chloroplast genomes will be useful for identifying varieties and resources; this concept is also valuable in the identification of the origin of cultivated crops and their close relatives to enhance breeding or transfer of useful traits. Molecular techniques to sequence the genomes of single chloroplasts could help to eliminate chloroplast-like sequences that are present in the mitochondrial or nuclear genome. The ability to sequence chloroplast genomes using minimal leaf materials could help us to understand variations in different segments of a variegated leaf in horticultural crops. Further, determining complete chloroplast genome sequences from fossils or recently extinct plants could shed more light on chloroplast genome evolution; help us to understand these species’ inadequate fitness to cope with environmental changes; and help us to build new phylogenetic trees. The technology for isolating DNA from fossils is already available [<xref ref-type="bibr" rid="CR166">166</xref>–<xref ref-type="bibr" rid="CR168">168</xref>]. All of these goals can be accomplished with less expensive and more accurate genome sequences, utilizing longer read sequencing technology and new bioinformatics tools.</p></sec><sec id="Sec20"><title>Abbreviations</title><p>ACE2, Angiotensin-converting enzyme 2; BAC, bacterial artificial chromosome; <italic>Bt</italic>, <italic>Bacillus thuringiensis</italic>; CTB, Cholera toxin B subunit; cGMP, Current Good Manufacturing Processes; CTB, Cholera toxin B subunit; dsRNA, double-stranded RNA; FIX, clotting factor IX; <italic>infA</italic>, <italic>translation initiation factor 1</italic>; IR, inverted repeat; LSC, large single copy; ndh, NAD(P)H dehydrogenase; NCBI, National Center for Biotechnology Information; NGS, next-generation sequencing; RNAi, RNA interference; SSC, small single copy; γ-TMT, γ-Tocopherol methyltransferase; TSP, total soluble protein; UTR, untranslated region; Ang (1–7), Angiotensin (1–7)</p></sec></body><back><app-group><app id="App1"><sec id="Sec21"><title>Additional file</title><p><media position="anchor" xlink:href="13059_2016_1004_MOESM1_ESM.docx" id="MOESM1"><label>Additional file 1: Table S1.</label><caption><p>The chloroplast genes which are absent in specific species, their knock out phenotypes and transfer to nuclear genomes. (DOCX 23 kb)</p></caption></media></p></sec></app></app-group><ack><title>Acknowledgements</title><p>We acknowledge valuable contributions from editors of <italic>Genome Biology</italic> (Drs Dominique Morneau and Ripudaman Bains) to enhance the flow and presentation to non-specialists and reviewers for their critical comments.</p><sec id="FPar1"><title>Funding</title><p>Research from the Daniell Laboratory included in this review was supported by the Bill and Melinda Gates Foundation (OPP1031406), the National Institutes of Health (NIH; R01 HL107904, HL109442, GM 63879, EY 024564), Novo Nordisk, Bayer, and Department of Energy ARPA-E grants to Henry Daniell.</p></sec><sec id="FPar2"><title>Authors’ contributions</title><p>HD and CSL wrote this review. MY assembled Table <xref rid="Tab2" ref-type="table">2</xref> and Figs. <xref rid="Fig3" ref-type="fig">3</xref> and <xref rid="Fig4" ref-type="fig">4</xref> with guidance from HD. WJC assembled Table <xref rid="Tab1" ref-type="table">1</xref> and Figs. <xref rid="Fig1" ref-type="fig">1</xref> and <xref rid="Fig2" ref-type="fig">2</xref> with guidance from CSL. All authors read and approved the final manuscript.</p></sec><sec id="FPar3"><title>Competing interests</title><p>Henry Daniell, as a pioneer in the field of chloroplast genetic engineering, has several patents in this field but has no financial conflict of interest to declare. A complete list of published patents is available at the Google Scholar weblink: <ext-link ext-link-type="uri" xlink:href="http://scholar.google.com/citations?user=7sow4jwAAAAJ&hl=en">http://scholar.google.com/citations?user=7sow4jwAAAAJ&hl=en</ext-link></p></sec></ack><ref-list id="Bib1"><title>References</title><ref id="CR1"><label>1.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Bobik</surname><given-names>K</given-names></name><name><surname>Burch-Smith</surname><given-names>TM</given-names></name></person-group><article-title>Chloroplast signaling within, between and beyond cells</article-title><source>Front Plant Sci</source><year>2015</year><volume>6</volume><fpage>781</fpage><pub-id pub-id-type="doi">10.3389/fpls.2015.00781</pub-id><pub-id pub-id-type="pmid">26500659</pub-id></element-citation></ref><ref id="CR2"><label>2.</label><mixed-citation publication-type="other">Daniell H, Chan H-T, Pasoreck EK. Vaccination through chloroplast genetics: affordable protein drugs for the prevention and treatment of inherited or infectious human diseases. Annu Rev Genet. 2016. In Press.</mixed-citation></ref><ref id="CR3"><label>3.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Shinozaki</surname><given-names>K</given-names></name><name><surname>Ohme</surname><given-names>M</given-names></name><name><surname>Tanaka</surname><given-names>M</given-names></name><name><surname>Wakasugi</surname><given-names>T</given-names></name><name><surname>Hayashida</surname><given-names>N</given-names></name><name><surname>Matsubayashi</surname><given-names>T</given-names></name><etal></etal></person-group><article-title>The complete nucleotide sequence of the tobacco chloroplast genome: its gene organization and expression</article-title><source>EMBO J</source><year>1986</year><volume>5</volume><fpage>2043</fpage><lpage>2049</lpage><pub-id pub-id-type="pmid">16453699</pub-id></element-citation></ref><ref id="CR4"><label>4.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Wambugu</surname><given-names>P</given-names></name><name><surname>Brozynska</surname><given-names>M</given-names></name><name><surname>Furtado</surname><given-names>A</given-names></name><name><surname>Waters</surname><given-names>D</given-names></name><name><surname>Henry</surname><given-names>R</given-names></name></person-group><article-title>Relationships of wild and domesticated rices (<italic>Oryza</italic> AA genome species) based upon whole chloroplast genome sequences</article-title><source>Sci Rep</source><year>2015</year><volume>5</volume><fpage>13957</fpage><pub-id pub-id-type="doi">10.1038/srep13957</pub-id><pub-id pub-id-type="pmid">26355750</pub-id></element-citation></ref><ref id="CR5"><label>5.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Brozynska</surname><given-names>M</given-names></name><name><surname>Furtado</surname><given-names>A</given-names></name><name><surname>Henry</surname><given-names>RJ</given-names></name></person-group><article-title>Genomics of crop wild relatives: expanding the gene pool for crop improvement</article-title><source>Plant Biotechnol J</source><year>2016</year><volume>14</volume><fpage>1070</fpage><lpage>1085</lpage><pub-id pub-id-type="doi">10.1111/pbi.12454</pub-id><pub-id pub-id-type="pmid">26311018</pub-id></element-citation></ref><ref id="CR6"><label>6.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Su</surname><given-names>J</given-names></name><name><surname>Zhu</surname><given-names>L</given-names></name><name><surname>Sherman</surname><given-names>A</given-names></name><name><surname>Wang</surname><given-names>X</given-names></name><name><surname>Lin</surname><given-names>S</given-names></name><name><surname>Kamesh</surname><given-names>A</given-names></name><etal></etal></person-group><article-title>Low cost industrial production of coagulation factor IX bioencapsulated in lettuce cells for oral tolerance induction in hemophilia B</article-title><source>Biomaterials</source><year>2015</year><volume>70</volume><fpage>84</fpage><lpage>93</lpage><pub-id pub-id-type="doi">10.1016/j.biomaterials.2015.08.004</pub-id><pub-id pub-id-type="pmid">26302233</pub-id></element-citation></ref><ref id="CR7"><label>7.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Jansen</surname><given-names>RK</given-names></name><name><surname>Wojciechowski</surname><given-names>MF</given-names></name><name><surname>Sanniyasi</surname><given-names>E</given-names></name><name><surname>Lee</surname><given-names>SB</given-names></name><name><surname>Daniell</surname><given-names>H</given-names></name></person-group><article-title>Complete plastid genome sequence of the chickpea (<italic>Cicer arietinum</italic>) and the phylogenetic distribution of <italic>rps12</italic> and <italic>clpP</italic> intron losses among legumes (Leguminosae)</article-title><source>Mol Phylogenet Evol</source><year>2008</year><volume>48</volume><fpage>1204</fpage><lpage>1217</lpage><pub-id pub-id-type="doi">10.1016/j.ympev.2008.06.013</pub-id><pub-id pub-id-type="pmid">18638561</pub-id></element-citation></ref><ref id="CR8"><label>8.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Saski</surname><given-names>C</given-names></name><name><surname>Lee</surname><given-names>SB</given-names></name><name><surname>Fjellheim</surname><given-names>S</given-names></name><name><surname>Guda</surname><given-names>C</given-names></name><name><surname>Jansen</surname><given-names>RK</given-names></name><name><surname>Luo</surname><given-names>H</given-names></name><etal></etal></person-group><article-title>Complete chloroplast genome sequences of <italic>Hordeum vulgare</italic>, <italic>Sorghum bicolor</italic> and <italic>Agrostis stolonifera</italic>, and comparative analyses with other grass genomes</article-title><source>Theor Appl Genet</source><year>2007</year><volume>115</volume><fpage>571</fpage><lpage>590</lpage><pub-id pub-id-type="doi">10.1007/s00122-007-0567-4</pub-id><pub-id pub-id-type="pmid">17534593</pub-id></element-citation></ref><ref id="CR9"><label>9.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Ruhlman</surname><given-names>T</given-names></name><name><surname>Lee</surname><given-names>SB</given-names></name><name><surname>Jansen</surname><given-names>RK</given-names></name><name><surname>Hostetler</surname><given-names>JB</given-names></name><name><surname>Tallon</surname><given-names>LJ</given-names></name><name><surname>Town</surname><given-names>CD</given-names></name><name><surname>Daniell</surname><given-names>H</given-names></name></person-group><article-title>Complete plastid genome sequence of <italic>Daucus carota</italic>: implications for biotechnology and phylogeny of angiosperms</article-title><source>BMC Genomics</source><year>2006</year><volume>7</volume><fpage>222</fpage><pub-id pub-id-type="doi">10.1186/1471-2164-7-222</pub-id><pub-id pub-id-type="pmid">16945140</pub-id></element-citation></ref><ref id="CR10"><label>10.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Samson</surname><given-names>N</given-names></name><name><surname>Bausher</surname><given-names>MG</given-names></name><name><surname>Lee</surname><given-names>SB</given-names></name><name><surname>Jansen</surname><given-names>RK</given-names></name><name><surname>Daniell</surname><given-names>H</given-names></name></person-group><article-title>The complete nucleotide sequence of the coffee (<italic>Coffea arabica</italic> L.) chloroplast genome: organization and implications for biotechnology and phylogenetic relationships amongst angiosperms</article-title><source>Plant Biotechnol J</source><year>2007</year><volume>5</volume><fpage>339</fpage><lpage>353</lpage><pub-id pub-id-type="doi">10.1111/j.1467-7652.2007.00245.x</pub-id><pub-id pub-id-type="pmid">17309688</pub-id></element-citation></ref><ref id="CR11"><label>11.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Lee</surname><given-names>SB</given-names></name><name><surname>Kaittanis</surname><given-names>C</given-names></name><name><surname>Jansen</surname><given-names>RK</given-names></name><name><surname>Hostetler</surname><given-names>JB</given-names></name><name><surname>Tallon</surname><given-names>LJ</given-names></name><name><surname>Town</surname><given-names>CD</given-names></name><name><surname>Daniell</surname><given-names>H</given-names></name></person-group><article-title>The complete chloroplast genome sequence of <italic>Gossypium hirsutum</italic>: organization and phylogenetic relationships to other angiosperms</article-title><source>BMC Genomics</source><year>2006</year><volume>7</volume><fpage>61</fpage><pub-id pub-id-type="doi">10.1186/1471-2164-7-61</pub-id><pub-id pub-id-type="pmid">16553962</pub-id></element-citation></ref><ref id="CR12"><label>12.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Bausher</surname><given-names>MG</given-names></name><name><surname>Singh</surname><given-names>ND</given-names></name><name><surname>Lee</surname><given-names>SB</given-names></name><name><surname>Jansen</surname><given-names>RK</given-names></name><name><surname>Daniell</surname><given-names>H</given-names></name></person-group><article-title>The complete chloroplast genome sequence of <italic>Citrus sinensis</italic> (L.) Osbeck var 'Ridge Pineapple': organization and phylogenetic relationships to other angiosperms</article-title><source>BMC Plant Biol</source><year>2006</year><volume>6</volume><fpage>21</fpage><pub-id pub-id-type="doi">10.1186/1471-2229-6-21</pub-id><pub-id pub-id-type="pmid">17010212</pub-id></element-citation></ref><ref id="CR13"><label>13.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Daniell</surname><given-names>H</given-names></name><name><surname>Lee</surname><given-names>SB</given-names></name><name><surname>Grevich</surname><given-names>J</given-names></name><name><surname>Saski</surname><given-names>C</given-names></name><name><surname>Quesada-Vargas</surname><given-names>T</given-names></name><name><surname>Guda</surname><given-names>C</given-names></name><etal></etal></person-group><article-title>Complete chloroplast genome sequences of <italic>Solanum bulbocastanum</italic>, <italic>Solanum lycopersicum</italic> and comparative analyses with other Solanaceae genomes</article-title><source>Theor Appl Genet</source><year>2006</year><volume>112</volume><fpage>1503</fpage><lpage>1518</lpage><pub-id pub-id-type="doi">10.1007/s00122-006-0254-x</pub-id><pub-id pub-id-type="pmid">16575560</pub-id></element-citation></ref><ref id="CR14"><label>14.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Jansen</surname><given-names>RK</given-names></name><name><surname>Saski</surname><given-names>C</given-names></name><name><surname>Lee</surname><given-names>SB</given-names></name><name><surname>Hansen</surname><given-names>AK</given-names></name><name><surname>Daniell</surname><given-names>H</given-names></name></person-group><article-title>Complete plastid genome sequences of three rosids (<italic>Castanea</italic>, <italic>Prunus</italic>, <italic>Theobroma</italic>): evidence for at least two independent transfers of <italic>rpl22</italic> to the nucleus</article-title><source>Mol Biol Evol</source><year>2011</year><volume>28</volume><fpage>835</fpage><lpage>847</lpage><pub-id pub-id-type="doi">10.1093/molbev/msq261</pub-id><pub-id pub-id-type="pmid">20935065</pub-id></element-citation></ref><ref id="CR15"><label>15.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Wolfe</surname><given-names>KH</given-names></name><name><surname>Morden</surname><given-names>CW</given-names></name><name><surname>Palmer</surname><given-names>JD</given-names></name></person-group><article-title>Function and evolution of a minimal plastid genome from a nonphotosynthetic parasitic plant</article-title><source>Proc Natl Acad Sci U S A</source><year>1992</year><volume>89</volume><fpage>10648</fpage><lpage>10652</lpage><pub-id pub-id-type="doi">10.1073/pnas.89.22.10648</pub-id><pub-id pub-id-type="pmid">1332054</pub-id></element-citation></ref><ref id="CR16"><label>16.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Bortiri</surname><given-names>E</given-names></name><name><surname>Coleman-Derr</surname><given-names>D</given-names></name><name><surname>Lazo</surname><given-names>GR</given-names></name><name><surname>Anderson</surname><given-names>OD</given-names></name><name><surname>Gu</surname><given-names>YQ</given-names></name></person-group><article-title>The complete chloroplast genome sequence of <italic>Brachypodium distachyon</italic>: sequence comparison and phylogenetic analysis of eight grass plastomes</article-title><source>BMC Res Notes</source><year>2008</year><volume>1</volume><fpage>61</fpage><pub-id pub-id-type="doi">10.1186/1756-0500-1-61</pub-id><pub-id pub-id-type="pmid">18710514</pub-id></element-citation></ref><ref id="CR17"><label>17.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Sato</surname><given-names>S</given-names></name><name><surname>Nakamura</surname><given-names>Y</given-names></name><name><surname>Kaneko</surname><given-names>T</given-names></name><name><surname>Asamizu</surname><given-names>E</given-names></name><name><surname>Tabata</surname><given-names>S</given-names></name></person-group><article-title>Complete structure of the chloroplast genome of <italic>Arabidopsis thaliana</italic></article-title><source>DNA Res</source><year>1999</year><volume>6</volume><fpage>283</fpage><lpage>290</lpage><pub-id pub-id-type="doi">10.1093/dnares/6.5.283</pub-id><pub-id pub-id-type="pmid">10574454</pub-id></element-citation></ref><ref id="CR18"><label>18.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Saski</surname><given-names>C</given-names></name><name><surname>Lee</surname><given-names>SB</given-names></name><name><surname>Daniell</surname><given-names>H</given-names></name><name><surname>Wood</surname><given-names>TC</given-names></name><name><surname>Tomkins</surname><given-names>J</given-names></name><name><surname>Kim</surname><given-names>HG</given-names></name><name><surname>Jansen</surname><given-names>RK</given-names></name></person-group><article-title>Complete chloroplast genome sequence of <italic>Glycine max</italic> and comparative analyses with other legume genomes</article-title><source>Plant Mol Biol</source><year>2005</year><volume>59</volume><fpage>309</fpage><lpage>322</lpage><pub-id pub-id-type="doi">10.1007/s11103-005-8882-0</pub-id><pub-id pub-id-type="pmid">16247559</pub-id></element-citation></ref><ref id="CR19"><label>19.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Jansen</surname><given-names>RK</given-names></name><name><surname>Kaittanis</surname><given-names>C</given-names></name><name><surname>Saski</surname><given-names>C</given-names></name><name><surname>Lee</surname><given-names>SB</given-names></name><name><surname>Tomkins</surname><given-names>J</given-names></name><name><surname>Alverson</surname><given-names>AJ</given-names></name><name><surname>Daniell</surname><given-names>H</given-names></name></person-group><article-title>Phylogenetic analyses of <italic>Vitis</italic> (Vitaceae) based on complete chloroplast genome sequences: effects of taxon sampling and phylogenetic methods on resolving relationships among rosids</article-title><source>BMC Evol Biol</source><year>2006</year><volume>6</volume><fpage>32</fpage><pub-id pub-id-type="doi">10.1186/1471-2148-6-32</pub-id><pub-id pub-id-type="pmid">16603088</pub-id></element-citation></ref><ref id="CR20"><label>20.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Daniell</surname><given-names>H</given-names></name><name><surname>Wurdack</surname><given-names>KJ</given-names></name><name><surname>Kanagaraj</surname><given-names>A</given-names></name><name><surname>Lee</surname><given-names>SB</given-names></name><name><surname>Saski</surname><given-names>C</given-names></name><name><surname>Jansen</surname><given-names>RK</given-names></name></person-group><article-title>The complete nucleotide sequence of the cassava (<italic>Manihot esculenta</italic>) chloroplast genome and the evolution of <italic>atpF</italic> in Malpighiales: RNA editing and multiple losses of a group II intron</article-title><source>Theor Appl Genet</source><year>2008</year><volume>116</volume><fpage>723</fpage><lpage>737</lpage><pub-id pub-id-type="doi">10.1007/s00122-007-0706-y</pub-id><pub-id pub-id-type="pmid">18214421</pub-id></element-citation></ref><ref id="CR21"><label>21.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Wu</surname><given-names>J</given-names></name><name><surname>Liu</surname><given-names>B</given-names></name><name><surname>Cheng</surname><given-names>F</given-names></name><name><surname>Ramchiary</surname><given-names>N</given-names></name><name><surname>Choi</surname><given-names>SR</given-names></name><name><surname>Lim</surname><given-names>YP</given-names></name><name><surname>Wang</surname><given-names>X-W</given-names></name></person-group><article-title>Sequencing of chloroplast genome using whole cellular DNA and Solexa sequencing technology</article-title><source>Front Plant Sci</source><year>2012</year><volume>3</volume><fpage>234</fpage><pub-id pub-id-type="pmid">23125844</pub-id></element-citation></ref><ref id="CR22"><label>22.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Grivet</surname><given-names>D</given-names></name><name><surname>Heinze</surname><given-names>B</given-names></name><name><surname>Vendramin</surname><given-names>G</given-names></name><name><surname>Petit</surname><given-names>R</given-names></name></person-group><article-title>Genome walking with consensus primers: application to the large single copy region of chloroplast DNA</article-title><source>Mol Ecol Notes</source><year>2001</year><volume>1</volume><fpage>345</fpage><lpage>349</lpage><pub-id pub-id-type="doi">10.1046/j.1471-8278.2001.00107.x</pub-id></element-citation></ref><ref id="CR23"><label>23.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Goremykin</surname><given-names>V</given-names></name><name><surname>Hirsch-Ernst</surname><given-names>K</given-names></name><name><surname>Wölfl</surname><given-names>S</given-names></name><name><surname>Hellwig</surname><given-names>F</given-names></name></person-group><article-title>The chloroplast genome of the 'basal' angiosperm <italic>Calycanthus fertilis</italic>–structural and phylogenetic analyses</article-title><source>Plant Syst Evol</source><year>2003</year><volume>242</volume><fpage>119</fpage><lpage>135</lpage><pub-id pub-id-type="doi">10.1007/s00606-003-0056-4</pub-id></element-citation></ref><ref id="CR24"><label>24.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Goremykin</surname><given-names>VV</given-names></name><name><surname>Hirsch-Ernst</surname><given-names>KI</given-names></name><name><surname>Wolfl</surname><given-names>S</given-names></name><name><surname>Hellwig</surname><given-names>FH</given-names></name></person-group><article-title>The chloroplast genome of <italic>Nymphaea alba</italic>: whole-genome analyses and the problem of identifying the most basal angiosperm</article-title><source>Mol Biol Evol</source><year>2004</year><volume>21</volume><fpage>1445</fpage><lpage>1454</lpage><pub-id pub-id-type="doi">10.1093/molbev/msh147</pub-id><pub-id pub-id-type="pmid">15084683</pub-id></element-citation></ref><ref id="CR25"><label>25.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Goremykin</surname><given-names>VV</given-names></name><name><surname>Hirsch-Ernst</surname><given-names>KI</given-names></name><name><surname>Wölfl</surname><given-names>S</given-names></name><name><surname>Hellwig</surname><given-names>FH</given-names></name></person-group><article-title>Analysis of the <italic>Amborella trichopoda</italic> chloroplast genome sequence suggests that <italic>Amborella</italic> is not a basal angiosperm</article-title><source>Mol Biol Evol</source><year>2003</year><volume>20</volume><fpage>1499</fpage><lpage>1505</lpage><pub-id pub-id-type="doi">10.1093/molbev/msg159</pub-id><pub-id pub-id-type="pmid">12832641</pub-id></element-citation></ref><ref id="CR26"><label>26.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Dhingra</surname><given-names>A</given-names></name><name><surname>Folta</surname><given-names>KM</given-names></name></person-group><article-title>ASAP: amplification, sequencing & annotation of plastomes</article-title><source>BMC Genomics</source><year>2005</year><volume>6</volume><fpage>176</fpage><pub-id pub-id-type="doi">10.1186/1471-2164-6-176</pub-id><pub-id pub-id-type="pmid">16336644</pub-id></element-citation></ref><ref id="CR27"><label>27.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Heinze</surname><given-names>B</given-names></name></person-group><article-title>A database of PCR primers for the chloroplast genomes of higher plants</article-title><source>Plant Methods</source><year>2007</year><volume>3</volume><fpage>4</fpage><pub-id pub-id-type="doi">10.1186/1746-4811-3-4</pub-id><pub-id pub-id-type="pmid">17326828</pub-id></element-citation></ref><ref id="CR28"><label>28.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Wu</surname><given-names>FH</given-names></name><name><surname>Kan</surname><given-names>DP</given-names></name><name><surname>Lee</surname><given-names>SB</given-names></name><name><surname>Daniell</surname><given-names>H</given-names></name><name><surname>Lee</surname><given-names>YW</given-names></name><name><surname>Lin</surname><given-names>CC</given-names></name><etal></etal></person-group><article-title>Complete nucleotide sequence of <italic>Dendrocalamus latiflorus</italic> and <italic>Bambusa oldhamii</italic> chloroplast genomes</article-title><source>Tree Physiol</source><year>2009</year><volume>29</volume><fpage>847</fpage><lpage>856</lpage><pub-id pub-id-type="doi">10.1093/treephys/tpp015</pub-id><pub-id pub-id-type="pmid">19324693</pub-id></element-citation></ref><ref id="CR29"><label>29.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Leseberg</surname><given-names>CH</given-names></name><name><surname>Duvall</surname><given-names>MR</given-names></name></person-group><article-title>The complete chloroplast genome of <italic>Coix lacryma-jobi</italic> and a comparative molecular evolutionary analysis of plastomes in cereals</article-title><source>J Mol Evol</source><year>2009</year><volume>69</volume><fpage>311</fpage><lpage>318</lpage><pub-id pub-id-type="doi">10.1007/s00239-009-9275-9</pub-id><pub-id pub-id-type="pmid">19777151</pub-id></element-citation></ref><ref id="CR30"><label>30.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Dong</surname><given-names>W</given-names></name><name><surname>Xu</surname><given-names>C</given-names></name><name><surname>Cheng</surname><given-names>T</given-names></name><name><surname>Lin</surname><given-names>K</given-names></name><name><surname>Zhou</surname><given-names>S</given-names></name></person-group><article-title>Sequencing angiosperm plastid genomes made easy: a complete set of universal primers and a case study on the phylogeny of saxifragales</article-title><source>Genome Biol Evol</source><year>2013</year><volume>5</volume><fpage>989</fpage><lpage>997</lpage><pub-id pub-id-type="doi">10.1093/gbe/evt063</pub-id><pub-id pub-id-type="pmid">23595020</pub-id></element-citation></ref><ref id="CR31"><label>31.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Mardanov</surname><given-names>AV</given-names></name><name><surname>Ravin</surname><given-names>NV</given-names></name><name><surname>Kuznetsov</surname><given-names>BB</given-names></name><name><surname>Samigullin</surname><given-names>TH</given-names></name><name><surname>Antonov</surname><given-names>AS</given-names></name><name><surname>Kolganova</surname><given-names>TV</given-names></name><name><surname>Skyabin</surname><given-names>KG</given-names></name></person-group><article-title>Complete sequence of the duckweed (<italic>Lemna minor</italic>) chloroplast genome: structural organization and phylogenetic relationships to other angiosperms</article-title><source>J Mol Evol</source><year>2008</year><volume>66</volume><fpage>555</fpage><lpage>564</lpage><pub-id pub-id-type="doi">10.1007/s00239-008-9091-7</pub-id><pub-id pub-id-type="pmid">18463914</pub-id></element-citation></ref><ref id="CR32"><label>32.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Lin</surname><given-names>CS</given-names></name><name><surname>Chen</surname><given-names>JJ</given-names></name><name><surname>Huang</surname><given-names>YT</given-names></name><name><surname>Chan</surname><given-names>MT</given-names></name><name><surname>Daniell</surname><given-names>H</given-names></name><name><surname>Chang</surname><given-names>WJ</given-names></name><etal></etal></person-group><article-title>The location and translocation of <italic>ndh</italic> genes of chloroplast origin in the Orchidaceae family</article-title><source>Sci Rep</source><year>2015</year><volume>5</volume><fpage>9040</fpage><pub-id pub-id-type="doi">10.1038/srep09040</pub-id><pub-id pub-id-type="pmid">25761566</pub-id></element-citation></ref><ref id="CR33"><label>33.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Moore</surname><given-names>MJ</given-names></name><name><surname>Dhingra</surname><given-names>A</given-names></name><name><surname>Soltis</surname><given-names>PS</given-names></name><name><surname>Shaw</surname><given-names>R</given-names></name><name><surname>Farmerie</surname><given-names>WG</given-names></name><name><surname>Folta</surname><given-names>KM</given-names></name><name><surname>Soltis</surname><given-names>DE</given-names></name></person-group><article-title>Rapid and accurate pyrosequencing of angiosperm plastid genomes</article-title><source>BMC Plant Biol</source><year>2006</year><volume>6</volume><fpage>17</fpage><pub-id pub-id-type="doi">10.1186/1471-2229-6-17</pub-id><pub-id pub-id-type="pmid">16934154</pub-id></element-citation></ref><ref id="CR34"><label>34.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Wang</surname><given-names>W</given-names></name><name><surname>Messing</surname><given-names>J</given-names></name></person-group><article-title>High-throughput sequencing of three Lemnoideae (duckweeds) chloroplast genomes from total DNA</article-title><source>PLoS One</source><year>2011</year><volume>6</volume><pub-id pub-id-type="doi">10.1371/journal.pone.0024670</pub-id><pub-id pub-id-type="pmid">21931804</pub-id></element-citation></ref><ref id="CR35"><label>35.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Cronn</surname><given-names>R</given-names></name><name><surname>Liston</surname><given-names>A</given-names></name><name><surname>Parks</surname><given-names>M</given-names></name><name><surname>Gernandt</surname><given-names>DS</given-names></name><name><surname>Shen</surname><given-names>R</given-names></name><name><surname>Mockler</surname><given-names>T</given-names></name></person-group><article-title>Multiplex sequencing of plant chloroplast genomes using Solexa sequencing-by-synthesis technology</article-title><source>Nucleic Acids Res</source><year>2008</year><volume>36</volume><pub-id pub-id-type="doi">10.1093/nar/gkn502</pub-id><pub-id pub-id-type="pmid">18753151</pub-id></element-citation></ref><ref id="CR36"><label>36.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Pan</surname><given-names>IC</given-names></name><name><surname>Liao</surname><given-names>DC</given-names></name><name><surname>Wu</surname><given-names>FH</given-names></name><name><surname>Daniell</surname><given-names>H</given-names></name><name><surname>Singh</surname><given-names>ND</given-names></name><name><surname>Chang</surname><given-names>C</given-names></name><etal></etal></person-group><article-title>Complete chloroplast genome sequence of an orchid model plant candidate: <italic>Erycina pusilla</italic> apply in tropical oncidium breeding</article-title><source>PLoS One</source><year>2012</year><volume>7</volume><pub-id pub-id-type="doi">10.1371/journal.pone.0034738</pub-id><pub-id pub-id-type="pmid">22496851</pub-id></element-citation></ref><ref id="CR37"><label>37.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Atherton</surname><given-names>RA</given-names></name><name><surname>McComish</surname><given-names>BJ</given-names></name><name><surname>Shepherd</surname><given-names>LD</given-names></name><name><surname>Berry</surname><given-names>LA</given-names></name><name><surname>Albert</surname><given-names>NW</given-names></name><name><surname>Lockhart</surname><given-names>PJ</given-names></name></person-group><article-title>Whole genome sequencing of enriched chloroplast DNA using the Illumina GAII platform</article-title><source>Plant Methods</source><year>2010</year><volume>6</volume><fpage>22</fpage><pub-id pub-id-type="doi">10.1186/1746-4811-6-22</pub-id><pub-id pub-id-type="pmid">20920211</pub-id></element-citation></ref><ref id="CR38"><label>38.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Jackman</surname><given-names>SD</given-names></name><name><surname>Warren</surname><given-names>RL</given-names></name><name><surname>Gibb</surname><given-names>EA</given-names></name><name><surname>Vandervalk</surname><given-names>BP</given-names></name><name><surname>Mohamadi</surname><given-names>H</given-names></name><name><surname>Chu</surname><given-names>J</given-names></name><etal></etal></person-group><article-title>Organellar genomes of white spruce (<italic>Picea glauca</italic>): assembly and annotation</article-title><source>Genome Biol Evol</source><year>2016</year><volume>8</volume><fpage>29</fpage><lpage>41</lpage><pub-id pub-id-type="doi">10.1093/gbe/evv244</pub-id><pub-id pub-id-type="pmid">26645680</pub-id></element-citation></ref><ref id="CR39"><label>39.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Ferrarini</surname><given-names>M</given-names></name><name><surname>Moretto</surname><given-names>M</given-names></name><name><surname>Ward</surname><given-names>JA</given-names></name><name><surname>Šurbanovski</surname><given-names>N</given-names></name><name><surname>Stevanović</surname><given-names>V</given-names></name><name><surname>Giongo</surname><given-names>L</given-names></name><etal></etal></person-group><article-title>An evaluation of the PacBio RS platform for sequencing and <italic>de novo</italic> assembly of a chloroplast genome</article-title><source>BMC Genomics</source><year>2013</year><volume>14</volume><fpage>670</fpage><pub-id pub-id-type="doi">10.1186/1471-2164-14-670</pub-id><pub-id pub-id-type="pmid">24083400</pub-id></element-citation></ref><ref id="CR40"><label>40.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Wu</surname><given-names>Z</given-names></name><name><surname>Gui</surname><given-names>S</given-names></name><name><surname>Quan</surname><given-names>Z</given-names></name><name><surname>Pan</surname><given-names>L</given-names></name><name><surname>Wang</surname><given-names>S</given-names></name><name><surname>Ke</surname><given-names>W</given-names></name><etal></etal></person-group><article-title>A precise chloroplast genome of <italic>Nelumbo nucifera</italic> (Nelumbonaceae) evaluated with Sanger, Illumina MiSeq, and PacBio RS II sequencing platforms: insight into the plastid evolution of basal eudicots</article-title><source>BMC Plant Biol</source><year>2014</year><volume>14</volume><fpage>289</fpage><pub-id pub-id-type="doi">10.1186/s12870-014-0289-0</pub-id><pub-id pub-id-type="pmid">25407166</pub-id></element-citation></ref><ref id="CR41"><label>41.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Li</surname><given-names>Q</given-names></name><name><surname>Li</surname><given-names>Y</given-names></name><name><surname>Song</surname><given-names>J</given-names></name><name><surname>Xu</surname><given-names>H</given-names></name><name><surname>Xu</surname><given-names>J</given-names></name><name><surname>Zhu</surname><given-names>Y</given-names></name><etal></etal></person-group><article-title>High‐accuracy de novo assembly and SNP detection of chloroplast genomes using a SMRT circular consensus sequencing strategy</article-title><source>New Phytol</source><year>2014</year><volume>204</volume><fpage>1041</fpage><lpage>1049</lpage><pub-id pub-id-type="doi">10.1111/nph.12966</pub-id><pub-id pub-id-type="pmid">25103547</pub-id></element-citation></ref><ref id="CR42"><label>42.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Redwan</surname><given-names>R</given-names></name><name><surname>Saidin</surname><given-names>A</given-names></name><name><surname>Kumar</surname><given-names>S</given-names></name></person-group><article-title>Complete chloroplast genome sequence of MD-2 pineapple and its comparative analysis among nine other plants from the subclass Commelinidae</article-title><source>BMC Plant Biol</source><year>2015</year><volume>15</volume><fpage>196</fpage><pub-id pub-id-type="doi">10.1186/s12870-015-0587-1</pub-id><pub-id pub-id-type="pmid">26264372</pub-id></element-citation></ref><ref id="CR43"><label>43.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Chen</surname><given-names>X</given-names></name><name><surname>Li</surname><given-names>Q</given-names></name><name><surname>Li</surname><given-names>Y</given-names></name><name><surname>Qian</surname><given-names>J</given-names></name><name><surname>Han</surname><given-names>J</given-names></name></person-group><article-title>Chloroplast genome of <italic>Aconitum barbatum</italic> var. <italic>puberulum</italic> (Ranunculaceae) derived from CCS reads using the PacBio RS platform</article-title><source>Frontiers Plant Sci</source><year>2015</year><volume>6</volume><fpage>42</fpage></element-citation></ref><ref id="CR44"><label>44.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Eid</surname><given-names>J</given-names></name><name><surname>Fehr</surname><given-names>A</given-names></name><name><surname>Gray</surname><given-names>J</given-names></name><name><surname>Luong</surname><given-names>K</given-names></name><name><surname>Lyle</surname><given-names>J</given-names></name><name><surname>Otto</surname><given-names>G</given-names></name><etal></etal></person-group><article-title>Real-time DNA sequencing from single polymerase molecules</article-title><source>Science</source><year>2009</year><volume>323</volume><fpage>133</fpage><lpage>138</lpage><pub-id pub-id-type="doi">10.1126/science.1162986</pub-id><pub-id pub-id-type="pmid">19023044</pub-id></element-citation></ref><ref id="CR45"><label>45.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>English</surname><given-names>AC</given-names></name><name><surname>Richards</surname><given-names>S</given-names></name><name><surname>Han</surname><given-names>Y</given-names></name><name><surname>Wang</surname><given-names>M</given-names></name><name><surname>Vee</surname><given-names>V</given-names></name><name><surname>Qu</surname><given-names>J</given-names></name><etal></etal></person-group><article-title>Mind the gap: upgrading genomes with Pacific Biosciences RS long-read sequencing technology</article-title><source>PLoS One</source><year>2012</year><volume>7</volume><pub-id pub-id-type="doi">10.1371/journal.pone.0047768</pub-id><pub-id pub-id-type="pmid">23185243</pub-id></element-citation></ref><ref id="CR46"><label>46.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Chin</surname><given-names>CS</given-names></name><name><surname>Alexander</surname><given-names>DH</given-names></name><name><surname>Marks</surname><given-names>P</given-names></name><name><surname>Klammer</surname><given-names>AA</given-names></name><name><surname>Drake</surname><given-names>J</given-names></name><name><surname>Heiner</surname><given-names>C</given-names></name><etal></etal></person-group><article-title>Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data</article-title><source>Nat Methods</source><year>2013</year><volume>10</volume><fpage>563</fpage><lpage>569</lpage><pub-id pub-id-type="doi">10.1038/nmeth.2474</pub-id><pub-id pub-id-type="pmid">23644548</pub-id></element-citation></ref><ref id="CR47"><label>47.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Oldenburg</surname><given-names>DJ</given-names></name><name><surname>Bendich</surname><given-names>AJ</given-names></name></person-group><article-title>DNA maintenance in plastids and mitochondria of plants</article-title><source>Frontiers Plant Sci</source><year>2015</year><volume>6</volume><fpage>883</fpage><pub-id pub-id-type="doi">10.3389/fpls.2015.00883</pub-id></element-citation></ref><ref id="CR48"><label>48.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Oldenburg</surname><given-names>DJ</given-names></name><name><surname>Bendich</surname><given-names>AJ</given-names></name></person-group><article-title>The linear plastid chromosomes of maize: terminal sequences, structures, and implications for DNA replication</article-title><source>Curr Genet</source><year>2016</year><volume>62</volume><fpage>431</fpage><lpage>442</lpage><pub-id pub-id-type="doi">10.1007/s00294-015-0548-0</pub-id><pub-id pub-id-type="pmid">26650613</pub-id></element-citation></ref><ref id="CR49"><label>49.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Jansen</surname><given-names>RK</given-names></name><name><surname>Cai</surname><given-names>Z</given-names></name><name><surname>Raubeson</surname><given-names>LA</given-names></name><name><surname>Daniell</surname><given-names>H</given-names></name><name><surname>Leebens-Mack</surname><given-names>J</given-names></name><name><surname>Müller</surname><given-names>KF</given-names></name><etal></etal></person-group><article-title>Analysis of 81 genes from 64 plastid genomes resolves relationships in angiosperms and identifies genome-scale evolutionary patterns</article-title><source>Proc Natl Acad Sci U S A</source><year>2007</year><volume>104</volume><fpage>19369</fpage><lpage>19374</lpage><pub-id pub-id-type="doi">10.1073/pnas.0709121104</pub-id><pub-id pub-id-type="pmid">18048330</pub-id></element-citation></ref><ref id="CR50"><label>50.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Pillon</surname><given-names>Y</given-names></name><name><surname>Chase</surname><given-names>MW</given-names></name></person-group><article-title>Taxonomic exaggeration and its effects on orchid conservation</article-title><source>Conserv Biol</source><year>2007</year><volume>21</volume><fpage>263</fpage><lpage>265</lpage><pub-id pub-id-type="doi">10.1111/j.1523-1739.2006.00573.x</pub-id><pub-id pub-id-type="pmid">17298532</pub-id></element-citation></ref><ref id="CR51"><label>51.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Chang</surname><given-names>CC</given-names></name><name><surname>Lin</surname><given-names>HC</given-names></name><name><surname>Lin</surname><given-names>IP</given-names></name><name><surname>Chow</surname><given-names>TY</given-names></name><name><surname>Chen</surname><given-names>HH</given-names></name><name><surname>Chen</surname><given-names>WH</given-names></name><etal></etal></person-group><article-title>The chloroplast genome of <italic>Phalaenopsis aphrodite</italic> (Orchidaceae): comparative analysis of evolutionary rate with that of grasses and its phylogenetic implications</article-title><source>Mol Biol Evol</source><year>2006</year><volume>23</volume><fpage>279</fpage><lpage>291</lpage><pub-id pub-id-type="doi">10.1093/molbev/msj029</pub-id><pub-id pub-id-type="pmid">16207935</pub-id></element-citation></ref><ref id="CR52"><label>52.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Jheng</surname><given-names>CF</given-names></name><name><surname>Chen</surname><given-names>TC</given-names></name><name><surname>Lin</surname><given-names>JY</given-names></name><name><surname>Chen</surname><given-names>TC</given-names></name><name><surname>Wu</surname><given-names>WL</given-names></name><name><surname>Chang</surname><given-names>CC</given-names></name></person-group><article-title>The comparative chloroplast genomic analysis of photosynthetic orchids and developing DNA markers to distinguish <italic>Phalaenopsis</italic> orchids</article-title><source>Plant Sci</source><year>2012</year><volume>190</volume><fpage>62</fpage><lpage>73</lpage><pub-id pub-id-type="doi">10.1016/j.plantsci.2012.04.001</pub-id><pub-id pub-id-type="pmid">22608520</pub-id></element-citation></ref><ref id="CR53"><label>53.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Kim</surname><given-names>GB</given-names></name><name><surname>Kwon</surname><given-names>Y</given-names></name><name><surname>Yu</surname><given-names>HJ</given-names></name><name><surname>Lim</surname><given-names>KB</given-names></name><name><surname>Seo</surname><given-names>JH</given-names></name><name><surname>Mun</surname><given-names>JH</given-names></name></person-group><article-title>The complete chloroplast genome of <italic>Phalaenopsis</italic> 'Tiny Star'</article-title><source>Mitochondrial DNA</source><year>2016</year><volume>27</volume><fpage>1300</fpage><lpage>1302</lpage><pub-id pub-id-type="doi">10.3109/19401736.2014.945566</pub-id><pub-id pub-id-type="pmid">25093401</pub-id></element-citation></ref><ref id="CR54"><label>54.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Wu</surname><given-names>FH</given-names></name><name><surname>Chan</surname><given-names>MT</given-names></name><name><surname>Liao</surname><given-names>DC</given-names></name><name><surname>Hsu</surname><given-names>CT</given-names></name><name><surname>Lee</surname><given-names>YW</given-names></name><name><surname>Daniell</surname><given-names>H</given-names></name><etal></etal></person-group><article-title>Complete chloroplast genome of Oncidium Gower Ramsey and evaluation of molecular markers for identification and breeding in Oncidiinae</article-title><source>BMC Plant Biol</source><year>2010</year><volume>10</volume><fpage>68</fpage><pub-id pub-id-type="doi">10.1186/1471-2229-10-68</pub-id><pub-id pub-id-type="pmid">20398375</pub-id></element-citation></ref><ref id="CR55"><label>55.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Yang</surname><given-names>JB</given-names></name><name><surname>Tang</surname><given-names>M</given-names></name><name><surname>Li</surname><given-names>HT</given-names></name><name><surname>Zhang</surname><given-names>ZR</given-names></name><name><surname>Li</surname><given-names>DZ</given-names></name></person-group><article-title>Complete chloroplast genome of the genus <italic>Cymbidium</italic>: lights into the species identification, phylogenetic implications and population genetic analyses</article-title><source>BMC Evol Biol</source><year>2013</year><volume>13</volume><fpage>84</fpage><pub-id pub-id-type="doi">10.1186/1471-2148-13-84</pub-id><pub-id pub-id-type="pmid">23597078</pub-id></element-citation></ref><ref id="CR56"><label>56.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Luo</surname><given-names>J</given-names></name><name><surname>Hou</surname><given-names>BW</given-names></name><name><surname>Niu</surname><given-names>ZT</given-names></name><name><surname>Liu</surname><given-names>W</given-names></name><name><surname>Xue</surname><given-names>QY</given-names></name><name><surname>Ding</surname><given-names>XY</given-names></name></person-group><article-title>Comparative chloroplast genomes of photosynthetic orchids: insights into evolution of the Orchidaceae and development of molecular markers for phylogenetic applications</article-title><source>PLoS One</source><year>2014</year><volume>9</volume><pub-id pub-id-type="doi">10.1371/journal.pone.0099016</pub-id><pub-id pub-id-type="pmid">24911363</pub-id></element-citation></ref><ref id="CR57"><label>57.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Li</surname><given-names>J</given-names></name><name><surname>Chen</surname><given-names>C</given-names></name><name><surname>Wang</surname><given-names>ZZ</given-names></name></person-group><article-title>The complete chloroplast genome of the <italic>Dendrobium strongylanthum</italic> (Orchidaceae: Epidendroideae)</article-title><source>Mitochondrial DNA</source><year>2016</year><volume>27</volume><fpage>3048</fpage><lpage>3049</lpage><pub-id pub-id-type="pmid">26153739</pub-id></element-citation></ref><ref id="CR58"><label>58.</label><mixed-citation publication-type="other">da Rocha Perini V, Leles B, Furtado C, Prosdocimi F. Complete chloroplast genome of the orchid <italic>Cattleya crispata</italic> (Orchidaceae:Laeliinae), a Neotropical rupiculous species. Mitochondrial DNA. 2015. doi:10.3109/19401736.2014.1003850.</mixed-citation></ref><ref id="CR59"><label>59.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Tsitrone</surname><given-names>A</given-names></name><name><surname>Kirkpatrick</surname><given-names>M</given-names></name><name><surname>Levin</surname><given-names>DA</given-names></name></person-group><article-title>A model for chloroplast capture</article-title><source>Evolution</source><year>2003</year><volume>57</volume><fpage>1776</fpage><lpage>1782</lpage><pub-id pub-id-type="doi">10.1111/j.0014-3820.2003.tb00585.x</pub-id><pub-id pub-id-type="pmid">14503619</pub-id></element-citation></ref><ref id="CR60"><label>60.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Soltis</surname><given-names>DE</given-names></name><name><surname>Kuzoff</surname><given-names>RK</given-names></name></person-group><article-title>Discordance between nuclear and chloroplast phylogenies in the heuchera group (Saxifragaceae)</article-title><source>Evolution</source><year>1995</year><volume>49</volume><fpage>727</fpage><lpage>742</lpage><pub-id pub-id-type="doi">10.2307/2410326</pub-id></element-citation></ref><ref id="CR61"><label>61.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Rieseberg</surname><given-names>LH</given-names></name><name><surname>Soltis</surname><given-names>DE</given-names></name></person-group><article-title>Phylogenetic consequences of cytoplasmic gene flow in plants</article-title><source>Evol Trends Plants</source><year>1991</year><volume>5</volume><fpage>65</fpage><lpage>84</lpage></element-citation></ref><ref id="CR62"><label>62.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Maier</surname><given-names>RM</given-names></name><name><surname>Neckermann</surname><given-names>K</given-names></name><name><surname>Igloi</surname><given-names>GL</given-names></name><name><surname>Kossel</surname><given-names>H</given-names></name></person-group><article-title>Complete sequence of the maize chloroplast genome: gene content, hotspots of divergence and fine tuning of genetic information by transcript editing</article-title><source>J Mol Biol</source><year>1995</year><volume>251</volume><fpage>614</fpage><lpage>628</lpage><pub-id pub-id-type="doi">10.1006/jmbi.1995.0460</pub-id><pub-id pub-id-type="pmid">7666415</pub-id></element-citation></ref><ref id="CR63"><label>63.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Ogihara</surname><given-names>Y</given-names></name><name><surname>Isono</surname><given-names>K</given-names></name><name><surname>Kojima</surname><given-names>T</given-names></name><name><surname>Endo</surname><given-names>A</given-names></name><name><surname>Hanaoka</surname><given-names>M</given-names></name><name><surname>Shiina</surname><given-names>T</given-names></name><etal></etal></person-group><article-title>Structural features of a wheat plastome as revealed by complete sequencing of chloroplast DNA</article-title><source>Mol Genet Genomics</source><year>2002</year><volume>266</volume><fpage>740</fpage><lpage>746</lpage><pub-id pub-id-type="doi">10.1007/s00438-001-0606-9</pub-id><pub-id pub-id-type="pmid">11810247</pub-id></element-citation></ref><ref id="CR64"><label>64.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Middleton</surname><given-names>CP</given-names></name><name><surname>Senerchia</surname><given-names>N</given-names></name><name><surname>Stein</surname><given-names>N</given-names></name><name><surname>Akhunov</surname><given-names>ED</given-names></name><name><surname>Keller</surname><given-names>B</given-names></name><name><surname>Wicker</surname><given-names>T</given-names></name><name><surname>Kilian</surname><given-names>B</given-names></name></person-group><article-title>Sequencing of chloroplast genomes from wheat, barley, rye and their relatives provides a detailed insight into the evolution of the Triticeae tribe</article-title><source>PLoS One</source><year>2014</year><volume>9</volume><pub-id pub-id-type="doi">10.1371/journal.pone.0085761</pub-id><pub-id pub-id-type="pmid">24614886</pub-id></element-citation></ref><ref id="CR65"><label>65.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Brozynska</surname><given-names>M</given-names></name><name><surname>Omar</surname><given-names>ES</given-names></name><name><surname>Furtado</surname><given-names>A</given-names></name><name><surname>Crayn</surname><given-names>D</given-names></name><name><surname>Simon</surname><given-names>B</given-names></name><name><surname>Ishikawa</surname><given-names>R</given-names></name><name><surname>Henry</surname><given-names>RJ</given-names></name></person-group><article-title>Chloroplast genome of novel rice germplasm identified in northern Australia</article-title><source>Tropical Plant Biol</source><year>2014</year><volume>7</volume><fpage>111</fpage><lpage>120</lpage><pub-id pub-id-type="doi">10.1007/s12042-014-9142-8</pub-id></element-citation></ref><ref id="CR66"><label>66.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Waters</surname><given-names>DL</given-names></name><name><surname>Nock</surname><given-names>CJ</given-names></name><name><surname>Ishikawa</surname><given-names>R</given-names></name><name><surname>Rice</surname><given-names>N</given-names></name><name><surname>Henry</surname><given-names>RJ</given-names></name></person-group><article-title>Chloroplast genome sequence confirms distinctness of Australian and Asian wild rice</article-title><source>Ecol Evol</source><year>2012</year><volume>2</volume><fpage>211</fpage><lpage>217</lpage><pub-id pub-id-type="doi">10.1002/ece3.66</pub-id><pub-id pub-id-type="pmid">22408737</pub-id></element-citation></ref><ref id="CR67"><label>67.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Sotowa</surname><given-names>M</given-names></name><name><surname>Ootsuka</surname><given-names>K</given-names></name><name><surname>Kobayashi</surname><given-names>Y</given-names></name><name><surname>Hao</surname><given-names>Y</given-names></name><name><surname>Tanaka</surname><given-names>K</given-names></name><name><surname>Ichitani</surname><given-names>K</given-names></name><etal></etal></person-group><article-title>Molecular relationships between Australian annual wild rice, <italic>Oryza meridionalis</italic>, and two related perennial forms</article-title><source>Rice</source><year>2013</year><volume>6</volume><fpage>26</fpage><pub-id pub-id-type="doi">10.1186/1939-8433-6-26</pub-id><pub-id pub-id-type="pmid">24280095</pub-id></element-citation></ref><ref id="CR68"><label>68.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Xu</surname><given-names>Q</given-names></name><name><surname>Xiong</surname><given-names>G</given-names></name><name><surname>Li</surname><given-names>P</given-names></name><name><surname>He</surname><given-names>F</given-names></name><name><surname>Huang</surname><given-names>Y</given-names></name><name><surname>Wang</surname><given-names>K</given-names></name><etal></etal></person-group><article-title>Analysis of complete nucleotide sequences of 12 <italic>Gossypium</italic> chloroplast genomes: origin and evolution of allotetraploids</article-title><source>PLoS One</source><year>2012</year><volume>7</volume><pub-id pub-id-type="doi">10.1371/journal.pone.0037128</pub-id><pub-id pub-id-type="pmid">22876273</pub-id></element-citation></ref><ref id="CR69"><label>69.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Ibrahim</surname><given-names>RI</given-names></name><name><surname>Azuma</surname><given-names>J</given-names></name><name><surname>Sakamoto</surname><given-names>M</given-names></name></person-group><article-title>Complete nucleotide sequence of the cotton (<italic>Gossypium barbadense</italic> L.) chloroplast genome with a comparative analysis of sequences among 9 dicot plants</article-title><source>Genes Genet Syst</source><year>2006</year><volume>81</volume><fpage>311</fpage><lpage>321</lpage><pub-id pub-id-type="doi">10.1266/ggs.81.311</pub-id><pub-id pub-id-type="pmid">17159292</pub-id></element-citation></ref><ref id="CR70"><label>70.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Li</surname><given-names>P</given-names></name><name><surname>Li</surname><given-names>Z</given-names></name><name><surname>Liu</surname><given-names>H</given-names></name><name><surname>Hua</surname><given-names>J</given-names></name></person-group><article-title>Cytoplasmic diversity of the cotton genus as revealed by chloroplast microsatellite markers</article-title><source>Genet Resour Crop Evol</source><year>2014</year><volume>61</volume><fpage>107</fpage><lpage>119</lpage><pub-id pub-id-type="doi">10.1007/s10722-013-0018-9</pub-id></element-citation></ref><ref id="CR71"><label>71.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Pickersgill</surname><given-names>B</given-names></name><name><surname>Debouck</surname><given-names>DG</given-names></name></person-group><article-title>Domestication patterns in common bean (<italic>Phaseolus vulgaris</italic> L.) and the origin of the Mesoamerican and Andean cultivated races</article-title><source>Theor Appl Genet</source><year>2005</year><volume>110</volume><fpage>432</fpage><lpage>444</lpage><pub-id pub-id-type="doi">10.1007/s00122-004-1842-2</pub-id><pub-id pub-id-type="pmid">15655667</pub-id></element-citation></ref><ref id="CR72"><label>72.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Palmer</surname><given-names>JD</given-names></name><name><surname>Osorio</surname><given-names>B</given-names></name><name><surname>Thompson</surname><given-names>WF</given-names></name></person-group><article-title>Evolutionary significance of inversions in legume chloroplast DNAs</article-title><source>Curr Genet</source><year>1988</year><volume>14</volume><fpage>65</fpage><lpage>74</lpage><pub-id pub-id-type="doi">10.1007/BF00405856</pub-id></element-citation></ref><ref id="CR73"><label>73.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Sherman-Broyles</surname><given-names>S</given-names></name><name><surname>Bombarely</surname><given-names>A</given-names></name><name><surname>Grimwood</surname><given-names>J</given-names></name><name><surname>Schmutz</surname><given-names>J</given-names></name><name><surname>Doyle</surname><given-names>J</given-names></name></person-group><article-title>Complete plastome sequences from <italic>Glycine syndetika</italic> and six additional perennial wild relatives of soybean</article-title><source>G3 (Bethesda)</source><year>2014</year><volume>4</volume><fpage>2023</fpage><lpage>2033</lpage><pub-id pub-id-type="doi">10.1534/g3.114.012690</pub-id><pub-id pub-id-type="pmid">25155272</pub-id></element-citation></ref><ref id="CR74"><label>74.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Sabir</surname><given-names>J</given-names></name><name><surname>Schwarz</surname><given-names>E</given-names></name><name><surname>Ellison</surname><given-names>N</given-names></name><name><surname>Zhang</surname><given-names>J</given-names></name><name><surname>Baeshen</surname><given-names>NA</given-names></name><name><surname>Mutwakil</surname><given-names>M</given-names></name><etal></etal></person-group><article-title>Evolutionary and biotechnology implications of plastid genome variation in the inverted-repeat-lacking clade of legumes</article-title><source>Plant Biotechnol J</source><year>2014</year><volume>12</volume><fpage>743</fpage><lpage>754</lpage><pub-id pub-id-type="doi">10.1111/pbi.12179</pub-id><pub-id pub-id-type="pmid">24618204</pub-id></element-citation></ref><ref id="CR75"><label>75.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Cai</surname><given-names>Z</given-names></name><name><surname>Guisinger</surname><given-names>M</given-names></name><name><surname>Kim</surname><given-names>H-G</given-names></name><name><surname>Ruck</surname><given-names>E</given-names></name><name><surname>Blazier</surname><given-names>JC</given-names></name><name><surname>McMurtry</surname><given-names>V</given-names></name><etal></etal></person-group><article-title>Extensive reorganization of the plastid genome of <italic>Trifolium subterraneum</italic> (Fabaceae) is associated with numerous repeated sequences and novel DNA insertions</article-title><source>J Mol Evol</source><year>2008</year><volume>67</volume><fpage>696</fpage><lpage>704</lpage><pub-id pub-id-type="doi">10.1007/s00239-008-9180-7</pub-id><pub-id pub-id-type="pmid">19018585</pub-id></element-citation></ref><ref id="CR76"><label>76.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Magee</surname><given-names>AM</given-names></name><name><surname>Aspinall</surname><given-names>S</given-names></name><name><surname>Rice</surname><given-names>DW</given-names></name><name><surname>Cusack</surname><given-names>BP</given-names></name><name><surname>Semon</surname><given-names>M</given-names></name><name><surname>Perry</surname><given-names>AS</given-names></name><etal></etal></person-group><article-title>Localized hypermutation and associated gene losses in legume chloroplast genomes</article-title><source>Genome Res</source><year>2010</year><volume>20</volume><fpage>1700</fpage><lpage>1710</lpage><pub-id pub-id-type="doi">10.1101/gr.111955.110</pub-id><pub-id pub-id-type="pmid">20978141</pub-id></element-citation></ref><ref id="CR77"><label>77.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Bogdanova</surname><given-names>VS</given-names></name><name><surname>Zaytseva</surname><given-names>OO</given-names></name><name><surname>Mglinets</surname><given-names>AV</given-names></name><name><surname>Shatskaya</surname><given-names>NV</given-names></name><name><surname>Kosterin</surname><given-names>OE</given-names></name><name><surname>Vasiliev</surname><given-names>GV</given-names></name></person-group><article-title>Nuclear-cytoplasmic conflict in pea (<italic>Pisum sativum</italic> L.) is associated with nuclear and plastidic candidate genes encoding acetyl-CoA carboxylase subunits</article-title><source>PLoS One</source><year>2015</year><volume>10</volume><fpage>e0119835</fpage><pub-id pub-id-type="doi">10.1371/journal.pone.0119835</pub-id><pub-id pub-id-type="pmid">25789472</pub-id></element-citation></ref><ref id="CR78"><label>78.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Guo</surname><given-names>X</given-names></name><name><surname>Castillo-Ramírez</surname><given-names>S</given-names></name><name><surname>González</surname><given-names>V</given-names></name><name><surname>Bustos</surname><given-names>P</given-names></name><name><surname>Fernández-Vázquez</surname><given-names>JL</given-names></name><name><surname>Santamaría</surname><given-names>RI</given-names></name><etal></etal></person-group><article-title>Rapid evolutionary change of common bean (<italic>Phaseolus vulgaris</italic> L.) plastome, and the genomic diversification of legume chloroplasts</article-title><source>BMC Genomics</source><year>2007</year><volume>8</volume><fpage>228</fpage><pub-id pub-id-type="doi">10.1186/1471-2164-8-228</pub-id><pub-id pub-id-type="pmid">17623083</pub-id></element-citation></ref><ref id="CR79"><label>79.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Tangphatsornruang</surname><given-names>S</given-names></name><name><surname>Sangsrakru</surname><given-names>D</given-names></name><name><surname>Chanprasert</surname><given-names>J</given-names></name><name><surname>Uthaipaisanwong</surname><given-names>P</given-names></name><name><surname>Yoocha</surname><given-names>T</given-names></name><name><surname>Jomchai</surname><given-names>N</given-names></name><name><surname>Tragoonrung</surname><given-names>S</given-names></name></person-group><article-title>The chloroplast genome sequence of mungbean (<italic>Vigna radiata</italic>) determined by high-throughput pyrosequencing: structural organization and phylogenetic relationships</article-title><source>DNA Res</source><year>2010</year><volume>17</volume><fpage>11</fpage><lpage>22</lpage><pub-id pub-id-type="doi">10.1093/dnares/dsp025</pub-id><pub-id pub-id-type="pmid">20007682</pub-id></element-citation></ref><ref id="CR80"><label>80.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Martin</surname><given-names>GE</given-names></name><name><surname>Rousseau-Gueutin</surname><given-names>M</given-names></name><name><surname>Cordonnier</surname><given-names>S</given-names></name><name><surname>Lima</surname><given-names>O</given-names></name><name><surname>Michon-Coudouel</surname><given-names>S</given-names></name><name><surname>Naquin</surname><given-names>D</given-names></name><etal></etal></person-group><article-title>The first complete chloroplast genome of the Genistoid legume <italic>Lupinus luteus</italic>: evidence for a novel major lineage-specific rearrangement and new insights regarding plastome evolution in the legume family</article-title><source>Ann Bot</source><year>2014</year><volume>113</volume><fpage>1197</fpage><lpage>1210</lpage><pub-id pub-id-type="doi">10.1093/aob/mcu050</pub-id><pub-id pub-id-type="pmid">24769537</pub-id></element-citation></ref><ref id="CR81"><label>81.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Kazakoff</surname><given-names>SH</given-names></name><name><surname>Imelfort</surname><given-names>M</given-names></name><name><surname>Edwards</surname><given-names>D</given-names></name><name><surname>Koehorst</surname><given-names>J</given-names></name><name><surname>Biswas</surname><given-names>B</given-names></name><name><surname>Batley</surname><given-names>J</given-names></name><etal></etal></person-group><article-title>Capturing the biofuel wellhead and powerhouse: the chloroplast and mitochondrial genomes of the leguminous feedstock tree <italic>Pongamia pinnata</italic></article-title><source>PLoS One</source><year>2012</year><volume>7</volume><pub-id pub-id-type="doi">10.1371/journal.pone.0051687</pub-id><pub-id pub-id-type="pmid">23272141</pub-id></element-citation></ref><ref id="CR82"><label>82.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Schwarz</surname><given-names>EN</given-names></name><name><surname>Ruhlman</surname><given-names>TA</given-names></name><name><surname>Sabir</surname><given-names>JS</given-names></name><name><surname>Hajrah</surname><given-names>NH</given-names></name><name><surname>Alharbi</surname><given-names>NS</given-names></name><name><surname>Al‐Malki</surname><given-names>AL</given-names></name><etal></etal></person-group><article-title>Plastid genome sequences of legumes reveal parallel inversions and multiple losses of <italic>rps16</italic> in papilionoids</article-title><source>J Syst Evol</source><year>2015</year><volume>53</volume><fpage>458</fpage><lpage>468</lpage><pub-id pub-id-type="doi">10.1111/jse.12179</pub-id></element-citation></ref><ref id="CR83"><label>83.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Su</surname><given-names>HJ</given-names></name><name><surname>Hogenhout</surname><given-names>SA</given-names></name><name><surname>Al-Sadi</surname><given-names>AM</given-names></name><name><surname>Kuo</surname><given-names>CH</given-names></name></person-group><article-title>Complete chloroplast genome sequence of Omani Lime (<italic>Citrus aurantiifolia</italic>) and comparative analysis within the Rosids</article-title><source>PLoS One</source><year>2014</year><volume>9</volume><pub-id pub-id-type="doi">10.1371/journal.pone.0113049</pub-id><pub-id pub-id-type="pmid">25398081</pub-id></element-citation></ref><ref id="CR84"><label>84.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Carbonell-Caballero</surname><given-names>J</given-names></name><name><surname>Alonso</surname><given-names>R</given-names></name><name><surname>Ibañez</surname><given-names>V</given-names></name><name><surname>Terol</surname><given-names>J</given-names></name><name><surname>Talon</surname><given-names>M</given-names></name><name><surname>Dopazo</surname><given-names>J</given-names></name></person-group><article-title>A phylogenetic analysis of 34 chloroplast genomes elucidates the relationships between wild and domestic species within the genus <italic>Citrus</italic></article-title><source>Mol Biol Evol</source><year>2015</year><volume>32</volume><fpage>2015</fpage><lpage>2035</lpage><pub-id pub-id-type="doi">10.1093/molbev/msv082</pub-id><pub-id pub-id-type="pmid">25873589</pub-id></element-citation></ref><ref id="CR85"><label>85.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Caspermeyer</surname><given-names>J</given-names></name></person-group><article-title>Most comprehensive study to date reveals evolutionary history of <italic>Citrus</italic></article-title><source>Mol Biol Evol</source><year>2015</year><volume>32</volume><fpage>2217</fpage><lpage>2218</lpage></element-citation></ref><ref id="CR86"><label>86.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Chen</surname><given-names>SL</given-names></name><name><surname>Xiao</surname><given-names>PG</given-names></name></person-group><article-title>Molecular evolution and positive Darwinian selection of the chloroplast maturase matK</article-title><source>J Plant Res</source><year>2010</year><volume>123</volume><fpage>241</fpage><lpage>247</lpage><pub-id pub-id-type="doi">10.1007/s10265-009-0261-5</pub-id><pub-id pub-id-type="pmid">19943076</pub-id></element-citation></ref><ref id="CR87"><label>87.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Peng</surname><given-names>L</given-names></name><name><surname>Yamamoto</surname><given-names>H</given-names></name><name><surname>Shikanai</surname><given-names>T</given-names></name></person-group><article-title>Structure and biogenesis of the chloroplast NAD(P)H dehydrogenase complex</article-title><source>Biochim Biophys Acta</source><year>1807</year><volume>2011</volume><fpage>945</fpage><lpage>953</lpage></element-citation></ref><ref id="CR88"><label>88.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Ma</surname><given-names>PF</given-names></name><name><surname>Zhang</surname><given-names>YX</given-names></name><name><surname>Guo</surname><given-names>ZH</given-names></name><name><surname>Li</surname><given-names>DZ</given-names></name></person-group><article-title>Evidence for horizontal transfer of mitochondrial DNA to the plastid genome in a bamboo genus</article-title><source>Sci Rep</source><year>2015</year><volume>5</volume><fpage>11608</fpage><pub-id pub-id-type="doi">10.1038/srep11608</pub-id><pub-id pub-id-type="pmid">26100509</pub-id></element-citation></ref><ref id="CR89"><label>89.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Zhang</surname><given-names>YJ</given-names></name><name><surname>Ma</surname><given-names>PF</given-names></name><name><surname>Li</surname><given-names>DZ</given-names></name></person-group><article-title>High-throughput sequencing of six bamboo chloroplast genomes: phylogenetic implications for temperate woody bamboos (Poaceae: Bambusoideae)</article-title><source>PLoS One</source><year>2011</year><volume>6</volume><pub-id pub-id-type="doi">10.1371/journal.pone.0020596</pub-id><pub-id pub-id-type="pmid">21655229</pub-id></element-citation></ref><ref id="CR90"><label>90.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Burke</surname><given-names>SV</given-names></name><name><surname>Grennan</surname><given-names>CP</given-names></name><name><surname>Duvall</surname><given-names>MR</given-names></name></person-group><article-title>Plastome sequences of two New World bamboos–<italic>Arundinaria gigantea</italic> and <italic>Cryptochloa strictiflora</italic> (Poaceae)–extend phylogenomic understanding of Bambusoideae</article-title><source>Am J Bot</source><year>2012</year><volume>99</volume><fpage>1951</fpage><lpage>1961</lpage><pub-id pub-id-type="doi">10.3732/ajb.1200365</pub-id><pub-id pub-id-type="pmid">23221496</pub-id></element-citation></ref><ref id="CR91"><label>91.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Gao</surname><given-names>J</given-names></name><name><surname>Li</surname><given-names>K</given-names></name><name><surname>Gao</surname><given-names>LZ</given-names></name></person-group><article-title>The complete chloroplast genome sequence of the <italic>Bambusa multiplex</italic> (Poaceae: Bambusoideae)</article-title><source>Mitochondrial DNA</source><year>2014</year><volume>18</volume><fpage>1</fpage><lpage>3</lpage></element-citation></ref><ref id="CR92"><label>92.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Wysocki</surname><given-names>WP</given-names></name><name><surname>Clark</surname><given-names>LG</given-names></name><name><surname>Attigala</surname><given-names>L</given-names></name><name><surname>Ruiz-Sanchez</surname><given-names>E</given-names></name><name><surname>Duvall</surname><given-names>MR</given-names></name></person-group><article-title>Evolution of the bamboos (Bambusoideae; Poaceae): a full plastome phylogenomic analysis</article-title><source>BMC Evol Biol</source><year>2015</year><volume>15</volume><fpage>50</fpage><pub-id pub-id-type="doi">10.1186/s12862-015-0321-5</pub-id><pub-id pub-id-type="pmid">25887467</pub-id></element-citation></ref><ref id="CR93"><label>93.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Ma</surname><given-names>PF</given-names></name><name><surname>Zhang</surname><given-names>YX</given-names></name><name><surname>Zeng</surname><given-names>CX</given-names></name><name><surname>Guo</surname><given-names>ZH</given-names></name><name><surname>Li</surname><given-names>DZ</given-names></name></person-group><article-title>Chloroplast phylogenomic analyses resolve deep-level relationships of an intractable bamboo tribe Arundinarieae (Poaceae)</article-title><source>Syst Biol</source><year>2014</year><volume>63</volume><fpage>933</fpage><lpage>950</lpage><pub-id pub-id-type="doi">10.1093/sysbio/syu054</pub-id><pub-id pub-id-type="pmid">25092479</pub-id></element-citation></ref><ref id="CR94"><label>94.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Smith</surname><given-names>DR</given-names></name></person-group><article-title>Mitochondrion-to-plastid DNA, transfer: it happens</article-title><source>New Phytol</source><year>2014</year><volume>202</volume><fpage>736</fpage><lpage>738</lpage><pub-id pub-id-type="doi">10.1111/nph.12704</pub-id><pub-id pub-id-type="pmid">24467712</pub-id></element-citation></ref><ref id="CR95"><label>95.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Timmis</surname><given-names>JN</given-names></name><name><surname>Ayliffe</surname><given-names>MA</given-names></name><name><surname>Huang</surname><given-names>CY</given-names></name><name><surname>Martin</surname><given-names>W</given-names></name></person-group><article-title>Endosymbiotic gene transfer: organelle genomes forge eukaryotic chromosomes</article-title><source>Nat Rev Genet</source><year>2004</year><volume>5</volume><fpage>123</fpage><lpage>135</lpage><pub-id pub-id-type="doi">10.1038/nrg1271</pub-id><pub-id pub-id-type="pmid">14735123</pub-id></element-citation></ref><ref id="CR96"><label>96.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Li</surname><given-names>H</given-names></name><name><surname>Chiu</surname><given-names>CC</given-names></name></person-group><article-title>Protein transport into chloroplasts</article-title><source>Annu Rev Plant Biol</source><year>2010</year><volume>61</volume><fpage>157</fpage><lpage>180</lpage><pub-id pub-id-type="doi">10.1146/annurev-arplant-042809-112222</pub-id><pub-id pub-id-type="pmid">20192748</pub-id></element-citation></ref><ref id="CR97"><label>97.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Barrett</surname><given-names>CF</given-names></name><name><surname>Freudenstein</surname><given-names>JV</given-names></name><name><surname>Li</surname><given-names>J</given-names></name><name><surname>Mayfield-Jones</surname><given-names>DR</given-names></name><name><surname>Perez</surname><given-names>L</given-names></name><name><surname>Pires</surname><given-names>JC</given-names></name><name><surname>Santos</surname><given-names>C</given-names></name></person-group><article-title>Investigating the path of plastid genome degradation in an early-transitional clade of heterotrophic orchids, and implications for heterotrophic angiosperms</article-title><source>Mol Biol Evol</source><year>2014</year><volume>31</volume><fpage>3095</fpage><lpage>3112</lpage><pub-id pub-id-type="doi">10.1093/molbev/msu252</pub-id><pub-id pub-id-type="pmid">25172958</pub-id></element-citation></ref><ref id="CR98"><label>98.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Tiller</surname><given-names>N</given-names></name><name><surname>Bock</surname><given-names>R</given-names></name></person-group><article-title>The translational apparatus of plastids and its role in plant development</article-title><source>Mol Plant</source><year>2014</year><volume>7</volume><fpage>1105</fpage><lpage>1120</lpage><pub-id pub-id-type="doi">10.1093/mp/ssu022</pub-id><pub-id pub-id-type="pmid">24589494</pub-id></element-citation></ref><ref id="CR99"><label>99.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Hazkani-Covo</surname><given-names>E</given-names></name><name><surname>Zeller</surname><given-names>RM</given-names></name><name><surname>Martin</surname><given-names>W</given-names></name></person-group><article-title>Molecular poltergeists: mitochondrial DNA copies (numts) in sequenced nuclear genomes</article-title><source>PLoS Genet</source><year>2010</year><volume>6</volume><pub-id pub-id-type="doi">10.1371/journal.pgen.1000834</pub-id><pub-id pub-id-type="pmid">20168995</pub-id></element-citation></ref><ref id="CR100"><label>100.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Smith</surname><given-names>DR</given-names></name><name><surname>Crosby</surname><given-names>K</given-names></name><name><surname>Lee</surname><given-names>RW</given-names></name></person-group><article-title>Correlation between nuclear plastid DNA abundance and plastid number supports the limited transfer window hypothesis</article-title><source>Genome Biol Evol</source><year>2011</year><volume>3</volume><fpage>365</fpage><lpage>371</lpage><pub-id pub-id-type="doi">10.1093/gbe/evr001</pub-id><pub-id pub-id-type="pmid">21292629</pub-id></element-citation></ref><ref id="CR101"><label>101.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Cummings</surname><given-names>HS</given-names></name><name><surname>Hershey</surname><given-names>JWB</given-names></name></person-group><article-title>Translation initiation-factor <italic>IF1</italic> is essential for cell viability in <italic>Escherichia coli</italic></article-title><source>J Bacteriol</source><year>1994</year><volume>176</volume><fpage>198</fpage><lpage>205</lpage><pub-id pub-id-type="pmid">8282696</pub-id></element-citation></ref><ref id="CR102"><label>102.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Millen</surname><given-names>RS</given-names></name><name><surname>Olmstead</surname><given-names>RG</given-names></name><name><surname>Adams</surname><given-names>KL</given-names></name><name><surname>Palmer</surname><given-names>JD</given-names></name><name><surname>Lao</surname><given-names>NT</given-names></name><name><surname>Heggie</surname><given-names>L</given-names></name><etal></etal></person-group><article-title>Many parallel losses of infA from chloroplast DNA during angiosperm evolution with multiple independent transfers to the nucleus</article-title><source>Plant Cell</source><year>2001</year><volume>13</volume><fpage>645</fpage><lpage>658</lpage><pub-id pub-id-type="doi">10.1105/tpc.13.3.645</pub-id><pub-id pub-id-type="pmid">11251102</pub-id></element-citation></ref><ref id="CR103"><label>103.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Gantt</surname><given-names>JS</given-names></name><name><surname>Baldauf</surname><given-names>SL</given-names></name><name><surname>Calie</surname><given-names>PJ</given-names></name><name><surname>Weeden</surname><given-names>NF</given-names></name><name><surname>Palmer</surname><given-names>JD</given-names></name></person-group><article-title>Transfer of <italic>rpl22</italic> to the nucleus greatly preceded its loss from the chloroplast and involved the gain of an intron</article-title><source>EMBO J</source><year>1991</year><volume>10</volume><fpage>3073</fpage><lpage>3078</lpage><pub-id pub-id-type="pmid">1915281</pub-id></element-citation></ref><ref id="CR104"><label>104.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Park</surname><given-names>S</given-names></name><name><surname>Jansen</surname><given-names>RK</given-names></name><name><surname>Park</surname><given-names>S</given-names></name></person-group><article-title>Complete plastome sequence of <italic>Thalictrum coreanum</italic> (Ranunculaceae) and transfer of the <italic>rpl32</italic> gene to the nucleus in the ancestor of the subfamily Thalictroideae</article-title><source>BMC Plant Biol</source><year>2015</year><volume>15</volume><fpage>40</fpage><pub-id pub-id-type="doi">10.1186/s12870-015-0432-6</pub-id><pub-id pub-id-type="pmid">25652741</pub-id></element-citation></ref><ref id="CR105"><label>105.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Ueda</surname><given-names>M</given-names></name><name><surname>Fujimoto</surname><given-names>M</given-names></name><name><surname>Arimura</surname><given-names>S</given-names></name><name><surname>Murata</surname><given-names>J</given-names></name><name><surname>Tsutsumi</surname><given-names>N</given-names></name><name><surname>Kadowaki</surname><given-names>K</given-names></name></person-group><article-title>Loss of the <italic>rpl32</italic> gene from the chloroplast genome and subsequent acquisition of a preexisting transit peptide within the nuclear gene in <italic>Populus</italic></article-title><source>Gene</source><year>2007</year><volume>402</volume><fpage>51</fpage><lpage>56</lpage><pub-id pub-id-type="doi">10.1016/j.gene.2007.07.019</pub-id><pub-id pub-id-type="pmid">17728076</pub-id></element-citation></ref><ref id="CR106"><label>106.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Cusack</surname><given-names>BP</given-names></name><name><surname>Wolfe</surname><given-names>KH</given-names></name></person-group><article-title>When gene marriages don’t work out: divorce by subfunctionalization</article-title><source>Trends Genet</source><year>2007</year><volume>23</volume><fpage>270</fpage><lpage>272</lpage><pub-id pub-id-type="doi">10.1016/j.tig.2007.03.010</pub-id><pub-id pub-id-type="pmid">17418444</pub-id></element-citation></ref><ref id="CR107"><label>107.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Ueda</surname><given-names>M</given-names></name><name><surname>Kuniyoshi</surname><given-names>T</given-names></name><name><surname>Yamamoto</surname><given-names>H</given-names></name><name><surname>Sugimoto</surname><given-names>K</given-names></name><name><surname>Ishizaki</surname><given-names>K</given-names></name><name><surname>Kohchi</surname><given-names>T</given-names></name><etal></etal></person-group><article-title>Composition and physiological function of the chloroplast NADH dehydrogenase-like complex in <italic>Marchantia polymorpha</italic></article-title><source>Plant J</source><year>2012</year><volume>72</volume><fpage>683</fpage><lpage>693</lpage><pub-id pub-id-type="doi">10.1111/j.1365-313X.2012.05115.x</pub-id><pub-id pub-id-type="pmid">22862786</pub-id></element-citation></ref><ref id="CR108"><label>108.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Munekage</surname><given-names>Y</given-names></name><name><surname>Hashimoto</surname><given-names>M</given-names></name><name><surname>Miyake</surname><given-names>C</given-names></name><name><surname>Tomizawa</surname><given-names>K-I</given-names></name><name><surname>Endo</surname><given-names>T</given-names></name><name><surname>Tasaka</surname><given-names>M</given-names></name><name><surname>Shikanai</surname><given-names>T</given-names></name></person-group><article-title>Cyclic electron flow around photosystem I is essential for photosynthesis</article-title><source>Nature</source><year>2004</year><volume>429</volume><fpage>579</fpage><lpage>582</lpage><pub-id pub-id-type="doi">10.1038/nature02598</pub-id><pub-id pub-id-type="pmid">15175756</pub-id></element-citation></ref><ref id="CR109"><label>109.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Peltier</surname><given-names>G</given-names></name><name><surname>Cournac</surname><given-names>L</given-names></name></person-group><article-title>Chlororespiration</article-title><source>Annu Rev Plant Biol</source><year>2002</year><volume>53</volume><fpage>523</fpage><lpage>550</lpage><pub-id pub-id-type="doi">10.1146/annurev.arplant.53.100301.135242</pub-id><pub-id pub-id-type="pmid">12227339</pub-id></element-citation></ref><ref id="CR110"><label>110.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Wakasugi</surname><given-names>T</given-names></name><name><surname>Tsudzuki</surname><given-names>J</given-names></name><name><surname>Ito</surname><given-names>S</given-names></name><name><surname>Nakashima</surname><given-names>K</given-names></name><name><surname>Tsudzuki</surname><given-names>T</given-names></name><name><surname>Sugiura</surname><given-names>M</given-names></name></person-group><article-title>Loss of all <italic>ndh</italic> genes as determined by sequencing the entire chloroplast genome of the black pine <italic>Pinus thunbergii</italic></article-title><source>Proc Natl Acad Sci U S A</source><year>1994</year><volume>91</volume><fpage>9794</fpage><lpage>9798</lpage><pub-id pub-id-type="doi">10.1073/pnas.91.21.9794</pub-id><pub-id pub-id-type="pmid">7937893</pub-id></element-citation></ref><ref id="CR111"><label>111.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Sanderson</surname><given-names>MJ</given-names></name><name><surname>Copetti</surname><given-names>D</given-names></name><name><surname>Búrquez</surname><given-names>A</given-names></name><name><surname>Bustamante</surname><given-names>E</given-names></name><name><surname>Charboneau</surname><given-names>JL</given-names></name><name><surname>Eguiarte</surname><given-names>LE</given-names></name><etal></etal></person-group><article-title>Exceptional reduction of the plastid genome of saguaro cactus (<italic>Carnegiea gigantea</italic>): loss of the <italic>ndh</italic> gene suite and inverted repeat</article-title><source>Am J Bot</source><year>2015</year><volume>102</volume><fpage>1115</fpage><lpage>1127</lpage><pub-id pub-id-type="doi">10.3732/ajb.1500184</pub-id><pub-id pub-id-type="pmid">26199368</pub-id></element-citation></ref><ref id="CR112"><label>112.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>McCoy</surname><given-names>SR</given-names></name><name><surname>Kuehl</surname><given-names>JV</given-names></name><name><surname>Boore</surname><given-names>JL</given-names></name><name><surname>Raubeson</surname><given-names>LA</given-names></name></person-group><article-title>The complete plastid genome sequence of <italic>Welwitschia mirabilis</italic>: an unusually compact plastome with accelerated divergence rates</article-title><source>BMC Evol Biol</source><year>2008</year><volume>8</volume><fpage>130</fpage><pub-id pub-id-type="doi">10.1186/1471-2148-8-130</pub-id><pub-id pub-id-type="pmid">18452621</pub-id></element-citation></ref><ref id="CR113"><label>113.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Braukmann</surname><given-names>TWA</given-names></name><name><surname>Kuzmina</surname><given-names>M</given-names></name><name><surname>Stefanović</surname><given-names>S</given-names></name></person-group><article-title>Loss of all plastid <italic>ndh</italic> genes in Gnetales and conifers: extent and evolutionary significance for the seed plant phylogeny</article-title><source>Curr Genet</source><year>2009</year><volume>55</volume><fpage>323</fpage><lpage>337</lpage><pub-id pub-id-type="doi">10.1007/s00294-009-0249-7</pub-id><pub-id pub-id-type="pmid">19449185</pub-id></element-citation></ref><ref id="CR114"><label>114.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Blazier</surname><given-names>J</given-names></name><name><surname>Guisinger</surname><given-names>MM</given-names></name><name><surname>Jansen</surname><given-names>RK</given-names></name></person-group><article-title>Recent loss of plastid-encoded <italic>ndh</italic> genes within <italic>Erodium</italic> (Geraniaceae)</article-title><source>Plant Mol Biol</source><year>2011</year><volume>76</volume><fpage>263</fpage><lpage>272</lpage><pub-id pub-id-type="doi">10.1007/s11103-011-9753-5</pub-id><pub-id pub-id-type="pmid">21327834</pub-id></element-citation></ref><ref id="CR115"><label>115.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Weng</surname><given-names>M-L</given-names></name><name><surname>Blazier</surname><given-names>JC</given-names></name><name><surname>Govindu</surname><given-names>M</given-names></name><name><surname>Jansen</surname><given-names>RK</given-names></name></person-group><article-title>Reconstruction of the ancestral plastid genome in Geraniaceae reveals a correlation between genome rearrangements, repeats and nucleotide substitution rates</article-title><source>Mol Biol Evol</source><year>2014</year><volume>31</volume><fpage>645</fpage><lpage>659</lpage><pub-id pub-id-type="doi">10.1093/molbev/mst257</pub-id><pub-id pub-id-type="pmid">24336877</pub-id></element-citation></ref><ref id="CR116"><label>116.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Ranade</surname><given-names>SS</given-names></name><name><surname>García-Gil</surname><given-names>MR</given-names></name><name><surname>Rosselló</surname><given-names>JA</given-names></name></person-group><article-title>Non-functional plastid <italic>ndh</italic> gene fragments are present in the nuclear genome of Norway spruce (<italic>Picea abies</italic> L. Karsch): insights from in silico analysis of nuclear and organellar genomes</article-title><source>Mol Genet Genomics</source><year>2016</year><volume>291</volume><fpage>935</fpage><lpage>941</lpage><pub-id pub-id-type="doi">10.1007/s00438-015-1159-7</pub-id><pub-id pub-id-type="pmid">26732267</pub-id></element-citation></ref><ref id="CR117"><label>117.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Ruhlman</surname><given-names>TA</given-names></name><name><surname>Chang</surname><given-names>WJ</given-names></name><name><surname>Chen</surname><given-names>JJ</given-names></name><name><surname>Huang</surname><given-names>YT</given-names></name><name><surname>Chan</surname><given-names>MT</given-names></name><name><surname>Zhang</surname><given-names>J</given-names></name><etal></etal></person-group><article-title>NDH expression marks major transitions in plant evolution and reveals coordinate intracellular gene loss</article-title><source>BMC Plant Biol</source><year>2015</year><volume>15</volume><fpage>100</fpage><pub-id pub-id-type="doi">10.1186/s12870-015-0484-7</pub-id><pub-id pub-id-type="pmid">25886915</pub-id></element-citation></ref><ref id="CR118"><label>118.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Takabayashi</surname><given-names>A</given-names></name><name><surname>Endo</surname><given-names>T</given-names></name><name><surname>Shikanai</surname><given-names>T</given-names></name><name><surname>Sato</surname><given-names>F</given-names></name></person-group><article-title>Post-illumination reduction of the plastoquinone pool in chloroplast transformants in which chloroplastic NAD(P)H dehydrogenase was inactivated</article-title><source>Biosci Biotechnol Biochem</source><year>2002</year><volume>66</volume><fpage>2107</fpage><lpage>2111</lpage><pub-id pub-id-type="doi">10.1271/bbb.66.2107</pub-id><pub-id pub-id-type="pmid">12450121</pub-id></element-citation></ref><ref id="CR119"><label>119.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Burrows</surname><given-names>PA</given-names></name><name><surname>Sazanov</surname><given-names>LA</given-names></name><name><surname>Svab</surname><given-names>Z</given-names></name><name><surname>Maliga</surname><given-names>P</given-names></name><name><surname>Nixon</surname><given-names>PJ</given-names></name></person-group><article-title>Identification of a functional respiratory complex in chloroplasts through analysis of tobacco mutants containing disrupted plastid <italic>ndh</italic> genes</article-title><source>EMBO J</source><year>1998</year><volume>17</volume><fpage>868</fpage><lpage>876</lpage><pub-id pub-id-type="doi">10.1093/emboj/17.4.868</pub-id><pub-id pub-id-type="pmid">9463365</pub-id></element-citation></ref><ref id="CR120"><label>120.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Kofer</surname><given-names>W</given-names></name><name><surname>Koop</surname><given-names>H-U</given-names></name><name><surname>Wanner</surname><given-names>G</given-names></name><name><surname>Steinmüller</surname><given-names>K</given-names></name></person-group><article-title>Mutagenesis of the genes encoding subunits A, C, H, I, J and K of the plastid NAD(P)H-plastoquinone-oxidoreductase in tobacco by polyethylene glycol-mediated plastome transformation</article-title><source>Mol Gen Genet</source><year>1998</year><volume>258</volume><fpage>166</fpage><lpage>173</lpage><pub-id pub-id-type="doi">10.1007/s004380050719</pub-id><pub-id pub-id-type="pmid">9613585</pub-id></element-citation></ref><ref id="CR121"><label>121.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Shikanai</surname><given-names>T</given-names></name><name><surname>Endo</surname><given-names>T</given-names></name><name><surname>Hashimoto</surname><given-names>T</given-names></name><name><surname>Yamada</surname><given-names>Y</given-names></name><name><surname>Asada</surname><given-names>K</given-names></name><name><surname>Yokota</surname><given-names>A</given-names></name></person-group><article-title>Directed disruption of the tobacco <italic>ndhB</italic> gene impairs cyclic electron flow around photosystem I</article-title><source>Proc Natl Acad Sci U S A</source><year>1998</year><volume>95</volume><fpage>9705</fpage><lpage>9709</lpage><pub-id pub-id-type="doi">10.1073/pnas.95.16.9705</pub-id><pub-id pub-id-type="pmid">9689145</pub-id></element-citation></ref><ref id="CR122"><label>122.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Jin</surname><given-names>S</given-names></name><name><surname>Daniell</surname><given-names>H</given-names></name></person-group><article-title>The engineered chloroplast genome just got smarter</article-title><source>Trends Plant Sci</source><year>2015</year><volume>20</volume><fpage>622</fpage><lpage>640</lpage><pub-id pub-id-type="doi">10.1016/j.tplants.2015.07.004</pub-id><pub-id pub-id-type="pmid">26440432</pub-id></element-citation></ref><ref id="CR123"><label>123.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Daniell</surname><given-names>H</given-names></name></person-group><article-title>Transgene containment by maternal inheritance: effective or elusive?</article-title><source>Proc Natl Acad Sci U S A</source><year>2007</year><volume>104</volume><fpage>6879</fpage><lpage>6880</lpage><pub-id pub-id-type="doi">10.1073/pnas.0702219104</pub-id><pub-id pub-id-type="pmid">17440039</pub-id></element-citation></ref><ref id="CR124"><label>124.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Dheeraj</surname><given-names>V</given-names></name><name><surname>Daniell</surname><given-names>H</given-names></name></person-group><article-title>Chloroplast vector systems for biotechnology applications</article-title><source>Plant Physiol</source><year>2007</year><volume>145</volume><fpage>1129</fpage><lpage>1143</lpage><pub-id pub-id-type="doi">10.1104/pp.107.106690</pub-id><pub-id pub-id-type="pmid">18056863</pub-id></element-citation></ref><ref id="CR125"><label>125.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Dunne</surname><given-names>A</given-names></name><name><surname>Maple‐Grødem</surname><given-names>J</given-names></name><name><surname>Gargano</surname><given-names>D</given-names></name><name><surname>Haslam</surname><given-names>RP</given-names></name><name><surname>Napier</surname><given-names>JA</given-names></name><name><surname>Chua</surname><given-names>NH</given-names></name><etal></etal></person-group><article-title>Modifying fatty acid profiles through a new cytokinin‐based plastid transformation system</article-title><source>Plant J</source><year>2014</year><volume>80</volume><fpage>1131</fpage><lpage>1138</lpage><pub-id pub-id-type="doi">10.1111/tpj.12684</pub-id><pub-id pub-id-type="pmid">25280363</pub-id></element-citation></ref><ref id="CR126"><label>126.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Kavanagh</surname><given-names>TA</given-names></name><name><surname>Thanh</surname><given-names>ND</given-names></name><name><surname>Lao</surname><given-names>NT</given-names></name><name><surname>McGrath</surname><given-names>N</given-names></name><name><surname>Peter</surname><given-names>SO</given-names></name><name><surname>Horváth</surname><given-names>EM</given-names></name><etal></etal></person-group><article-title>Homeologous plastid DNA transformation in tobacco is mediated by multiple recombination events</article-title><source>Genetics</source><year>1999</year><volume>152</volume><fpage>1111</fpage><lpage>1122</lpage><pub-id pub-id-type="pmid">10388829</pub-id></element-citation></ref><ref id="CR127"><label>127.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Guda</surname><given-names>C</given-names></name><name><surname>Lee</surname><given-names>SB</given-names></name><name><surname>Daniell</surname><given-names>H</given-names></name></person-group><article-title>Stable expression of a biodegradable protein-based polymer in tobacco chloroplasts</article-title><source>Plant Cell Rep</source><year>2000</year><volume>19</volume><fpage>257</fpage><lpage>262</lpage><pub-id pub-id-type="doi">10.1007/s002990050008</pub-id></element-citation></ref><ref id="CR128"><label>128.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Ruhlman</surname><given-names>T</given-names></name><name><surname>Verma</surname><given-names>D</given-names></name><name><surname>Samson</surname><given-names>N</given-names></name><name><surname>Daniell</surname><given-names>H</given-names></name></person-group><article-title>The role of heterologous chloroplast sequence elements in transgene integration and expression</article-title><source>Plant Physiol</source><year>2010</year><volume>152</volume><fpage>2088</fpage><lpage>2104</lpage><pub-id pub-id-type="doi">10.1104/pp.109.152017</pub-id><pub-id pub-id-type="pmid">20130101</pub-id></element-citation></ref><ref id="CR129"><label>129.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Daniell</surname><given-names>H</given-names></name><name><surname>Datta</surname><given-names>R</given-names></name><name><surname>Varma</surname><given-names>S</given-names></name><name><surname>Gray</surname><given-names>S</given-names></name><name><surname>Lee</surname><given-names>SB</given-names></name></person-group><article-title>Containment of herbicide resistance through genetic engineering of the chloroplast genome</article-title><source>Nat Biotechnol</source><year>1998</year><volume>16</volume><fpage>345</fpage><lpage>348</lpage><pub-id pub-id-type="doi">10.1038/nbt0498-345</pub-id><pub-id pub-id-type="pmid">9555724</pub-id></element-citation></ref><ref id="CR130"><label>130.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Krichevsky</surname><given-names>A</given-names></name><name><surname>Meyers</surname><given-names>B</given-names></name><name><surname>Vainstein</surname><given-names>A</given-names></name><name><surname>Maliga</surname><given-names>P</given-names></name><name><surname>Citovsky</surname><given-names>V</given-names></name></person-group><article-title>Autoluminescent plants</article-title><source>PLoS One</source><year>2010</year><volume>5</volume><pub-id pub-id-type="doi">10.1371/journal.pone.0015461</pub-id><pub-id pub-id-type="pmid">21103397</pub-id></element-citation></ref><ref id="CR131"><label>131.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Daniell</surname><given-names>H</given-names></name><name><surname>Vivekananda</surname><given-names>J</given-names></name><name><surname>Nielsen</surname><given-names>B</given-names></name><name><surname>Ye</surname><given-names>G</given-names></name><name><surname>Tewari</surname><given-names>K</given-names></name><name><surname>Sanford</surname><given-names>J</given-names></name></person-group><article-title>Transient foreign gene expression in chloroplasts of cultured tobacco cells after biolistic delivery of chloroplast vectors</article-title><source>Proc Natl Acad Sci U S A</source><year>1990</year><volume>87</volume><fpage>88</fpage><lpage>92</lpage><pub-id pub-id-type="doi">10.1073/pnas.87.1.88</pub-id><pub-id pub-id-type="pmid">2404285</pub-id></element-citation></ref><ref id="CR132"><label>132.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Klein</surname><given-names>RR</given-names></name><name><surname>Mullet</surname><given-names>JE</given-names></name></person-group><article-title>Control of gene expression during higher plant chloroplast biogenesis. Protein synthesis and transcript levels of <italic>psbA</italic>, <italic>psaA</italic>-<italic>psaB</italic>, and <italic>rbcL</italic> in dark-grown and illuminated barley seedlings</article-title><source>J Biol Chem</source><year>1987</year><volume>262</volume><fpage>4341</fpage><lpage>4348</lpage><pub-id pub-id-type="pmid">3558409</pub-id></element-citation></ref><ref id="CR133"><label>133.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Wurbs</surname><given-names>D</given-names></name><name><surname>Ruf</surname><given-names>S</given-names></name><name><surname>Bock</surname><given-names>R</given-names></name></person-group><article-title>Contained metabolic engineering in tomatoes by expression of carotenoid biosynthesis genes from the plastid genome</article-title><source>Plant J</source><year>2007</year><volume>49</volume><fpage>276</fpage><lpage>288</lpage><pub-id pub-id-type="doi">10.1111/j.1365-313X.2006.02960.x</pub-id><pub-id pub-id-type="pmid">17241450</pub-id></element-citation></ref><ref id="CR134"><label>134.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>McBride</surname><given-names>KE</given-names></name><name><surname>Schaaf</surname><given-names>DJ</given-names></name><name><surname>Daley</surname><given-names>M</given-names></name><name><surname>Stalker</surname><given-names>DM</given-names></name></person-group><article-title>Controlled expression of plastid transgenes in plants based on a nuclear DNA-encoded and plastid-targeted T7 RNA polymerase</article-title><source>Proc Natl Acad Sci U S A</source><year>1994</year><volume>91</volume><fpage>7301</fpage><lpage>7305</lpage><pub-id pub-id-type="doi">10.1073/pnas.91.15.7301</pub-id><pub-id pub-id-type="pmid">8041784</pub-id></element-citation></ref><ref id="CR135"><label>135.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Kumar</surname><given-names>S</given-names></name><name><surname>Dhingra</surname><given-names>A</given-names></name><name><surname>Daniell</surname><given-names>H</given-names></name></person-group><article-title>Plastid-expressed betaine aldehyde dehydrogenase gene in carrot cultured cells, roots, and leaves confers enhanced salt tolerance</article-title><source>Plant Physiol</source><year>2004</year><volume>136</volume><fpage>2843</fpage><lpage>2854</lpage><pub-id pub-id-type="doi">10.1104/pp.104.045187</pub-id><pub-id pub-id-type="pmid">15347789</pub-id></element-citation></ref><ref id="CR136"><label>136.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Dhingra</surname><given-names>A</given-names></name><name><surname>Portis</surname><given-names>AR</given-names><suffix>Jr</suffix></name><name><surname>Daniell</surname><given-names>H</given-names></name></person-group><article-title>Enhanced translation of a chloroplast-expressed <italic>RbcS</italic> gene restores small subunit levels and photosynthesis in nuclear <italic>RbcS</italic> antisense plants</article-title><source>Proc Natl Acad Sci U S A</source><year>2004</year><volume>101</volume><fpage>6315</fpage><lpage>6320</lpage><pub-id pub-id-type="doi">10.1073/pnas.0400981101</pub-id><pub-id pub-id-type="pmid">15067115</pub-id></element-citation></ref><ref id="CR137"><label>137.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>De Cosa</surname><given-names>B</given-names></name><name><surname>Moar</surname><given-names>W</given-names></name><name><surname>Lee</surname><given-names>SB</given-names></name><name><surname>Miller</surname><given-names>M</given-names></name><name><surname>Daniell</surname><given-names>H</given-names></name></person-group><article-title>Overexpression of the Bt cry2Aa2 operon in chloroplasts leads to formation of insecticidal crystals</article-title><source>Nat Biotechnol</source><year>2001</year><volume>19</volume><fpage>71</fpage><lpage>74</lpage><pub-id pub-id-type="doi">10.1038/83559</pub-id><pub-id pub-id-type="pmid">11135556</pub-id></element-citation></ref><ref id="CR138"><label>138.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Ruf</surname><given-names>S</given-names></name><name><surname>Hermann</surname><given-names>M</given-names></name><name><surname>Berger</surname><given-names>IJ</given-names></name><name><surname>Carrer</surname><given-names>H</given-names></name><name><surname>Bock</surname><given-names>R</given-names></name></person-group><article-title>Stable genetic transformation of tomato plastids and expression of a foreign protein in fruit</article-title><source>Nat Biotechnol</source><year>2001</year><volume>19</volume><fpage>870</fpage><lpage>875</lpage><pub-id pub-id-type="doi">10.1038/nbt0901-870</pub-id><pub-id pub-id-type="pmid">11533648</pub-id></element-citation></ref><ref id="CR139"><label>139.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Zhou</surname><given-names>F</given-names></name><name><surname>Badillo-Corona</surname><given-names>JA</given-names></name><name><surname>Karcher</surname><given-names>D</given-names></name><name><surname>Gonzalez-Rabade</surname><given-names>N</given-names></name><name><surname>Piepenburg</surname><given-names>K</given-names></name><name><surname>Borchers</surname><given-names>AM</given-names></name><etal></etal></person-group><article-title>High-level expression of human immunodeficiency virus antigens from the tobacco and tomato plastid genomes</article-title><source>Plant Biotechnol J</source><year>2008</year><volume>6</volume><fpage>897</fpage><lpage>913</lpage><pub-id pub-id-type="doi">10.1111/j.1467-7652.2008.00356.x</pub-id><pub-id pub-id-type="pmid">19548344</pub-id></element-citation></ref><ref id="CR140"><label>140.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Lee</surname><given-names>SB</given-names></name><name><surname>Li</surname><given-names>B</given-names></name><name><surname>Jin</surname><given-names>S</given-names></name><name><surname>Daniell</surname><given-names>H</given-names></name></person-group><article-title>Expression and characterization of antimicrobial peptides Retrocyclin-101 and Protegrin-1 in chloroplasts to control viral and bacterial infections</article-title><source>Plant Biotechnol J</source><year>2011</year><volume>9</volume><fpage>100</fpage><lpage>115</lpage><pub-id pub-id-type="doi">10.1111/j.1467-7652.2010.00538.x</pub-id><pub-id pub-id-type="pmid">20553419</pub-id></element-citation></ref><ref id="CR141"><label>141.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Jin</surname><given-names>S</given-names></name><name><surname>Kanagaraj</surname><given-names>A</given-names></name><name><surname>Verma</surname><given-names>D</given-names></name><name><surname>Lange</surname><given-names>T</given-names></name><name><surname>Daniell</surname><given-names>H</given-names></name></person-group><article-title>Release of hormones from conjugates: chloroplast expression of beta-glucosidase results in elevated phytohormone levels associated with significant increase in biomass and protection from aphids or whiteflies conferred by sucrose esters</article-title><source>Plant Physiol</source><year>2011</year><volume>155</volume><fpage>222</fpage><lpage>235</lpage><pub-id pub-id-type="doi">10.1104/pp.110.160754</pub-id><pub-id pub-id-type="pmid">21068365</pub-id></element-citation></ref><ref id="CR142"><label>142.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Jin</surname><given-names>S</given-names></name><name><surname>Zhang</surname><given-names>X</given-names></name><name><surname>Daniell</surname><given-names>H</given-names></name></person-group><article-title><italic>Pinellia ternata</italic> agglutinin expression in chloroplasts confers broad spectrum resistance against aphid, whitefly, Lepidopteran insects, bacterial and viral pathogens</article-title><source>Plant Biotechnol J</source><year>2012</year><volume>10</volume><fpage>313</fpage><lpage>327</lpage><pub-id pub-id-type="doi">10.1111/j.1467-7652.2011.00663.x</pub-id><pub-id pub-id-type="pmid">22077160</pub-id></element-citation></ref><ref id="CR143"><label>143.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Liu</surname><given-names>CW</given-names></name><name><surname>Lin</surname><given-names>CC</given-names></name><name><surname>Chen</surname><given-names>JJ</given-names></name><name><surname>Tseng</surname><given-names>MJ</given-names></name></person-group><article-title>Stable chloroplast transformation in cabbage (<italic>Brassica oleracea</italic> L. var. <italic>capitata</italic> L.) by particle bombardment</article-title><source>Plant Cell Rep</source><year>2007</year><volume>26</volume><fpage>1733</fpage><lpage>1744</lpage><pub-id pub-id-type="doi">10.1007/s00299-007-0374-z</pub-id><pub-id pub-id-type="pmid">17569052</pub-id></element-citation></ref><ref id="CR144"><label>144.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Dufourmantel</surname><given-names>N</given-names></name><name><surname>Pelissier</surname><given-names>B</given-names></name><name><surname>Garcon</surname><given-names>F</given-names></name><name><surname>Peltier</surname><given-names>G</given-names></name><name><surname>Ferullo</surname><given-names>JM</given-names></name><name><surname>Tissot</surname><given-names>G</given-names></name></person-group><article-title>Generation of fertile transplastomic soybean</article-title><source>Plant Mol Biol</source><year>2004</year><volume>55</volume><fpage>479</fpage><lpage>489</lpage><pub-id pub-id-type="doi">10.1007/s11103-004-0192-4</pub-id><pub-id pub-id-type="pmid">15604694</pub-id></element-citation></ref><ref id="CR145"><label>145.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Dufourmantel</surname><given-names>N</given-names></name><name><surname>Tissot</surname><given-names>G</given-names></name><name><surname>Goutorbe</surname><given-names>F</given-names></name><name><surname>Garcon</surname><given-names>F</given-names></name><name><surname>Muhr</surname><given-names>C</given-names></name><name><surname>Jansens</surname><given-names>S</given-names></name><etal></etal></person-group><article-title>Generation and analysis of soybean plastid transformants expressing <italic>Bacillus thuringiensis</italic> Cry1Ab protoxin</article-title><source>Plant Mol Biol</source><year>2005</year><volume>58</volume><fpage>659</fpage><lpage>668</lpage><pub-id pub-id-type="doi">10.1007/s11103-005-7405-3</pub-id><pub-id pub-id-type="pmid">16158241</pub-id></element-citation></ref><ref id="CR146"><label>146.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Singh</surname><given-names>AK</given-names></name><name><surname>Verma</surname><given-names>SS</given-names></name><name><surname>Bansal</surname><given-names>KC</given-names></name></person-group><article-title>Plastid transformation in eggplant (<italic>Solanum melongena</italic> L.)</article-title><source>Transgenic Res</source><year>2010</year><volume>19</volume><fpage>113</fpage><lpage>119</lpage><pub-id pub-id-type="doi">10.1007/s11248-009-9290-z</pub-id><pub-id pub-id-type="pmid">19562498</pub-id></element-citation></ref><ref id="CR147"><label>147.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Jin</surname><given-names>S</given-names></name><name><surname>Singh</surname><given-names>ND</given-names></name><name><surname>Li</surname><given-names>L</given-names></name><name><surname>Zhang</surname><given-names>X</given-names></name><name><surname>Daniell</surname><given-names>H</given-names></name></person-group><article-title>Engineered chloroplast dsRNA silences cytochrome p450 monooxygenase, V-ATPase and chitin synthase genes in the insect gut and disrupts <italic>Helicoverpa armigera</italic> larval development and pupation</article-title><source>Plant Biotechnol J</source><year>2015</year><volume>13</volume><fpage>435</fpage><lpage>446</lpage><pub-id pub-id-type="doi">10.1111/pbi.12355</pub-id><pub-id pub-id-type="pmid">25782349</pub-id></element-citation></ref><ref id="CR148"><label>148.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Zhang</surname><given-names>J</given-names></name><name><surname>Khan</surname><given-names>SA</given-names></name><name><surname>Hasse</surname><given-names>C</given-names></name><name><surname>Ruf</surname><given-names>S</given-names></name><name><surname>Heckel</surname><given-names>DG</given-names></name><name><surname>Bock</surname><given-names>R</given-names></name></person-group><article-title>Pest control. Full crop protection from an insect pest by expression of long double-stranded RNAs in plastids</article-title><source>Science</source><year>2015</year><volume>347</volume><fpage>991</fpage><lpage>994</lpage><pub-id pub-id-type="doi">10.1126/science.1261680</pub-id><pub-id pub-id-type="pmid">25722411</pub-id></element-citation></ref><ref id="CR149"><label>149.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Viitanen</surname><given-names>PV</given-names></name><name><surname>Devine</surname><given-names>AL</given-names></name><name><surname>Khan</surname><given-names>MS</given-names></name><name><surname>Deuel</surname><given-names>DL</given-names></name><name><surname>Van Dyk</surname><given-names>DE</given-names></name><name><surname>Daniell</surname><given-names>H</given-names></name></person-group><article-title>Metabolic engineering of the chloroplast genome using the <italic>Echerichia coli ubiC</italic> gene reveals that chorismate is a readily abundant plant precursor for p-hydroxybenzoic acid biosynthesis</article-title><source>Plant Physiol</source><year>2004</year><volume>136</volume><fpage>4048</fpage><lpage>4060</lpage><pub-id pub-id-type="doi">10.1104/pp.104.050054</pub-id><pub-id pub-id-type="pmid">15563620</pub-id></element-citation></ref><ref id="CR150"><label>150.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Verma</surname><given-names>D</given-names></name><name><surname>Kanagaraj</surname><given-names>A</given-names></name><name><surname>Jin</surname><given-names>SX</given-names></name><name><surname>Singh</surname><given-names>ND</given-names></name><name><surname>Kolattukudy</surname><given-names>PE</given-names></name><name><surname>Daniell</surname><given-names>H</given-names></name></person-group><article-title>Chloroplast-derived enzyme cocktails hydrolyse lignocellulosic biomass and release fermentable sugars</article-title><source>Plant Biotechnol J</source><year>2010</year><volume>8</volume><fpage>332</fpage><lpage>350</lpage><pub-id pub-id-type="doi">10.1111/j.1467-7652.2009.00486.x</pub-id><pub-id pub-id-type="pmid">20070870</pub-id></element-citation></ref><ref id="CR151"><label>151.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Schneider</surname><given-names>C</given-names></name></person-group><article-title>Chemistry and biology of vitamin E</article-title><source>Mol Nutr Food Res</source><year>2005</year><volume>49</volume><fpage>7</fpage><lpage>30</lpage><pub-id pub-id-type="doi">10.1002/mnfr.200400049</pub-id><pub-id pub-id-type="pmid">15580660</pub-id></element-citation></ref><ref id="CR152"><label>152.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Shintani</surname><given-names>D</given-names></name><name><surname>DellaPenna</surname><given-names>D</given-names></name></person-group><article-title>Elevating the vitamin E content of plants through metabolic engineering</article-title><source>Science</source><year>1998</year><volume>282</volume><fpage>2098</fpage><lpage>2100</lpage><pub-id pub-id-type="doi">10.1126/science.282.5396.2098</pub-id><pub-id pub-id-type="pmid">9851934</pub-id></element-citation></ref><ref id="CR153"><label>153.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Jin</surname><given-names>S</given-names></name><name><surname>Daniell</surname><given-names>H</given-names></name></person-group><article-title>Expression of gamma-tocopherol methyltransferase in chloroplasts results in massive proliferation of the inner envelope membrane and decreases susceptibility to salt and metal-induced oxidative stresses by reducing reactive oxygen species</article-title><source>Plant Biotechnol J</source><year>2014</year><volume>12</volume><fpage>1274</fpage><lpage>1285</lpage><pub-id pub-id-type="doi">10.1111/pbi.12224</pub-id><pub-id pub-id-type="pmid">25051898</pub-id></element-citation></ref><ref id="CR154"><label>154.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Apel</surname><given-names>W</given-names></name><name><surname>Bock</surname><given-names>R</given-names></name></person-group><article-title>Enhancement of carotenoid biosynthesis in transplastomic tomatoes by induced lycopene-to-provitamin A conversion</article-title><source>Plant Physiol</source><year>2009</year><volume>151</volume><fpage>59</fpage><lpage>66</lpage><pub-id pub-id-type="doi">10.1104/pp.109.140533</pub-id><pub-id pub-id-type="pmid">19587100</pub-id></element-citation></ref><ref id="CR155"><label>155.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Grabowski</surname><given-names>H</given-names></name><name><surname>Cockburn</surname><given-names>I</given-names></name><name><surname>Long</surname><given-names>G</given-names></name></person-group><article-title>The market for follow-on biologics: how will it evolve?</article-title><source>Health Aff</source><year>2006</year><volume>25</volume><fpage>1291</fpage><lpage>1301</lpage><pub-id pub-id-type="doi">10.1377/hlthaff.25.5.1291</pub-id></element-citation></ref><ref id="CR156"><label>156.</label><mixed-citation publication-type="other">Spök A, Karner S, Stein AJ, Rodríguez-Cerezo E. Plant molecular farming. Opportunities and challenges. JRC Scientific and Technical Reports 2008. <ext-link ext-link-type="uri" xlink:href="http://ftp.jrc.es/EURdoc/JRC43873.pdf">http://ftp.jrc.es/EURdoc/JRC43873.pdf</ext-link>. Accessed 17 May 2016.</mixed-citation></ref><ref id="CR157"><label>157.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Holtz</surname><given-names>BR</given-names></name><name><surname>Berquist</surname><given-names>BR</given-names></name><name><surname>Bennett</surname><given-names>LD</given-names></name><name><surname>Kommineni</surname><given-names>VJ</given-names></name><name><surname>Munigunti</surname><given-names>RK</given-names></name><name><surname>White</surname><given-names>EL</given-names></name><etal></etal></person-group><article-title>Commercial‐scale biotherapeutics manufacturing facility for plant‐made pharmaceuticals</article-title><source>Plant Biotechnol J</source><year>2015</year><volume>13</volume><fpage>1180</fpage><lpage>1190</lpage><pub-id pub-id-type="doi">10.1111/pbi.12469</pub-id><pub-id pub-id-type="pmid">26387511</pub-id></element-citation></ref><ref id="CR158"><label>158.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Kwon</surname><given-names>KC</given-names></name><name><surname>Daniell</surname><given-names>H</given-names></name></person-group><article-title>Low‐cost oral delivery of protein drugs bioencapsulated in plant cells</article-title><source>Plant Biotechnol J</source><year>2015</year><volume>13</volume><fpage>1017</fpage><lpage>1022</lpage><pub-id pub-id-type="doi">10.1111/pbi.12462</pub-id><pub-id pub-id-type="pmid">26333301</pub-id></element-citation></ref><ref id="CR159"><label>159.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>El Kaoutari</surname><given-names>A</given-names></name><name><surname>Armougom</surname><given-names>F</given-names></name><name><surname>Gordon</surname><given-names>JI</given-names></name><name><surname>Raoult</surname><given-names>D</given-names></name><name><surname>Henrissat</surname><given-names>B</given-names></name></person-group><article-title>The abundance and variety of carbohydrate-active enzymes in the human gut microbiota</article-title><source>Nat Rev Microbiol</source><year>2013</year><volume>11</volume><fpage>497</fpage><lpage>504</lpage><pub-id pub-id-type="doi">10.1038/nrmicro3050</pub-id><pub-id pub-id-type="pmid">23748339</pub-id></element-citation></ref><ref id="CR160"><label>160.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Kwon</surname><given-names>KC</given-names></name><name><surname>Nityanandam</surname><given-names>R</given-names></name><name><surname>New</surname><given-names>JS</given-names></name><name><surname>Daniell</surname><given-names>H</given-names></name></person-group><article-title>Oral delivery of bioencapsulated exendin-4 expressed in chloroplasts lowers blood glucose level in mice and stimulates insulin secretion in beta-TC6 cells</article-title><source>Plant Biotechnol J</source><year>2013</year><volume>11</volume><fpage>77</fpage><lpage>86</lpage><pub-id pub-id-type="doi">10.1111/pbi.12008</pub-id><pub-id pub-id-type="pmid">23078126</pub-id></element-citation></ref><ref id="CR161"><label>161.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Shenoy</surname><given-names>V</given-names></name><name><surname>Kwon</surname><given-names>KC</given-names></name><name><surname>Rathinasabapathy</surname><given-names>A</given-names></name><name><surname>Lin</surname><given-names>SN</given-names></name><name><surname>Jin</surname><given-names>GY</given-names></name><name><surname>Song</surname><given-names>CJ</given-names></name><etal></etal></person-group><article-title>Oral delivery of angiotensin-converting enzyme 2 and angiotensin-(1–7) bioencapsulated in plant cells attenuates pulmonary hypertension</article-title><source>Hypertension</source><year>2014</year><volume>64</volume><fpage>1248</fpage><lpage>1259</lpage><pub-id pub-id-type="doi">10.1161/HYPERTENSIONAHA.114.03871</pub-id><pub-id pub-id-type="pmid">25225206</pub-id></element-citation></ref><ref id="CR162"><label>162.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Kohli</surname><given-names>N</given-names></name><name><surname>Westerveld</surname><given-names>DR</given-names></name><name><surname>Ayache</surname><given-names>AC</given-names></name><name><surname>Verma</surname><given-names>A</given-names></name><name><surname>Shil</surname><given-names>P</given-names></name><name><surname>Prasad</surname><given-names>T</given-names></name><etal></etal></person-group><article-title>Oral delivery of bioencapsulated proteins across blood–brain and blood-retinal barriers</article-title><source>Mol Ther</source><year>2014</year><volume>22</volume><fpage>535</fpage><lpage>546</lpage><pub-id pub-id-type="doi">10.1038/mt.2013.273</pub-id><pub-id pub-id-type="pmid">24281246</pub-id></element-citation></ref><ref id="CR163"><label>163.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Chan</surname><given-names>HT</given-names></name><name><surname>Daniell</surname><given-names>H</given-names></name></person-group><article-title>Plant‐made oral vaccines against human infectious diseases—are we there yet?</article-title><source>Plant Biotechnol J</source><year>2015</year><volume>13</volume><fpage>1056</fpage><lpage>1070</lpage><pub-id pub-id-type="doi">10.1111/pbi.12471</pub-id><pub-id pub-id-type="pmid">26387509</pub-id></element-citation></ref><ref id="CR164"><label>164.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Davoodi-Semiromi</surname><given-names>A</given-names></name><name><surname>Schreiber</surname><given-names>M</given-names></name><name><surname>Nalapalli</surname><given-names>S</given-names></name><name><surname>Verma</surname><given-names>D</given-names></name><name><surname>Singh</surname><given-names>ND</given-names></name><name><surname>Banks</surname><given-names>RK</given-names></name><etal></etal></person-group><article-title>Chloroplast-derived vaccine antigens confer dual immunity against cholera and malaria by oral or injectable delivery</article-title><source>Plant Biotechnol J</source><year>2010</year><volume>8</volume><fpage>223</fpage><lpage>242</lpage><pub-id pub-id-type="doi">10.1111/j.1467-7652.2009.00479.x</pub-id><pub-id pub-id-type="pmid">20051036</pub-id></element-citation></ref><ref id="CR165"><label>165.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Lakshmi</surname><given-names>PS</given-names></name><name><surname>Verma</surname><given-names>D</given-names></name><name><surname>Yang</surname><given-names>X</given-names></name><name><surname>Lloyd</surname><given-names>B</given-names></name><name><surname>Daniell</surname><given-names>H</given-names></name></person-group><article-title>Low cost tuberculosis vaccine antigens in capsules: expression in chloroplasts, bio-encapsulation, stability and functional evaluation in vitro</article-title><source>PLoS One</source><year>2013</year><volume>8</volume><pub-id pub-id-type="doi">10.1371/journal.pone.0054708</pub-id><pub-id pub-id-type="pmid">23355891</pub-id></element-citation></ref><ref id="CR166"><label>166.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Hagelberg</surname><given-names>E</given-names></name><name><surname>Hofreiter</surname><given-names>M</given-names></name><name><surname>Keyser</surname><given-names>C</given-names></name></person-group><article-title>Ancient DNA: the first three decades</article-title><source>Philos Trans R Soc Lond B Biol Sci</source><year>2015</year><volume>370</volume><fpage>20130371</fpage><pub-id pub-id-type="doi">10.1098/rstb.2013.0371</pub-id><pub-id pub-id-type="pmid">25487324</pub-id></element-citation></ref><ref id="CR167"><label>167.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Golenberg</surname><given-names>EM</given-names></name><name><surname>Giannasi</surname><given-names>DE</given-names></name><name><surname>Clegg</surname><given-names>MT</given-names></name><name><surname>Smiley</surname><given-names>CJ</given-names></name><name><surname>Durbin</surname><given-names>M</given-names></name><name><surname>Henderson</surname><given-names>D</given-names></name><name><surname>Zurawski</surname><given-names>G</given-names></name></person-group><article-title>Chloroplast DNA sequence from a Miocene <italic>Magnolia</italic> species</article-title><source>Nature</source><year>1990</year><volume>344</volume><fpage>656</fpage><lpage>658</lpage><pub-id pub-id-type="doi">10.1038/344656a0</pub-id><pub-id pub-id-type="pmid">2325772</pub-id></element-citation></ref><ref id="CR168"><label>168.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Rosselló</surname><given-names>JA</given-names></name></person-group><article-title>The never‐ending story of geologically ancient DNA: was the model plant <italic>Arabidopsis</italic> the source of Miocene Dominican amber?</article-title><source>Biol J Linn Soc</source><year>2014</year><volume>111</volume><fpage>234</fpage><lpage>240</lpage><pub-id pub-id-type="doi">10.1111/bij.12192</pub-id></element-citation></ref><ref id="CR169"><label>169.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Zhu</surname><given-names>A</given-names></name><name><surname>Guo</surname><given-names>W</given-names></name><name><surname>Gupta</surname><given-names>S</given-names></name><name><surname>Fan</surname><given-names>W</given-names></name><name><surname>Mower</surname><given-names>JP</given-names></name></person-group><article-title>Evolutionary dynamics of the plastid inverted repeat: the effects of expansion, contraction, and loss on substitution rates</article-title><source>New Phytol</source><year>2016</year><volume>209</volume><fpage>1747</fpage><lpage>1756</lpage><pub-id pub-id-type="doi">10.1111/nph.13743</pub-id><pub-id pub-id-type="pmid">26574731</pub-id></element-citation></ref><ref id="CR170"><label>170.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>von Kohn</surname><given-names>C</given-names></name><name><surname>Kielkowska</surname><given-names>A</given-names></name><name><surname>Havey</surname><given-names>MJ</given-names></name></person-group><article-title>Sequencing and annotation of the chloroplast DNAs and identification of polymorphisms distinguishing normal male-fertile and male-sterile cytoplasms of onion</article-title><source>Genome</source><year>2013</year><volume>56</volume><fpage>737</fpage><lpage>742</lpage><pub-id pub-id-type="doi">10.1139/gen-2013-0182</pub-id><pub-id pub-id-type="pmid">24433209</pub-id></element-citation></ref><ref id="CR171"><label>171.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Nashima</surname><given-names>K</given-names></name><name><surname>Terakami</surname><given-names>S</given-names></name><name><surname>Nishitani</surname><given-names>C</given-names></name><name><surname>Kunihisa</surname><given-names>M</given-names></name><name><surname>Shoda</surname><given-names>M</given-names></name><name><surname>Takeuchi</surname><given-names>M</given-names></name><etal></etal></person-group><article-title>Complete chloroplast genome sequence of pineapple (<italic>Ananas comosus</italic>)</article-title><source>Tree Genet Genomes</source><year>2015</year><volume>11</volume><fpage>60</fpage><pub-id pub-id-type="doi">10.1007/s11295-015-0892-8</pub-id></element-citation></ref><ref id="CR172"><label>172.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Downie</surname><given-names>SR</given-names></name><name><surname>Jansen</surname><given-names>RK</given-names></name></person-group><article-title>A comparative analysis of whole plastid genomes from the Apiales: expansion and contraction of the inverted repeat, mitochondrial to plastid transfer of DNA, and identification of highly divergent noncoding regions</article-title><source>Syst Botany</source><year>2015</year><volume>40</volume><fpage>336</fpage><lpage>351</lpage><pub-id pub-id-type="doi">10.1600/036364415X686620</pub-id></element-citation></ref><ref id="CR173"><label>173.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Liu</surname><given-names>Y</given-names></name><name><surname>Huo</surname><given-names>N</given-names></name><name><surname>Dong</surname><given-names>L</given-names></name><name><surname>Wang</surname><given-names>Y</given-names></name><name><surname>Zhang</surname><given-names>S</given-names></name><name><surname>Young</surname><given-names>HA</given-names></name><etal></etal></person-group><article-title>Complete chloroplast genome sequences of Mongolia medicine <italic>Artemisia frigida</italic> and phylogenetic relationships with other plants</article-title><source>PLoS One</source><year>2013</year><volume>8</volume><pub-id pub-id-type="doi">10.1371/journal.pone.0057533</pub-id><pub-id pub-id-type="pmid">23460871</pub-id></element-citation></ref><ref id="CR174"><label>174.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Schmitz-Linneweber</surname><given-names>C</given-names></name><name><surname>Regel</surname><given-names>R</given-names></name><name><surname>Du</surname><given-names>TG</given-names></name><name><surname>Hupfer</surname><given-names>H</given-names></name><name><surname>Herrmann</surname><given-names>RG</given-names></name><name><surname>Maier</surname><given-names>RM</given-names></name></person-group><article-title>The plastid chromosome of <italic>Atropa belladonna</italic> and its comparison with that of <italic>Nicotiana tabacum</italic>: the role of RNA editing in generating divergence in the process of plant speciation</article-title><source>Mol Biol Evol</source><year>2002</year><volume>19</volume><fpage>1602</fpage><lpage>1612</lpage><pub-id pub-id-type="doi">10.1093/oxfordjournals.molbev.a004222</pub-id><pub-id pub-id-type="pmid">12200487</pub-id></element-citation></ref><ref id="CR175"><label>175.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Hu</surname><given-names>Z-Y</given-names></name><name><surname>Hua</surname><given-names>W</given-names></name><name><surname>Huang</surname><given-names>S-M</given-names></name><name><surname>Wang</surname><given-names>H-Z</given-names></name></person-group><article-title>Complete chloroplast genome sequence of rapeseed (<italic>Brassica napus</italic> L.) and its evolutionary implications</article-title><source>Genet Resour Crop Evol</source><year>2011</year><volume>58</volume><fpage>875</fpage><lpage>887</lpage><pub-id pub-id-type="doi">10.1007/s10722-010-9626-9</pub-id></element-citation></ref><ref id="CR176"><label>176.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Yang</surname><given-names>JB</given-names></name><name><surname>Li</surname><given-names>DZ</given-names></name><name><surname>Li</surname><given-names>HT</given-names></name></person-group><article-title>Highly effective sequencing whole chloroplast genomes of angiosperms by nine novel universal primer pairs</article-title><source>Mol Ecol Resour</source><year>2014</year><volume>14</volume><fpage>1024</fpage><lpage>1031</lpage><pub-id pub-id-type="doi">10.1111/1755-0998.12165</pub-id><pub-id pub-id-type="pmid">24620934</pub-id></element-citation></ref><ref id="CR177"><label>177.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Oh</surname><given-names>H</given-names></name><name><surname>Seo</surname><given-names>B</given-names></name><name><surname>Lee</surname><given-names>S</given-names></name><name><surname>Ahn</surname><given-names>D-H</given-names></name><name><surname>Jo</surname><given-names>E</given-names></name><name><surname>Park</surname><given-names>J-K</given-names></name><name><surname>Min</surname><given-names>G-S</given-names></name></person-group><article-title>Two complete chloroplast genome sequences of <italic>Cannabis sativa</italic> varieties</article-title><source>Mitochondrial DNA</source><year>2016</year><volume>27</volume><fpage>2835</fpage><lpage>2837</lpage><pub-id pub-id-type="doi">10.3109/19401736.2014.947603</pub-id><pub-id pub-id-type="pmid">26104156</pub-id></element-citation></ref><ref id="CR178"><label>178.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Jo</surname><given-names>YD</given-names></name><name><surname>Park</surname><given-names>J</given-names></name><name><surname>Kim</surname><given-names>J</given-names></name><name><surname>Song</surname><given-names>W</given-names></name><name><surname>Hur</surname><given-names>CG</given-names></name><name><surname>Lee</surname><given-names>YH</given-names></name><name><surname>Kang</surname><given-names>BC</given-names></name></person-group><article-title>Complete sequencing and comparative analyses of the pepper (<italic>Capsicum annuum</italic> L.) plastome revealed high frequency of tandem repeats and large insertion/deletions on pepper plastome</article-title><source>Plant Cell Rep</source><year>2011</year><volume>30</volume><fpage>217</fpage><lpage>229</lpage><pub-id pub-id-type="doi">10.1007/s00299-010-0929-2</pub-id><pub-id pub-id-type="pmid">20978766</pub-id></element-citation></ref><ref id="CR179"><label>179.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Ming</surname><given-names>R</given-names></name><name><surname>Hou</surname><given-names>S</given-names></name><name><surname>Feng</surname><given-names>Y</given-names></name><name><surname>Yu</surname><given-names>Q</given-names></name><name><surname>Dionne-Laporte</surname><given-names>A</given-names></name><name><surname>Saw</surname><given-names>JH</given-names></name><etal></etal></person-group><article-title>The draft genome of the transgenic tropical fruit tree papaya (<italic>Carica papaya</italic> Linnaeus)</article-title><source>Nature</source><year>2008</year><volume>452</volume><fpage>991</fpage><lpage>996</lpage><pub-id pub-id-type="doi">10.1038/nature06856</pub-id><pub-id pub-id-type="pmid">18432245</pub-id></element-citation></ref><ref id="CR180"><label>180.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Ku</surname><given-names>C</given-names></name><name><surname>Chung</surname><given-names>WC</given-names></name><name><surname>Chen</surname><given-names>LL</given-names></name><name><surname>Kuo</surname><given-names>CH</given-names></name></person-group><article-title>The complete plastid genome sequence of Madagascar periwinkle <italic>Catharanthus roseus</italic> (L.) G. Don: plastid genome evolution, molecular marker identification, and phylogenetic implications in asterids</article-title><source>PLoS One</source><year>2013</year><volume>8</volume><pub-id pub-id-type="doi">10.1371/journal.pone.0068518</pub-id><pub-id pub-id-type="pmid">23825699</pub-id></element-citation></ref><ref id="CR181"><label>181.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Mariac</surname><given-names>C</given-names></name><name><surname>Scarcelli</surname><given-names>N</given-names></name><name><surname>Pouzadou</surname><given-names>J</given-names></name><name><surname>Barnaud</surname><given-names>A</given-names></name><name><surname>Billot</surname><given-names>C</given-names></name><name><surname>Faye</surname><given-names>A</given-names></name><etal></etal></person-group><article-title>Cost-effective enrichment hybridization capture of chloroplast genomes at deep multiplexing levels for population genetics and phylogeography studies</article-title><source>Mol Ecol Resour</source><year>2014</year><volume>14</volume><fpage>1103</fpage><lpage>1113</lpage><pub-id pub-id-type="doi">10.1111/1755-0998.12258</pub-id><pub-id pub-id-type="pmid">24690362</pub-id></element-citation></ref><ref id="CR182"><label>182.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Ahmed</surname><given-names>I</given-names></name><name><surname>Biggs</surname><given-names>PJ</given-names></name><name><surname>Matthews</surname><given-names>PJ</given-names></name><name><surname>Collins</surname><given-names>LJ</given-names></name><name><surname>Hendy</surname><given-names>MD</given-names></name><name><surname>Lockhart</surname><given-names>PJ</given-names></name></person-group><article-title>Mutational dynamics of aroid chloroplast genomes</article-title><source>Genome Biol Evol</source><year>2012</year><volume>4</volume><fpage>1316</fpage><lpage>1323</lpage><pub-id pub-id-type="doi">10.1093/gbe/evs110</pub-id><pub-id pub-id-type="pmid">23204304</pub-id></element-citation></ref><ref id="CR183"><label>183.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Plader</surname><given-names>W</given-names></name><name><surname>Yukawa</surname><given-names>Y</given-names></name><name><surname>Sugiura</surname><given-names>M</given-names></name><name><surname>Malepszy</surname><given-names>S</given-names></name></person-group><article-title>The complete structure of the cucumber (<italic>Cucumis sativus</italic> L.) chloroplast genome: its composition and comparative analysis</article-title><source>Cell Mol Biol Lett</source><year>2007</year><volume>12</volume><fpage>584</fpage><lpage>594</lpage><pub-id pub-id-type="doi">10.2478/s11658-007-0029-7</pub-id><pub-id pub-id-type="pmid">17607527</pub-id></element-citation></ref><ref id="CR184"><label>184.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Barrett</surname><given-names>CF</given-names></name><name><surname>Specht</surname><given-names>CD</given-names></name><name><surname>Leebens-Mack</surname><given-names>J</given-names></name><name><surname>Stevenson</surname><given-names>DW</given-names></name><name><surname>Zomlefer</surname><given-names>WB</given-names></name><name><surname>Davis</surname><given-names>JI</given-names></name></person-group><article-title>Resolving ancient radiations: can complete plastid gene sets elucidate deep relationships among the tropical gingers (Zingiberales)?</article-title><source>Ann Bot</source><year>2014</year><volume>113</volume><fpage>119</fpage><lpage>133</lpage><pub-id pub-id-type="doi">10.1093/aob/mct264</pub-id><pub-id pub-id-type="pmid">24280362</pub-id></element-citation></ref><ref id="CR185"><label>185.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Wang</surname><given-names>B</given-names></name><name><surname>Han</surname><given-names>L</given-names></name><name><surname>Chen</surname><given-names>C</given-names></name><name><surname>Wang</surname><given-names>Z</given-names></name></person-group><article-title>The complete chloroplast genome sequence of <italic>Dieffenbachia seguine</italic> (Araceae)</article-title><source>Mitochondrial DNA</source><year>2016</year><volume>27</volume><fpage>2913</fpage><lpage>2914</lpage><pub-id pub-id-type="pmid">26153749</pub-id></element-citation></ref><ref id="CR186"><label>186.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Ye</surname><given-names>CY</given-names></name><name><surname>Lin</surname><given-names>Z</given-names></name><name><surname>Li</surname><given-names>G</given-names></name><name><surname>Wang</surname><given-names>YY</given-names></name><name><surname>Qiu</surname><given-names>J</given-names></name><name><surname>Fu</surname><given-names>F</given-names></name><name><surname>Zhang</surname><given-names>H</given-names></name><etal></etal></person-group><article-title><italic>Echinochloa</italic> chloroplast genomes: insights into the evolution and taxonomic identification of two weedy species</article-title><source>PLoS One</source><year>2014</year><volume>9</volume><pub-id pub-id-type="doi">10.1371/journal.pone.0113657</pub-id><pub-id pub-id-type="pmid">25427255</pub-id></element-citation></ref><ref id="CR187"><label>187.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Wu</surname><given-names>CS</given-names></name><name><surname>Lai</surname><given-names>YT</given-names></name><name><surname>Lin</surname><given-names>CP</given-names></name><name><surname>Wang</surname><given-names>YN</given-names></name><name><surname>Chaw</surname><given-names>SM</given-names></name></person-group><article-title>Evolution of reduced and compact chloroplast genomes (cpDNAs) in gnetophytes: selection toward a lower-cost strategy</article-title><source>Mol Phylogenet Evol</source><year>2009</year><volume>52</volume><fpage>115</fpage><lpage>124</lpage><pub-id pub-id-type="doi">10.1016/j.ympev.2008.12.026</pub-id><pub-id pub-id-type="pmid">19166950</pub-id></element-citation></ref><ref id="CR188"><label>188.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Logacheva</surname><given-names>MD</given-names></name><name><surname>Samigullin</surname><given-names>TH</given-names></name><name><surname>Dhingra</surname><given-names>A</given-names></name><name><surname>Penin</surname><given-names>AA</given-names></name></person-group><article-title>Comparative chloroplast genomics and phylogenetics of Fagopyrum esculentum ssp. ancestrale--a wild ancestor of cultivated buckwheat</article-title><source>BMC Plant Biol</source><year>2008</year><volume>8</volume><fpage>59</fpage><pub-id pub-id-type="doi">10.1186/1471-2229-8-59</pub-id><pub-id pub-id-type="pmid">18492277</pub-id></element-citation></ref><ref id="CR189"><label>189.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Cahoon</surname><given-names>AB</given-names></name><name><surname>Sharpe</surname><given-names>RM</given-names></name><name><surname>Mysayphonh</surname><given-names>C</given-names></name><name><surname>Thompson</surname><given-names>EJ</given-names></name><name><surname>Ward</surname><given-names>AD</given-names></name><name><surname>Lin</surname><given-names>A</given-names></name></person-group><article-title>The complete chloroplast genome of tall fescue (<italic>Lolium arundinaceum</italic>; Poaceae) and comparison of whole plastomes from the family Poaceae</article-title><source>Am J Bot</source><year>2010</year><volume>97</volume><fpage>49</fpage><lpage>58</lpage><pub-id pub-id-type="doi">10.3732/ajb.0900008</pub-id><pub-id pub-id-type="pmid">21622366</pub-id></element-citation></ref><ref id="CR190"><label>190.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Shulaev</surname><given-names>V</given-names></name><name><surname>Sargent</surname><given-names>DJ</given-names></name><name><surname>Crowhurst</surname><given-names>RN</given-names></name><name><surname>Mockler</surname><given-names>TC</given-names></name><name><surname>Folkerts</surname><given-names>O</given-names></name><name><surname>Delcher</surname><given-names>AL</given-names></name><etal></etal></person-group><article-title>The genome of woodland strawberry (<italic>Fragaria vesca</italic>)</article-title><source>Nat Genet</source><year>2011</year><volume>43</volume><fpage>109</fpage><lpage>116</lpage><pub-id pub-id-type="doi">10.1038/ng.740</pub-id><pub-id pub-id-type="pmid">21186353</pub-id></element-citation></ref><ref id="CR191"><label>191.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Dempewolf</surname><given-names>H</given-names></name><name><surname>Kane</surname><given-names>NC</given-names></name><name><surname>Ostevik</surname><given-names>KL</given-names></name><name><surname>Geleta</surname><given-names>M</given-names></name><name><surname>Barker</surname><given-names>MS</given-names></name><name><surname>Lai</surname><given-names>Z</given-names></name><etal></etal></person-group><article-title>Establishing genomic tools and resources for <italic>Guizotia abyssinica</italic> (L.f.) Cass.–the development of a library of expressed sequence tags, microsatellite loci, and the sequencing of its chloroplast genome</article-title><source>Mol Ecol Resour</source><year>2010</year><volume>10</volume><fpage>1048</fpage><lpage>1058</lpage><pub-id pub-id-type="doi">10.1111/j.1755-0998.2010.02859.x</pub-id><pub-id pub-id-type="pmid">21565115</pub-id></element-citation></ref><ref id="CR192"><label>192.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Timme</surname><given-names>RE</given-names></name><name><surname>Kuehl</surname><given-names>JV</given-names></name><name><surname>Boore</surname><given-names>JL</given-names></name><name><surname>Jansen</surname><given-names>RK</given-names></name></person-group><article-title>A comparative analysis of the <italic>Lactuca</italic> and <italic>Helianthus</italic> (Asteraceae) plastid genomes: identification of divergent regions and categorization of shared repeats</article-title><source>Am J Bot</source><year>2007</year><volume>94</volume><fpage>302</fpage><lpage>312</lpage><pub-id pub-id-type="doi">10.3732/ajb.94.3.302</pub-id><pub-id pub-id-type="pmid">21636403</pub-id></element-citation></ref><ref id="CR193"><label>193.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Barrett</surname><given-names>CF</given-names></name><name><surname>Davis</surname><given-names>JI</given-names></name><name><surname>Leebens‐Mack</surname><given-names>J</given-names></name><name><surname>Conran</surname><given-names>JG</given-names></name><name><surname>Stevenson</surname><given-names>DW</given-names></name></person-group><article-title>Plastid genomes and deep relationships among the commelinid monocot angiosperms</article-title><source>Cladistics</source><year>2013</year><volume>29</volume><fpage>65</fpage><lpage>87</lpage><pub-id pub-id-type="doi">10.1111/j.1096-0031.2012.00418.x</pub-id></element-citation></ref><ref id="CR194"><label>194.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Sanchez-Puerta</surname><given-names>MV</given-names></name><name><surname>Abbona</surname><given-names>CC</given-names></name></person-group><article-title>The chloroplast genome of <italic>Hyoscyamus niger</italic> and a phylogenetic study of the tribe Hyoscyameae (Solanaceae)</article-title><source>PLoS One</source><year>2014</year><volume>9</volume><pub-id pub-id-type="doi">10.1371/journal.pone.0098353</pub-id><pub-id pub-id-type="pmid">24851862</pub-id></element-citation></ref><ref id="CR195"><label>195.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Yan</surname><given-names>L</given-names></name><name><surname>Lai</surname><given-names>X</given-names></name><name><surname>Li</surname><given-names>X</given-names></name><name><surname>Wei</surname><given-names>C</given-names></name><name><surname>Tan</surname><given-names>X</given-names></name><name><surname>Zhang</surname><given-names>Y</given-names></name></person-group><article-title>Analyses of the complete genome and gene expression of chloroplast of sweet potato (<italic>Ipomoea batata</italic>)</article-title><source>PLoS One</source><year>2015</year><volume>10</volume><pub-id pub-id-type="doi">10.1371/journal.pone.0124083</pub-id><pub-id pub-id-type="pmid">25874767</pub-id></element-citation></ref><ref id="CR196"><label>196.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>McNeal</surname><given-names>JR</given-names></name><name><surname>Kuehl</surname><given-names>JV</given-names></name><name><surname>Boore</surname><given-names>JL</given-names></name><name><surname>de Pamphilis</surname><given-names>CW</given-names></name></person-group><article-title>Complete plastid genome sequences suggest strong selection for retention of photosynthetic genes in the parasitic plant genus <italic>Cuscuta</italic></article-title><source>BMC Plant Biol</source><year>2007</year><volume>7</volume><fpage>57</fpage><pub-id pub-id-type="doi">10.1186/1471-2229-7-57</pub-id><pub-id pub-id-type="pmid">17956636</pub-id></element-citation></ref><ref id="CR197"><label>197.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Kanamoto</surname><given-names>H</given-names></name><name><surname>Yamashita</surname><given-names>A</given-names></name><name><surname>Asao</surname><given-names>H</given-names></name><name><surname>Okumura</surname><given-names>S</given-names></name><name><surname>Takase</surname><given-names>H</given-names></name><name><surname>Hattori</surname><given-names>M</given-names></name><etal></etal></person-group><article-title>Efficient and stable transformation of <italic>Lactuca sativa</italic> L. cv. Cisco (lettuce) plastids</article-title><source>Transgenic Res</source><year>2006</year><volume>15</volume><fpage>205</fpage><lpage>217</lpage><pub-id pub-id-type="doi">10.1007/s11248-005-3997-2</pub-id><pub-id pub-id-type="pmid">16604461</pub-id></element-citation></ref><ref id="CR198"><label>198.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Mennes</surname><given-names>CB</given-names></name><name><surname>Lam</surname><given-names>VK</given-names></name><name><surname>Rudall</surname><given-names>PJ</given-names></name><name><surname>Lyon</surname><given-names>SP</given-names></name><name><surname>Graham</surname><given-names>SW</given-names></name><name><surname>Smets</surname><given-names>EF</given-names></name><name><surname>Merckx</surname><given-names>VS</given-names></name></person-group><article-title>Ancient Gondwana break‐up explains the distribution of the mycoheterotrophic family Corsiaceae (Liliales)</article-title><source>J Biogeogr</source><year>2015</year><volume>42</volume><fpage>1123</fpage><lpage>1136</lpage><pub-id pub-id-type="doi">10.1111/jbi.12486</pub-id></element-citation></ref><ref id="CR199"><label>199.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Hand</surname><given-names>ML</given-names></name><name><surname>Spangenberg</surname><given-names>GC</given-names></name><name><surname>Forster</surname><given-names>JW</given-names></name><name><surname>Cogan</surname><given-names>NO</given-names></name></person-group><article-title>Plastome sequence determination and comparative analysis for members of the <italic>Lolium-Festuca</italic> grass species complex</article-title><source>G3 (Bethsada)</source><year>2013</year><volume>3</volume><fpage>607</fpage><lpage>616</lpage><pub-id pub-id-type="doi">10.1534/g3.112.005264</pub-id></element-citation></ref><ref id="CR200"><label>200.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Kato</surname><given-names>T</given-names></name><name><surname>Kaneko</surname><given-names>T</given-names></name><name><surname>Sato</surname><given-names>S</given-names></name><name><surname>Nakamura</surname><given-names>Y</given-names></name><name><surname>Tabata</surname><given-names>S</given-names></name></person-group><article-title>Complete structure of the chloroplast genome of a legume, <italic>Lotus japonicus</italic></article-title><source>DNA Res</source><year>2000</year><volume>7</volume><fpage>323</fpage><lpage>330</lpage><pub-id pub-id-type="doi">10.1093/dnares/7.6.323</pub-id><pub-id pub-id-type="pmid">11214967</pub-id></element-citation></ref><ref id="CR201"><label>201.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Raubeson</surname><given-names>LA</given-names></name><name><surname>Peery</surname><given-names>R</given-names></name><name><surname>Chumley</surname><given-names>TW</given-names></name><name><surname>Dziubek</surname><given-names>C</given-names></name><name><surname>Fourcade</surname><given-names>HM</given-names></name><name><surname>Boore</surname><given-names>JL</given-names></name><name><surname>Jansen</surname><given-names>RK</given-names></name></person-group><article-title>Comparative chloroplast genomics: analyses including new sequences from the angiosperms <italic>Nuphar advena</italic> and <italic>Ranunculus macranthus</italic></article-title><source>BMC Genomics</source><year>2007</year><volume>8</volume><fpage>174</fpage><pub-id pub-id-type="doi">10.1186/1471-2164-8-174</pub-id><pub-id pub-id-type="pmid">17573971</pub-id></element-citation></ref><ref id="CR202"><label>202.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Hiratsuka</surname><given-names>J</given-names></name><name><surname>Shimada</surname><given-names>H</given-names></name><name><surname>Whittier</surname><given-names>R</given-names></name><name><surname>Ishibashi</surname><given-names>T</given-names></name><name><surname>Sakamoto</surname><given-names>M</given-names></name><name><surname>Mori</surname><given-names>M</given-names></name><etal></etal></person-group><article-title>The complete sequence of the rice (<italic>Oryza sativa</italic>) chloroplast genome: intermolecular recombination between distinct tRNA genes accounts for a major plastid DNA inversion during the evolution of the cereals</article-title><source>Mol Gen Genet</source><year>1989</year><volume>217</volume><fpage>185</fpage><lpage>194</lpage><pub-id pub-id-type="doi">10.1007/BF02464880</pub-id><pub-id pub-id-type="pmid">2770692</pub-id></element-citation></ref><ref id="CR203"><label>203.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Kim</surname><given-names>KJ</given-names></name><name><surname>Lee</surname><given-names>HL</given-names></name></person-group><article-title>Complete chloroplast genome sequences from Korean ginseng (<italic>Panax schinseng</italic> Nees) and comparative analysis of sequence evolution among 17 vascular plants</article-title><source>DNA Res</source><year>2004</year><volume>11</volume><fpage>247</fpage><lpage>261</lpage><pub-id pub-id-type="doi">10.1093/dnares/11.4.247</pub-id><pub-id pub-id-type="pmid">15500250</pub-id></element-citation></ref><ref id="CR204"><label>204.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Young</surname><given-names>HA</given-names></name><name><surname>Lanzatella</surname><given-names>CL</given-names></name><name><surname>Sarath</surname><given-names>G</given-names></name><name><surname>Tobias</surname><given-names>CM</given-names></name></person-group><article-title>Chloroplast genome variation in upland and lowland switchgrass</article-title><source>PLoS One</source><year>2011</year><volume>6</volume><pub-id pub-id-type="doi">10.1371/journal.pone.0023980</pub-id><pub-id pub-id-type="pmid">21887356</pub-id></element-citation></ref><ref id="CR205"><label>205.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Kumar</surname><given-names>S</given-names></name><name><surname>Hahn</surname><given-names>FM</given-names></name><name><surname>McMahan</surname><given-names>CM</given-names></name><name><surname>Cornish</surname><given-names>K</given-names></name><name><surname>Whalen</surname><given-names>MC</given-names></name></person-group><article-title>Comparative analysis of the complete sequence of the plastid genome of <italic>Parthenium argentatum</italic> and identification of DNA barcodes to differentiate <italic>Parthenium</italic> species and lines</article-title><source>BMC Plant Biol</source><year>2009</year><volume>9</volume><fpage>131</fpage><pub-id pub-id-type="doi">10.1186/1471-2229-9-131</pub-id><pub-id pub-id-type="pmid">19917140</pub-id></element-citation></ref><ref id="CR206"><label>206.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Chumley</surname><given-names>TW</given-names></name><name><surname>Palmer</surname><given-names>JD</given-names></name><name><surname>Mower</surname><given-names>JP</given-names></name><name><surname>Fourcade</surname><given-names>HM</given-names></name><name><surname>Calie</surname><given-names>PJ</given-names></name><name><surname>Boore</surname><given-names>JL</given-names></name><name><surname>Jansen</surname><given-names>RK</given-names></name></person-group><article-title>The complete chloroplast genome sequence of <italic>Pelargonium x hortorum</italic>: organization and evolution of the largest and most highly rearranged chloroplast genome of land plants</article-title><source>Mol Biol Evol</source><year>2006</year><volume>23</volume><fpage>2175</fpage><lpage>2190</lpage><pub-id pub-id-type="doi">10.1093/molbev/msl089</pub-id><pub-id pub-id-type="pmid">16916942</pub-id></element-citation></ref><ref id="CR207"><label>207.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Jeong</surname><given-names>YM</given-names></name><name><surname>Chung</surname><given-names>WH</given-names></name><name><surname>Mun</surname><given-names>JH</given-names></name><name><surname>Kim</surname><given-names>N</given-names></name><name><surname>Yu</surname><given-names>HJ</given-names></name></person-group><article-title>De novo assembly and characterization of the complete chloroplast genome of radish (<italic>Raphanus sativus</italic> L.)</article-title><source>Gene</source><year>2014</year><volume>551</volume><fpage>39</fpage><lpage>48</lpage><pub-id pub-id-type="doi">10.1016/j.gene.2014.08.038</pub-id><pub-id pub-id-type="pmid">25151309</pub-id></element-citation></ref><ref id="CR208"><label>208.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Rivarola</surname><given-names>M</given-names></name><name><surname>Foster</surname><given-names>JT</given-names></name><name><surname>Chan</surname><given-names>AP</given-names></name><name><surname>Williams</surname><given-names>AL</given-names></name><name><surname>Rice</surname><given-names>DW</given-names></name><name><surname>Liu</surname><given-names>X</given-names></name><etal></etal></person-group><article-title>Castor bean organelle genome sequencing and worldwide genetic diversity analysis</article-title><source>PLoS One</source><year>2011</year><volume>6</volume><pub-id pub-id-type="doi">10.1371/journal.pone.0021743</pub-id><pub-id pub-id-type="pmid">21750729</pub-id></element-citation></ref><ref id="CR209"><label>209.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Calsa Junior</surname><given-names>T</given-names></name><name><surname>Carraro</surname><given-names>DM</given-names></name><name><surname>Benatti</surname><given-names>MR</given-names></name><name><surname>Barbosa</surname><given-names>AC</given-names></name><name><surname>Kitajima</surname><given-names>JP</given-names></name><name><surname>Carrer</surname><given-names>H</given-names></name></person-group><article-title>Structural features and transcript-editing analysis of sugarcane (<italic>Saccharum officinarum</italic> L.) chloroplast genome</article-title><source>Curr Genet</source><year>2004</year><volume>46</volume><fpage>366</fpage><lpage>373</lpage><pub-id pub-id-type="doi">10.1007/s00294-004-0542-4</pub-id><pub-id pub-id-type="pmid">15526204</pub-id></element-citation></ref><ref id="CR210"><label>210.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Qian</surname><given-names>J</given-names></name><name><surname>Song</surname><given-names>J</given-names></name><name><surname>Gao</surname><given-names>H</given-names></name><name><surname>Zhu</surname><given-names>Y</given-names></name><name><surname>Xu</surname><given-names>J</given-names></name><name><surname>Pang</surname><given-names>X</given-names></name><etal></etal></person-group><article-title>The complete chloroplast genome sequence of the medicinal plant <italic>Salvia miltiorrhiza</italic></article-title><source>PLoS One</source><year>2013</year><volume>8</volume><pub-id pub-id-type="doi">10.1371/journal.pone.0057607</pub-id><pub-id pub-id-type="pmid">23460883</pub-id></element-citation></ref><ref id="CR211"><label>211.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Yi</surname><given-names>DK</given-names></name><name><surname>Kim</surname><given-names>KJ</given-names></name></person-group><article-title>Complete chloroplast genome sequences of important oilseed crop <italic>Sesamum indicum</italic> L</article-title><source>PLoS One</source><year>2012</year><volume>7</volume><pub-id pub-id-type="doi">10.1371/journal.pone.0035872</pub-id><pub-id pub-id-type="pmid">22606240</pub-id></element-citation></ref><ref id="CR212"><label>212.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Chung</surname><given-names>HJ</given-names></name><name><surname>Jung</surname><given-names>JD</given-names></name><name><surname>Park</surname><given-names>HW</given-names></name><name><surname>Kim</surname><given-names>JH</given-names></name><name><surname>Cha</surname><given-names>HW</given-names></name><name><surname>Min</surname><given-names>SR</given-names></name><etal></etal></person-group><article-title>The complete chloroplast genome sequences of <italic>Solanum tuberosum</italic> and comparative analysis with Solanaceae species identified the presence of a 241-bp deletion in cultivated potato chloroplast DNA sequence</article-title><source>Plant Cell Rep</source><year>2006</year><volume>25</volume><fpage>1369</fpage><lpage>1379</lpage><pub-id pub-id-type="doi">10.1007/s00299-006-0196-4</pub-id><pub-id pub-id-type="pmid">16835751</pub-id></element-citation></ref><ref id="CR213"><label>213.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Schmitz-Linneweber</surname><given-names>C</given-names></name><name><surname>Maier</surname><given-names>RM</given-names></name><name><surname>Alcaraz</surname><given-names>JP</given-names></name><name><surname>Cottet</surname><given-names>A</given-names></name><name><surname>Herrmann</surname><given-names>RG</given-names></name><name><surname>Mache</surname><given-names>R</given-names></name></person-group><article-title>The plastid chromosome of spinach (<italic>Spinacia oleracea</italic>): complete nucleotide sequence and gene organization</article-title><source>Plant Mol Biol</source><year>2001</year><volume>45</volume><fpage>307</fpage><lpage>315</lpage><pub-id pub-id-type="doi">10.1023/A:1006478403810</pub-id><pub-id pub-id-type="pmid">11292076</pub-id></element-citation></ref><ref id="CR214"><label>214.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Yi</surname><given-names>DK</given-names></name><name><surname>Yang</surname><given-names>JC</given-names></name><name><surname>So</surname><given-names>S</given-names></name><name><surname>Joo</surname><given-names>M</given-names></name><name><surname>Kim</surname><given-names>DK</given-names></name><name><surname>Shin</surname><given-names>CH</given-names></name><etal></etal></person-group><article-title>The complete plastid genome sequence of <italic>Abies koreana</italic> (Pinaceae: Abietoideae)</article-title><source>Mitochondrial DNA</source><year>2016</year><volume>27</volume><fpage>2351</fpage><lpage>2353</lpage><pub-id pub-id-type="pmid">25812052</pub-id></element-citation></ref><ref id="CR215"><label>215.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Yao</surname><given-names>X</given-names></name><name><surname>Tang</surname><given-names>P</given-names></name><name><surname>Li</surname><given-names>Z</given-names></name><name><surname>Li</surname><given-names>D</given-names></name><name><surname>Liu</surname><given-names>Y</given-names></name><name><surname>Huang</surname><given-names>H</given-names></name></person-group><article-title>The first complete chloroplast genome sequences in Actinidiaceae: genome structure and comparative analysis</article-title><source>PLoS One</source><year>2015</year><volume>10</volume><pub-id pub-id-type="doi">10.1371/journal.pone.0129347</pub-id><pub-id pub-id-type="pmid">26046631</pub-id></element-citation></ref><ref id="CR216"><label>216.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Hsu</surname><given-names>CY</given-names></name><name><surname>Wu</surname><given-names>CS</given-names></name><name><surname>Chaw</surname><given-names>SM</given-names></name></person-group><article-title>Ancient nuclear plastid DNA in the yew family (Taxaceae)</article-title><source>Genome Biol Evol</source><year>2014</year><volume>6</volume><fpage>2111</fpage><lpage>2121</lpage><pub-id pub-id-type="doi">10.1093/gbe/evu165</pub-id><pub-id pub-id-type="pmid">25084786</pub-id></element-citation></ref><ref id="CR217"><label>217.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Ruhsam</surname><given-names>M</given-names></name><name><surname>Rai</surname><given-names>HS</given-names></name><name><surname>Mathews</surname><given-names>S</given-names></name><name><surname>Ross</surname><given-names>TG</given-names></name><name><surname>Graham</surname><given-names>SW</given-names></name><name><surname>Raubeson</surname><given-names>LA</given-names></name><etal></etal></person-group><article-title>Does complete plastid genome sequencing improve species discrimination and phylogenetic resolution in <italic>Araucaria</italic>?</article-title><source>Mol Ecol Resour</source><year>2015</year><volume>15</volume><fpage>1067</fpage><lpage>1078</lpage><pub-id pub-id-type="doi">10.1111/1755-0998.12375</pub-id><pub-id pub-id-type="pmid">25611173</pub-id></element-citation></ref><ref id="CR218"><label>218.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Ma</surname><given-names>J</given-names></name><name><surname>Yang</surname><given-names>B</given-names></name><name><surname>Zhu</surname><given-names>W</given-names></name><name><surname>Sun</surname><given-names>L</given-names></name><name><surname>Tian</surname><given-names>J</given-names></name><name><surname>Wang</surname><given-names>X</given-names></name></person-group><article-title>The complete chloroplast genome sequence of <italic>Mahonia bealei</italic> (Berberidaceae) reveals a significant expansion of the inverted repeat and phylogenetic relationship with other angiosperms</article-title><source>Gene</source><year>2013</year><volume>528</volume><fpage>120</fpage><lpage>131</lpage><pub-id pub-id-type="doi">10.1016/j.gene.2013.07.037</pub-id><pub-id pub-id-type="pmid">23900198</pub-id></element-citation></ref><ref id="CR219"><label>219.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Hansen</surname><given-names>DR</given-names></name><name><surname>Dastidar</surname><given-names>SG</given-names></name><name><surname>Cai</surname><given-names>Z</given-names></name><name><surname>Penaflor</surname><given-names>C</given-names></name><name><surname>Kuehl</surname><given-names>JV</given-names></name><name><surname>Boore</surname><given-names>JL</given-names></name><name><surname>Jansen</surname><given-names>RK</given-names></name></person-group><article-title>Phylogenetic and evolutionary implications of complete chloroplast genome sequences of four early-diverging angiosperms: <italic>Buxus</italic> (Buxaceae), <italic>Chloranthus</italic> (Chloranthaceae), <italic>Dioscorea</italic> (Dioscoreaceae), and <italic>Illicium</italic> (Schisandraceae)</article-title><source>Mol Phylogenet Evol</source><year>2007</year><volume>45</volume><fpage>547</fpage><lpage>563</lpage><pub-id pub-id-type="doi">10.1016/j.ympev.2007.06.004</pub-id><pub-id pub-id-type="pmid">17644003</pub-id></element-citation></ref><ref id="CR220"><label>220.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Wu</surname><given-names>CS</given-names></name><name><surname>Chaw</surname><given-names>SM</given-names></name></person-group><article-title>Highly rearranged and size-variable chloroplast genomes in conifers II clade (cupressophytes): evolution towards shorter intergenic spacers</article-title><source>Plant Biotechnol J</source><year>2014</year><volume>12</volume><fpage>344</fpage><lpage>353</lpage><pub-id pub-id-type="doi">10.1111/pbi.12141</pub-id><pub-id pub-id-type="pmid">24283260</pub-id></element-citation></ref><ref id="CR221"><label>221.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Shi</surname><given-names>C</given-names></name><name><surname>Liu</surname><given-names>Y</given-names></name><name><surname>Huang</surname><given-names>H</given-names></name><name><surname>Xia</surname><given-names>EH</given-names></name><name><surname>Zhang</surname><given-names>HB</given-names></name><name><surname>Gao</surname><given-names>LZ</given-names></name></person-group><article-title>Contradiction between plastid gene transcription and function due to complex posttranscriptional splicing: an exemplary study of <italic>ycf15</italic> function and evolution in angiosperms</article-title><source>PLoS One</source><year>2013</year><volume>8</volume><pub-id pub-id-type="doi">10.1371/journal.pone.0059620</pub-id><pub-id pub-id-type="pmid">23527231</pub-id></element-citation></ref><ref id="CR222"><label>222.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Huang</surname><given-names>H</given-names></name><name><surname>Shi</surname><given-names>C</given-names></name><name><surname>Liu</surname><given-names>Y</given-names></name><name><surname>Mao</surname><given-names>SY</given-names></name><name><surname>Gao</surname><given-names>LZ</given-names></name></person-group><article-title>Thirteen <italic>Camellia</italic> chloroplast genome sequences determined by high-throughput sequencing: genome structure and phylogenetic relationships</article-title><source>BMC Evol Biol</source><year>2014</year><volume>14</volume><fpage>151</fpage><pub-id pub-id-type="doi">10.1186/1471-2148-14-151</pub-id><pub-id pub-id-type="pmid">25001059</pub-id></element-citation></ref><ref id="CR223"><label>223.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Lin</surname><given-names>CP</given-names></name><name><surname>Huang</surname><given-names>JP</given-names></name><name><surname>Wu</surname><given-names>CS</given-names></name><name><surname>Hsu</surname><given-names>CY</given-names></name><name><surname>Chaw</surname><given-names>SM</given-names></name></person-group><article-title>Comparative chloroplast genomics reveals the evolution of Pinaceae genera and subfamilies</article-title><source>Genome Biol Evol</source><year>2010</year><volume>2</volume><fpage>504</fpage><lpage>517</lpage><pub-id pub-id-type="doi">10.1093/gbe/evq036</pub-id><pub-id pub-id-type="pmid">20651328</pub-id></element-citation></ref><ref id="CR224"><label>224.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Wu</surname><given-names>CS</given-names></name><name><surname>Wang</surname><given-names>YN</given-names></name><name><surname>Hsu</surname><given-names>CY</given-names></name><name><surname>Lin</surname><given-names>CP</given-names></name><name><surname>Chaw</surname><given-names>SM</given-names></name></person-group><article-title>Loss of different inverted repeat copies from the chloroplast genomes of Pinaceae and cupressophytes and influence of heterotachy on the evaluation of gymnosperm phylogeny</article-title><source>Genome Biol Evol</source><year>2011</year><volume>3</volume><fpage>1284</fpage><lpage>1295</lpage><pub-id pub-id-type="doi">10.1093/gbe/evr095</pub-id><pub-id pub-id-type="pmid">21933779</pub-id></element-citation></ref><ref id="CR225"><label>225.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Male</surname><given-names>PJ</given-names></name><name><surname>Bardon</surname><given-names>L</given-names></name><name><surname>Besnard</surname><given-names>G</given-names></name><name><surname>Coissac</surname><given-names>E</given-names></name><name><surname>Delsuc</surname><given-names>F</given-names></name><name><surname>Engel</surname><given-names>J</given-names></name><etal></etal></person-group><article-title>Genome skimming by shotgun sequencing helps resolve the phylogeny of a pantropical tree family</article-title><source>Mol Ecol Resour</source><year>2014</year><volume>14</volume><fpage>966</fpage><lpage>975</lpage><pub-id pub-id-type="pmid">24606032</pub-id></element-citation></ref><ref id="CR226"><label>226.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Huang</surname><given-names>YY</given-names></name><name><surname>Matzke</surname><given-names>AJ</given-names></name><name><surname>Matzke</surname><given-names>M</given-names></name></person-group><article-title>Complete sequence and comparative analysis of the chloroplast genome of coconut palm (<italic>Cocos nucifera</italic>)</article-title><source>PLoS One</source><year>2013</year><volume>8</volume><pub-id pub-id-type="doi">10.1371/journal.pone.0074736</pub-id><pub-id pub-id-type="pmid">24023703</pub-id></element-citation></ref><ref id="CR227"><label>227.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Bayly</surname><given-names>MJ</given-names></name><name><surname>Rigault</surname><given-names>P</given-names></name><name><surname>Spokevicius</surname><given-names>A</given-names></name><name><surname>Ladiges</surname><given-names>PY</given-names></name><name><surname>Ades</surname><given-names>PK</given-names></name><name><surname>Anderson</surname><given-names>C</given-names></name><etal></etal></person-group><article-title>Chloroplast genome analysis of Australian eucalypts--<italic>Eucalyptus</italic>, <italic>Corymbia</italic>, <italic>Angophora</italic>, <italic>Allosyncarpia</italic> and <italic>Stockwellia</italic> (Myrtaceae<italic>)</italic></article-title><source>Mol Phylogenet Evol</source><year>2013</year><volume>69</volume><fpage>704</fpage><lpage>716</lpage><pub-id pub-id-type="doi">10.1016/j.ympev.2013.07.006</pub-id><pub-id pub-id-type="pmid">23876290</pub-id></element-citation></ref><ref id="CR228"><label>228.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Hirao</surname><given-names>T</given-names></name><name><surname>Watanabe</surname><given-names>A</given-names></name><name><surname>Kurita</surname><given-names>M</given-names></name><name><surname>Kondo</surname><given-names>T</given-names></name><name><surname>Takata</surname><given-names>K</given-names></name></person-group><article-title>Complete nucleotide sequence of the <italic>Cryptomeria japonica</italic> D. Don. chloroplast genome and comparative chloroplast genomics: diversified genomic structure of coniferous species</article-title><source>BMC Plant Biol</source><year>2008</year><volume>8</volume><fpage>70</fpage><pub-id pub-id-type="doi">10.1186/1471-2229-8-70</pub-id><pub-id pub-id-type="pmid">18570682</pub-id></element-citation></ref><ref id="CR229"><label>229.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Uthaipaisanwong</surname><given-names>P</given-names></name><name><surname>Chanprasert</surname><given-names>J</given-names></name><name><surname>Shearman</surname><given-names>JR</given-names></name><name><surname>Sangsrakru</surname><given-names>D</given-names></name><name><surname>Yoocha</surname><given-names>T</given-names></name><name><surname>Jomchai</surname><given-names>N</given-names></name><etal></etal></person-group><article-title>Characterization of the chloroplast genome sequence of oil palm (<italic>Elaeis guineensis</italic> Jacq.)</article-title><source>Gene</source><year>2012</year><volume>500</volume><fpage>172</fpage><lpage>180</lpage><pub-id pub-id-type="doi">10.1016/j.gene.2012.03.061</pub-id><pub-id pub-id-type="pmid">22487870</pub-id></element-citation></ref><ref id="CR230"><label>230.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Steane</surname><given-names>D</given-names></name><name><surname>Jones</surname><given-names>R</given-names></name><name><surname>Vaillancourt</surname><given-names>R</given-names></name></person-group><article-title>A set of chloroplast microsatellite primers for <italic>Eucalyptus</italic> (Myrtaceae)</article-title><source>Mol Ecol Notes</source><year>2005</year><volume>5</volume><fpage>538</fpage><lpage>541</lpage><pub-id pub-id-type="doi">10.1111/j.1471-8286.2005.00981.x</pub-id></element-citation></ref><ref id="CR231"><label>231.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Tangphatsornruang</surname><given-names>S</given-names></name><name><surname>Uthaipaisanwong</surname><given-names>P</given-names></name><name><surname>Sangsrakru</surname><given-names>D</given-names></name><name><surname>Chanprasert</surname><given-names>J</given-names></name><name><surname>Yoocha</surname><given-names>T</given-names></name><name><surname>Jomchai</surname><given-names>N</given-names></name><name><surname>Tragoonrung</surname><given-names>S</given-names></name></person-group><article-title>Characterization of the complete chloroplast genome of <italic>Hevea brasiliensis</italic> reveals genome rearrangement, RNA editing sites and phylogenetic relationships</article-title><source>Gene</source><year>2011</year><volume>475</volume><fpage>104</fpage><lpage>112</lpage><pub-id pub-id-type="doi">10.1016/j.gene.2011.01.002</pub-id><pub-id pub-id-type="pmid">21241787</pub-id></element-citation></ref><ref id="CR232"><label>232.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Lee</surname><given-names>HL</given-names></name><name><surname>Jansen</surname><given-names>RK</given-names></name><name><surname>Chumley</surname><given-names>TW</given-names></name><name><surname>Kim</surname><given-names>KJ</given-names></name></person-group><article-title>Gene relocations within chloroplast genomes of <italic>Jasminum</italic> and <italic>Menodora</italic> (Oleaceae) are due to multiple, overlapping inversions</article-title><source>Mol Biol Evol</source><year>2007</year><volume>24</volume><fpage>1161</fpage><lpage>1180</lpage><pub-id pub-id-type="doi">10.1093/molbev/msm036</pub-id><pub-id pub-id-type="pmid">17329229</pub-id></element-citation></ref><ref id="CR233"><label>233.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Asif</surname><given-names>MH</given-names></name><name><surname>Mantri</surname><given-names>SS</given-names></name><name><surname>Sharma</surname><given-names>A</given-names></name><name><surname>Srivastava</surname><given-names>A</given-names></name><name><surname>Trivedi</surname><given-names>I</given-names></name><name><surname>Gupta</surname><given-names>P</given-names></name><etal></etal></person-group><article-title>Complete sequence and organisation of the <italic>Jatropha curcas</italic> (Euphorbiaceae) chloroplast genome</article-title><source>Tree Genet Genomes</source><year>2010</year><volume>6</volume><fpage>941</fpage><lpage>952</lpage><pub-id pub-id-type="doi">10.1007/s11295-010-0303-0</pub-id></element-citation></ref><ref id="CR234"><label>234.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Guo</surname><given-names>W</given-names></name><name><surname>Grewe</surname><given-names>F</given-names></name><name><surname>Cobo-Clark</surname><given-names>A</given-names></name><name><surname>Fan</surname><given-names>W</given-names></name><name><surname>Duan</surname><given-names>Z</given-names></name><name><surname>Adams</surname><given-names>RP</given-names></name><etal></etal></person-group><article-title>Predominant and substoichiometric isomers of the plastid genome coexist within <italic>Juniperus</italic> plants and have shifted multiple times during cupressophyte evolution</article-title><source>Genome Biol Evol</source><year>2014</year><volume>6</volume><fpage>580</fpage><lpage>590</lpage><pub-id pub-id-type="doi">10.1093/gbe/evu046</pub-id><pub-id pub-id-type="pmid">24586030</pub-id></element-citation></ref><ref id="CR235"><label>235.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Cai</surname><given-names>Z</given-names></name><name><surname>Penaflor</surname><given-names>C</given-names></name><name><surname>Kuehl</surname><given-names>JV</given-names></name><name><surname>Leebens-Mack</surname><given-names>J</given-names></name><name><surname>Carlson</surname><given-names>JE</given-names></name><name><surname>de Pamphilis</surname><given-names>CW</given-names></name><etal></etal></person-group><article-title>Complete plastid genome sequences of <italic>Drimys</italic>, <italic>Liriodendron</italic>, and <italic>Piper</italic>: implications for the phylogenetic relationships of magnoliids</article-title><source>BMC Evol Biol</source><year>2006</year><volume>6</volume><fpage>77</fpage><pub-id pub-id-type="doi">10.1186/1471-2148-6-77</pub-id><pub-id pub-id-type="pmid">17020608</pub-id></element-citation></ref><ref id="CR236"><label>236.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Chen</surname><given-names>J</given-names></name><name><surname>Hao</surname><given-names>Z</given-names></name><name><surname>Xu</surname><given-names>H</given-names></name><name><surname>Yang</surname><given-names>L</given-names></name><name><surname>Liu</surname><given-names>G</given-names></name><name><surname>Sheng</surname><given-names>Y</given-names></name><etal></etal></person-group><article-title>The complete chloroplast genome sequence of the relict woody plant <italic>Metasequoia glyptostroboides</italic> Hu et Cheng</article-title><source>Front Plant Sci</source><year>2015</year><volume>6</volume><fpage>447</fpage><pub-id pub-id-type="pmid">26136762</pub-id></element-citation></ref><ref id="CR237"><label>237.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Ravi</surname><given-names>V</given-names></name><name><surname>Khurana</surname><given-names>JP</given-names></name><name><surname>Tyagi</surname><given-names>AK</given-names></name><name><surname>Khurana</surname><given-names>P</given-names></name></person-group><article-title>The chloroplast genome of mulberry: complete nucleotide sequence, gene organization and comparative analysis</article-title><source>Tree Genet Genomes</source><year>2006</year><volume>3</volume><fpage>49</fpage><lpage>59</lpage><pub-id pub-id-type="doi">10.1007/s11295-006-0051-3</pub-id></element-citation></ref><ref id="CR238"><label>238.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Straub</surname><given-names>SC</given-names></name><name><surname>Moore</surname><given-names>MJ</given-names></name><name><surname>Soltis</surname><given-names>PS</given-names></name><name><surname>Soltis</surname><given-names>DE</given-names></name><name><surname>Liston</surname><given-names>A</given-names></name><name><surname>Livshultz</surname><given-names>T</given-names></name></person-group><article-title>Phylogenetic signal detection from an ancient rapid radiation: effects of noise reduction, long-branch attraction, and model selection in crown clade Apocynaceae</article-title><source>Mol Phylogenet Evol</source><year>2014</year><volume>80</volume><fpage>169</fpage><lpage>185</lpage><pub-id pub-id-type="doi">10.1016/j.ympev.2014.07.020</pub-id><pub-id pub-id-type="pmid">25109653</pub-id></element-citation></ref><ref id="CR239"><label>239.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Besnard</surname><given-names>G</given-names></name><name><surname>Hernández</surname><given-names>P</given-names></name><name><surname>Khadari</surname><given-names>B</given-names></name><name><surname>Dorado</surname><given-names>G</given-names></name><name><surname>Savolainen</surname><given-names>V</given-names></name></person-group><article-title>Genomic profiling of plastid DNA variation in the Mediterranean olive tree</article-title><source>BMC Plant Biol</source><year>2011</year><volume>11</volume><fpage>80</fpage><pub-id pub-id-type="doi">10.1186/1471-2229-11-80</pub-id><pub-id pub-id-type="pmid">21569271</pub-id></element-citation></ref><ref id="CR240"><label>240.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Yang</surname><given-names>M</given-names></name><name><surname>Zhang</surname><given-names>X</given-names></name><name><surname>Liu</surname><given-names>G</given-names></name><name><surname>Yin</surname><given-names>Y</given-names></name><name><surname>Chen</surname><given-names>K</given-names></name><name><surname>Yun</surname><given-names>Q</given-names></name><etal></etal></person-group><article-title>The complete chloroplast genome sequence of date palm (<italic>Phoenix dactylifera</italic> L.)</article-title><source>PLoS One</source><year>2010</year><volume>5</volume><pub-id pub-id-type="doi">10.1371/journal.pone.0012762</pub-id><pub-id pub-id-type="pmid">20856810</pub-id></element-citation></ref><ref id="CR241"><label>241.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Fang</surname><given-names>MF</given-names></name><name><surname>Wang</surname><given-names>YJ</given-names></name><name><surname>Zu</surname><given-names>YM</given-names></name><name><surname>Dong</surname><given-names>WL</given-names></name><name><surname>Wang</surname><given-names>RN</given-names></name><name><surname>Deng</surname><given-names>TT</given-names></name><name><surname>Li</surname><given-names>ZH</given-names></name></person-group><article-title>The complete chloroplast genome of the Taiwan red pine <italic>Pinus taiwanensis</italic> (Pinaceae)</article-title><source>Mitochondrial DNA</source><year>2016</year><volume>27</volume><fpage>2732</fpage><lpage>2733</lpage><pub-id pub-id-type="doi">10.3109/19401736.2014.926507</pub-id><pub-id pub-id-type="pmid">26057016</pub-id></element-citation></ref><ref id="CR242"><label>242.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Vieira Ldo</surname><given-names>N</given-names></name><name><surname>Faoro</surname><given-names>H</given-names></name><name><surname>Rogalski</surname><given-names>M</given-names></name><name><surname>Fraga</surname><given-names>HP</given-names></name><name><surname>Cardoso</surname><given-names>RL</given-names></name><name><surname>de Souza</surname><given-names>EM</given-names></name><etal></etal></person-group><article-title>The complete chloroplast genome sequence of <italic>Podocarpus lambertii</italic>: genome structure, evolutionary aspects, gene content and SSR detection</article-title><source>PLoS One</source><year>2014</year><volume>9</volume><pub-id pub-id-type="doi">10.1371/journal.pone.0090618</pub-id><pub-id pub-id-type="pmid">24594889</pub-id></element-citation></ref><ref id="CR243"><label>243.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Okumura</surname><given-names>S</given-names></name><name><surname>Sawada</surname><given-names>M</given-names></name><name><surname>Park</surname><given-names>YW</given-names></name><name><surname>Hayashi</surname><given-names>T</given-names></name><name><surname>Shimamura</surname><given-names>M</given-names></name><name><surname>Takase</surname><given-names>H</given-names></name><name><surname>Tomizawa</surname><given-names>K</given-names></name></person-group><article-title>Transformation of poplar (<italic>Populus alba</italic>) plastids and expression of foreign proteins in tree chloroplasts</article-title><source>Transgenic Res</source><year>2006</year><volume>15</volume><fpage>637</fpage><lpage>646</lpage><pub-id pub-id-type="doi">10.1007/s11248-006-9009-3</pub-id><pub-id pub-id-type="pmid">16952016</pub-id></element-citation></ref><ref id="CR244"><label>244.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Wang</surname><given-names>S</given-names></name><name><surname>Shi</surname><given-names>C</given-names></name><name><surname>Gao</surname><given-names>LZ</given-names></name></person-group><article-title>Plastid genome sequence of a wild woody oil species, <italic>Prinsepia utilis</italic>, provides insights into evolutionary and mutational patterns of Rosaceae chloroplast genomes</article-title><source>PLoS One</source><year>2013</year><volume>8</volume><pub-id pub-id-type="doi">10.1371/journal.pone.0073946</pub-id><pub-id pub-id-type="pmid">24023915</pub-id></element-citation></ref><ref id="CR245"><label>245.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Terakami</surname><given-names>S</given-names></name><name><surname>Matsumura</surname><given-names>Y</given-names></name><name><surname>Kurita</surname><given-names>K</given-names></name><name><surname>Kanamori</surname><given-names>H</given-names></name><name><surname>Katayose</surname><given-names>Y</given-names></name><name><surname>Yamamoto</surname><given-names>T</given-names></name><name><surname>Katayama</surname><given-names>H</given-names></name></person-group><article-title>Complete sequence of the chloroplast genome from pear (<italic>Pyrus pyrifolia</italic>): genome structure and comparative analysis</article-title><source>Tree Genet Genomes</source><year>2012</year><volume>8</volume><fpage>841</fpage><lpage>854</lpage><pub-id pub-id-type="doi">10.1007/s11295-012-0469-8</pub-id></element-citation></ref><ref id="CR246"><label>246.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Alexander</surname><given-names>LW</given-names></name><name><surname>Woeste</surname><given-names>KE</given-names></name></person-group><article-title>Pyrosequencing of the northern red oak (<italic>Quercus rubra</italic> L.) chloroplast genome reveals high quality polymorphisms for population management</article-title><source>Tree Genet Genomes</source><year>2014</year><volume>10</volume><fpage>803</fpage><lpage>812</lpage><pub-id pub-id-type="doi">10.1007/s11295-013-0681-1</pub-id></element-citation></ref><ref id="CR247"><label>247.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Yang</surname><given-names>B</given-names></name><name><surname>Li</surname><given-names>M</given-names></name><name><surname>Ma</surname><given-names>J</given-names></name><name><surname>Fu</surname><given-names>Z</given-names></name><name><surname>Xu</surname><given-names>X</given-names></name><name><surname>Chen</surname><given-names>Q</given-names></name><etal></etal></person-group><article-title>The complete chloroplast genome sequence of <italic>Sapindus mukorossi</italic></article-title><source>Mitochondrial DNA</source><year>2016</year><volume>27</volume><fpage>1825</fpage><lpage>1826</lpage><pub-id pub-id-type="pmid">25317637</pub-id></element-citation></ref><ref id="CR248"><label>248.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Fajardo</surname><given-names>D</given-names></name><name><surname>Senalik</surname><given-names>D</given-names></name><name><surname>Ames</surname><given-names>M</given-names></name><name><surname>Zhu</surname><given-names>H</given-names></name><name><surname>Steffan</surname><given-names>SA</given-names></name><name><surname>Harbut</surname><given-names>R</given-names></name><etal></etal></person-group><article-title>Complete plastid genome sequence of <italic>Vaccinium macrocarpon</italic>: structure, gene content, and rearrangements revealed by next generation sequencing</article-title><source>Tree Genet Genomes</source><year>2013</year><volume>9</volume><fpage>489</fpage><lpage>498</lpage><pub-id pub-id-type="doi">10.1007/s11295-012-0573-9</pub-id></element-citation></ref><ref id="CR249"><label>249.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Yap</surname><given-names>JY</given-names></name><name><surname>Rohner</surname><given-names>T</given-names></name><name><surname>Greenfield</surname><given-names>A</given-names></name><name><surname>Van Der Merwe</surname><given-names>M</given-names></name><name><surname>McPherson</surname><given-names>H</given-names></name><name><surname>Glenn</surname><given-names>W</given-names></name><etal></etal></person-group><article-title>Complete chloroplast genome of the wollemi pine (<italic>Wollemia nobilis</italic>): structure and evolution</article-title><source>PLoS One</source><year>2015</year><volume>10</volume><pub-id pub-id-type="doi">10.1371/journal.pone.0128126</pub-id><pub-id pub-id-type="pmid">26061691</pub-id></element-citation></ref><ref id="CR250"><label>250.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Shaw</surname><given-names>J</given-names></name><name><surname>Lickey</surname><given-names>EB</given-names></name><name><surname>Beck</surname><given-names>JT</given-names></name><name><surname>Farmer</surname><given-names>SB</given-names></name><name><surname>Liu</surname><given-names>W</given-names></name><name><surname>Miller</surname><given-names>J</given-names></name><etal></etal></person-group><article-title>The tortoise and the hare II: relative utility of 21 noncoding chloroplast DNA sequences for phylogenetic analysis</article-title><source>Am J Bot</source><year>2005</year><volume>92</volume><fpage>142</fpage><lpage>166</lpage><pub-id pub-id-type="doi">10.3732/ajb.92.1.142</pub-id><pub-id pub-id-type="pmid">21652394</pub-id></element-citation></ref><ref id="CR251"><label>251.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Ruhlman</surname><given-names>TA</given-names></name><name><surname>Rajasekaran</surname><given-names>K</given-names></name><name><surname>Cary</surname><given-names>JW</given-names></name></person-group><article-title>Expression of chloroperoxidase from <italic>Pseudomonas pyrrocinia</italic> in tobacco plastids for fungal resistance</article-title><source>Plant Sci</source><year>2014</year><volume>228</volume><fpage>98</fpage><lpage>106</lpage><pub-id pub-id-type="doi">10.1016/j.plantsci.2014.02.008</pub-id><pub-id pub-id-type="pmid">25438790</pub-id></element-citation></ref><ref id="CR252"><label>252.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Chakrabarti</surname><given-names>SK</given-names></name><name><surname>Lutz</surname><given-names>KA</given-names></name><name><surname>Lertwiriyawong</surname><given-names>B</given-names></name><name><surname>Svab</surname><given-names>Z</given-names></name><name><surname>Maliga</surname><given-names>P</given-names></name></person-group><article-title>Expression of the <italic>cry9Aa2 B.t</italic>. gene in tobacco chloroplasts confers resistance to potato tuber moth</article-title><source>Transgenic Res</source><year>2006</year><volume>15</volume><fpage>481</fpage><lpage>488</lpage><pub-id pub-id-type="doi">10.1007/s11248-006-0018-z</pub-id><pub-id pub-id-type="pmid">16906448</pub-id></element-citation></ref><ref id="CR253"><label>253.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>DeGray</surname><given-names>G</given-names></name><name><surname>Rajasekaran</surname><given-names>K</given-names></name><name><surname>Smith</surname><given-names>F</given-names></name><name><surname>Sanford</surname><given-names>J</given-names></name><name><surname>Daniell</surname><given-names>H</given-names></name></person-group><article-title>Expression of an antimicrobial peptide via the chloroplast genome to control phytopathogenic bacteria and fungi</article-title><source>Plant Physiol</source><year>2001</year><volume>127</volume><fpage>852</fpage><lpage>862</lpage><pub-id pub-id-type="doi">10.1104/pp.010233</pub-id><pub-id pub-id-type="pmid">11706168</pub-id></element-citation></ref><ref id="CR254"><label>254.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Chen</surname><given-names>PJ</given-names></name><name><surname>Senthilkumar</surname><given-names>R</given-names></name><name><surname>Jane</surname><given-names>WN</given-names></name><name><surname>He</surname><given-names>Y</given-names></name><name><surname>Tian</surname><given-names>Z</given-names></name><name><surname>Yeh</surname><given-names>KW</given-names></name></person-group><article-title>Transplastomic <italic>Nicotiana benthamiana</italic> plants expressing multiple defence genes encoding protease inhibitors and chitinase display broad-spectrum resistance against insects, pathogens and abiotic stresses</article-title><source>Plant Biotechnol J</source><year>2014</year><volume>12</volume><fpage>503</fpage><lpage>515</lpage><pub-id pub-id-type="doi">10.1111/pbi.12157</pub-id><pub-id pub-id-type="pmid">24479648</pub-id></element-citation></ref><ref id="CR255"><label>255.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Wang</surname><given-names>YP</given-names></name><name><surname>Wei</surname><given-names>ZY</given-names></name><name><surname>Zhang</surname><given-names>YY</given-names></name><name><surname>Lin</surname><given-names>CJ</given-names></name><name><surname>Zhong</surname><given-names>XF</given-names></name><name><surname>Wang</surname><given-names>YL</given-names></name><etal></etal></person-group><article-title>Chloroplast-expressed MSI-99 in tobacco improves disease resistance and displays inhibitory effect against rice blast fungus</article-title><source>Int J Mol Sci</source><year>2015</year><volume>16</volume><fpage>4628</fpage><lpage>4641</lpage><pub-id pub-id-type="doi">10.3390/ijms16034628</pub-id><pub-id pub-id-type="pmid">25739079</pub-id></element-citation></ref><ref id="CR256"><label>256.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>McBride</surname><given-names>KE</given-names></name><name><surname>Svab</surname><given-names>Z</given-names></name><name><surname>Schaaf</surname><given-names>DJ</given-names></name><name><surname>Hogan</surname><given-names>PS</given-names></name><name><surname>Stalker</surname><given-names>DM</given-names></name><name><surname>Maliga</surname><given-names>P</given-names></name></person-group><article-title>Amplification of a chimeric <italic>Bacillus</italic> gene in chloroplasts leads to an extraordinary level of an insecticidal protein in tobacco</article-title><source>Biotechnology (N Y)</source><year>1995</year><volume>13</volume><fpage>362</fpage><lpage>365</lpage><pub-id pub-id-type="doi">10.1038/nbt0495-362</pub-id><pub-id pub-id-type="pmid">9634777</pub-id></element-citation></ref><ref id="CR257"><label>257.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Kota</surname><given-names>M</given-names></name><name><surname>Daniell</surname><given-names>H</given-names></name><name><surname>Varma</surname><given-names>S</given-names></name><name><surname>Garczynski</surname><given-names>SF</given-names></name><name><surname>Gould</surname><given-names>F</given-names></name><name><surname>Moar</surname><given-names>WJ</given-names></name></person-group><article-title>Overexpression of the <italic>Bacillus thuringiensis</italic> (<italic>Bt</italic>) Cry2Aa2 protein in chloroplasts confers resistance to plants against susceptible and <italic>Bt</italic>-resistant insects</article-title><source>Proc Natl Acad Sci U S A</source><year>1999</year><volume>96</volume><fpage>1840</fpage><lpage>1845</lpage><pub-id pub-id-type="doi">10.1073/pnas.96.5.1840</pub-id><pub-id pub-id-type="pmid">10051556</pub-id></element-citation></ref><ref id="CR258"><label>258.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Lee</surname><given-names>SB</given-names></name><name><surname>Kwon</surname><given-names>HB</given-names></name><name><surname>Kwon</surname><given-names>SJ</given-names></name><name><surname>Park</surname><given-names>SC</given-names></name><name><surname>Jeong</surname><given-names>MJ</given-names></name><name><surname>Han</surname><given-names>SE</given-names></name><etal></etal></person-group><article-title>Accumulation of trehalose within transgenic chloroplasts confers drought tolerance</article-title><source>Mol Breeding</source><year>2003</year><volume>11</volume><fpage>1</fpage><lpage>13</lpage><pub-id pub-id-type="doi">10.1023/A:1022100404542</pub-id></element-citation></ref><ref id="CR259"><label>259.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Ruiz</surname><given-names>ON</given-names></name><name><surname>Hussein</surname><given-names>HS</given-names></name><name><surname>Terry</surname><given-names>N</given-names></name><name><surname>Daniell</surname><given-names>H</given-names></name></person-group><article-title>Phytoremediation of organomercurial compounds via chloroplast genetic engineering</article-title><source>Plant Physiol</source><year>2003</year><volume>132</volume><fpage>1344</fpage><lpage>1352</lpage><pub-id pub-id-type="doi">10.1104/pp.103.020958</pub-id><pub-id pub-id-type="pmid">12857816</pub-id></element-citation></ref><ref id="CR260"><label>260.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Ruiz</surname><given-names>ON</given-names></name><name><surname>Alvarez</surname><given-names>D</given-names></name><name><surname>Torres</surname><given-names>C</given-names></name><name><surname>Roman</surname><given-names>L</given-names></name><name><surname>Daniell</surname><given-names>H</given-names></name></person-group><article-title>Metallothionein expression in chloroplasts enhances mercury accumulation and phytoremediation capability</article-title><source>Plant Biotechnol J</source><year>2011</year><volume>9</volume><fpage>609</fpage><lpage>617</lpage><pub-id pub-id-type="doi">10.1111/j.1467-7652.2011.00616.x</pub-id><pub-id pub-id-type="pmid">21518240</pub-id></element-citation></ref><ref id="CR261"><label>261.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Lutz</surname><given-names>KA</given-names></name><name><surname>Knapp</surname><given-names>JE</given-names></name><name><surname>Maliga</surname><given-names>P</given-names></name></person-group><article-title>Expression of bar in the plastid genome confers herbicide resistance</article-title><source>Plant Physiol</source><year>2001</year><volume>125</volume><fpage>1585</fpage><lpage>1590</lpage><pub-id pub-id-type="doi">10.1104/pp.125.4.1585</pub-id><pub-id pub-id-type="pmid">11299340</pub-id></element-citation></ref><ref id="CR262"><label>262.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Ye</surname><given-names>GN</given-names></name><name><surname>Hajdukiewicz</surname><given-names>PT</given-names></name><name><surname>Broyles</surname><given-names>D</given-names></name><name><surname>Rodriguez</surname><given-names>D</given-names></name><name><surname>Xu</surname><given-names>CW</given-names></name><name><surname>Nehra</surname><given-names>N</given-names></name><name><surname>Staub</surname><given-names>JM</given-names></name></person-group><article-title>Plastid-expressed 5-enolpyruvylshikimate-3-phosphate synthase genes provide high level glyphosate tolerance in tobacco</article-title><source>Plant J</source><year>2001</year><volume>25</volume><fpage>261</fpage><lpage>270</lpage><pub-id pub-id-type="doi">10.1046/j.1365-313x.2001.00958.x</pub-id><pub-id pub-id-type="pmid">11208018</pub-id></element-citation></ref><ref id="CR263"><label>263.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Shimizu</surname><given-names>M</given-names></name><name><surname>Goto</surname><given-names>M</given-names></name><name><surname>Hanai</surname><given-names>M</given-names></name><name><surname>Shimizu</surname><given-names>T</given-names></name><name><surname>Izawa</surname><given-names>N</given-names></name><name><surname>Kanamoto</surname><given-names>H</given-names></name><etal></etal></person-group><article-title>Selectable tolerance to herbicides by mutated acetolactate synthase genes integrated into the chloroplast genome of tobacco</article-title><source>Plant Physiol</source><year>2008</year><volume>147</volume><fpage>1976</fpage><lpage>1983</lpage><pub-id pub-id-type="doi">10.1104/pp.108.120519</pub-id><pub-id pub-id-type="pmid">18515641</pub-id></element-citation></ref><ref id="CR264"><label>264.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Iamtham</surname><given-names>S</given-names></name><name><surname>Day</surname><given-names>A</given-names></name></person-group><article-title>Removal of antibiotic resistance genes from transgenic tobacco plastids</article-title><source>Nat Biotechnol</source><year>2000</year><volume>18</volume><fpage>1172</fpage><lpage>1176</lpage><pub-id pub-id-type="doi">10.1038/81161</pub-id><pub-id pub-id-type="pmid">11062436</pub-id></element-citation></ref><ref id="CR265"><label>265.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Dufourmantel</surname><given-names>N</given-names></name><name><surname>Dubald</surname><given-names>M</given-names></name><name><surname>Matringe</surname><given-names>M</given-names></name><name><surname>Canard</surname><given-names>H</given-names></name><name><surname>Garcon</surname><given-names>F</given-names></name><name><surname>Job</surname><given-names>C</given-names></name><etal></etal></person-group><article-title>Generation and characterization of soybean and marker-free tobacco plastid transformants over-expressing a bacterial 4-hydroxyphenylpyruvate dioxygenase which provides strong herbicide tolerance</article-title><source>Plant Biotechnol J</source><year>2007</year><volume>5</volume><fpage>118</fpage><lpage>133</lpage><pub-id pub-id-type="doi">10.1111/j.1467-7652.2006.00226.x</pub-id><pub-id pub-id-type="pmid">17207262</pub-id></element-citation></ref><ref id="CR266"><label>266.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Fouad</surname><given-names>WM</given-names></name><name><surname>Altpeter</surname><given-names>F</given-names></name></person-group><article-title>Transplastomic expression of bacterial L-aspartate-alpha-decarboxylase enhances photosynthesis and biomass production in response to high temperature stress</article-title><source>Transgenic Res</source><year>2009</year><volume>18</volume><fpage>707</fpage><lpage>718</lpage><pub-id pub-id-type="doi">10.1007/s11248-009-9258-z</pub-id><pub-id pub-id-type="pmid">19353301</pub-id></element-citation></ref><ref id="CR267"><label>267.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Lu</surname><given-names>Y</given-names></name><name><surname>Rijzaani</surname><given-names>H</given-names></name><name><surname>Karcher</surname><given-names>D</given-names></name><name><surname>Ruf</surname><given-names>S</given-names></name><name><surname>Bock</surname><given-names>R</given-names></name></person-group><article-title>Efficient metabolic pathway engineering in transgenic tobacco and tomato plastids with synthetic multigene operons</article-title><source>Proc Natl Acad Sci U S A</source><year>2013</year><volume>110</volume><fpage>E623</fpage><lpage>E632</lpage><pub-id pub-id-type="doi">10.1073/pnas.1216898110</pub-id><pub-id pub-id-type="pmid">23382222</pub-id></element-citation></ref><ref id="CR268"><label>268.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Ruiz</surname><given-names>ON</given-names></name><name><surname>Daniell</surname><given-names>H</given-names></name></person-group><article-title>Engineering cytoplasmic male sterility via the chloroplast genome by expression of beta-ketothiolase</article-title><source>Plant Physiol</source><year>2005</year><volume>138</volume><fpage>1232</fpage><lpage>1246</lpage><pub-id pub-id-type="doi">10.1104/pp.104.057729</pub-id><pub-id pub-id-type="pmid">16009998</pub-id></element-citation></ref><ref id="CR269"><label>269.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Yabuta</surname><given-names>Y</given-names></name><name><surname>Tanaka</surname><given-names>H</given-names></name><name><surname>Yoshimura</surname><given-names>S</given-names></name><name><surname>Suzuki</surname><given-names>A</given-names></name><name><surname>Tamoi</surname><given-names>M</given-names></name><name><surname>Maruta</surname><given-names>T</given-names></name><name><surname>Shigeoka</surname><given-names>S</given-names></name></person-group><article-title>Improvement of vitamin E quality and quantity in tobacco and lettuce by chloroplast genetic engineering</article-title><source>Transgenic Res</source><year>2013</year><volume>22</volume><fpage>391</fpage><lpage>402</lpage><pub-id pub-id-type="doi">10.1007/s11248-012-9656-5</pub-id><pub-id pub-id-type="pmid">22990376</pub-id></element-citation></ref><ref id="CR270"><label>270.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Harada</surname><given-names>H</given-names></name><name><surname>Maoka</surname><given-names>T</given-names></name><name><surname>Osawa</surname><given-names>A</given-names></name><name><surname>Hattan</surname><given-names>J</given-names></name><name><surname>Kanamoto</surname><given-names>H</given-names></name><name><surname>Shindo</surname><given-names>K</given-names></name><etal></etal></person-group><article-title>Construction of transplastomic lettuce (<italic>Lactuca sativa</italic>) dominantly producing astaxanthin fatty acid esters and detailed chemical analysis of generated carotenoids</article-title><source>Transgenic Res</source><year>2014</year><volume>23</volume><fpage>303</fpage><lpage>315</lpage><pub-id pub-id-type="doi">10.1007/s11248-013-9750-3</pub-id><pub-id pub-id-type="pmid">24287848</pub-id></element-citation></ref><ref id="CR271"><label>271.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Pengelly</surname><given-names>JJ</given-names></name><name><surname>Forster</surname><given-names>B</given-names></name><name><surname>von Caemmerer</surname><given-names>S</given-names></name><name><surname>Badger</surname><given-names>MR</given-names></name><name><surname>Price</surname><given-names>GD</given-names></name><name><surname>Whitney</surname><given-names>SM</given-names></name></person-group><article-title>Transplastomic integration of a cyanobacterial bicarbonate transporter into tobacco chloroplasts</article-title><source>J Exp Bot</source><year>2014</year><volume>65</volume><fpage>3071</fpage><lpage>3080</lpage><pub-id pub-id-type="doi">10.1093/jxb/eru156</pub-id><pub-id pub-id-type="pmid">24965541</pub-id></element-citation></ref><ref id="CR272"><label>272.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Sanz-Barrio</surname><given-names>R</given-names></name><name><surname>Corral-Martinez</surname><given-names>P</given-names></name><name><surname>Ancin</surname><given-names>M</given-names></name><name><surname>Segui-Simarro</surname><given-names>JM</given-names></name><name><surname>Farran</surname><given-names>I</given-names></name></person-group><article-title>Overexpression of plastidial thioredoxin f leads to enhanced starch accumulation in tobacco leaves</article-title><source>Plant Biotechnol J</source><year>2013</year><volume>11</volume><fpage>618</fpage><lpage>627</lpage><pub-id pub-id-type="doi">10.1111/pbi.12052</pub-id><pub-id pub-id-type="pmid">23398733</pub-id></element-citation></ref><ref id="CR273"><label>273.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Elghabi</surname><given-names>Z</given-names></name><name><surname>Karcher</surname><given-names>D</given-names></name><name><surname>Zhou</surname><given-names>F</given-names></name><name><surname>Ruf</surname><given-names>S</given-names></name><name><surname>Bock</surname><given-names>R</given-names></name></person-group><article-title>Optimization of the expression of the HIV fusion inhibitor cyanovirin-N from the tobacco plastid genome</article-title><source>Plant Biotechnol J</source><year>2011</year><volume>9</volume><fpage>599</fpage><lpage>608</lpage><pub-id pub-id-type="doi">10.1111/j.1467-7652.2011.00598.x</pub-id><pub-id pub-id-type="pmid">21309998</pub-id></element-citation></ref><ref id="CR274"><label>274.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Agrawal</surname><given-names>P</given-names></name><name><surname>Verma</surname><given-names>D</given-names></name><name><surname>Daniell</surname><given-names>H</given-names></name></person-group><article-title>Expression of <italic>Trichoderma reesei</italic> beta-mannanase in tobacco chloroplasts and its utilization in lignocellulosic woody biomass hydrolysis</article-title><source>PLoS One</source><year>2011</year><volume>6</volume><pub-id pub-id-type="doi">10.1371/journal.pone.0029302</pub-id><pub-id pub-id-type="pmid">22216240</pub-id></element-citation></ref><ref id="CR275"><label>275.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Verma</surname><given-names>D</given-names></name><name><surname>Jin</surname><given-names>S</given-names></name><name><surname>Kanagaraj</surname><given-names>A</given-names></name><name><surname>Singh</surname><given-names>ND</given-names></name><name><surname>Daniel</surname><given-names>J</given-names></name><name><surname>Kolattukudy</surname><given-names>PE</given-names></name><etal></etal></person-group><article-title>Expression of fungal cutinase and swollenin in tobacco chloroplasts reveals novel enzyme functions and/or substrates</article-title><source>PLoS One</source><year>2013</year><volume>8</volume><pub-id pub-id-type="doi">10.1371/journal.pone.0057187</pub-id><pub-id pub-id-type="pmid">23451186</pub-id></element-citation></ref><ref id="CR276"><label>276.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Saxena</surname><given-names>B</given-names></name><name><surname>Subramaniyan</surname><given-names>M</given-names></name><name><surname>Malhotra</surname><given-names>K</given-names></name><name><surname>Bhavesh</surname><given-names>NS</given-names></name><name><surname>Potlakayala</surname><given-names>SD</given-names></name><name><surname>Kumar</surname><given-names>S</given-names></name></person-group><article-title>Metabolic engineering of chloroplasts for artemisinic acid biosynthesis and impact on plant growth</article-title><source>J Biosci</source><year>2014</year><volume>39</volume><fpage>33</fpage><lpage>41</lpage><pub-id pub-id-type="doi">10.1007/s12038-013-9402-z</pub-id><pub-id pub-id-type="pmid">24499788</pub-id></element-citation></ref><ref id="CR277"><label>277.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Yu</surname><given-names>LX</given-names></name><name><surname>Gray</surname><given-names>BN</given-names></name><name><surname>Rutzke</surname><given-names>CJ</given-names></name><name><surname>Walker</surname><given-names>LP</given-names></name><name><surname>Wilson</surname><given-names>DB</given-names></name><name><surname>Hanson</surname><given-names>MR</given-names></name></person-group><article-title>Expression of thermostable microbial cellulases in the chloroplasts of nicotine-free tobacco</article-title><source>J Biotechnol</source><year>2007</year><volume>131</volume><fpage>362</fpage><lpage>369</lpage><pub-id pub-id-type="doi">10.1016/j.jbiotec.2007.07.942</pub-id><pub-id pub-id-type="pmid">17765995</pub-id></element-citation></ref><ref id="CR278"><label>278.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Petersen</surname><given-names>K</given-names></name><name><surname>Bock</surname><given-names>R</given-names></name></person-group><article-title>High-level expression of a suite of thermostable cell wall-degrading enzymes from the chloroplast genome</article-title><source>Plant Mol Biol</source><year>2011</year><volume>76</volume><fpage>311</fpage><lpage>321</lpage><pub-id pub-id-type="doi">10.1007/s11103-011-9742-8</pub-id><pub-id pub-id-type="pmid">21298465</pub-id></element-citation></ref><ref id="CR279"><label>279.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Arai</surname><given-names>Y</given-names></name><name><surname>Shikanai</surname><given-names>T</given-names></name><name><surname>Doi</surname><given-names>Y</given-names></name><name><surname>Yoshida</surname><given-names>S</given-names></name><name><surname>Yamaguchi</surname><given-names>I</given-names></name><name><surname>Nakashita</surname><given-names>H</given-names></name></person-group><article-title>Production of polyhydroxybutyrate by polycistronic expression of bacterial genes in tobacco plastid</article-title><source>Plant Cell Physiol</source><year>2004</year><volume>45</volume><fpage>1176</fpage><lpage>1184</lpage><pub-id pub-id-type="doi">10.1093/pcp/pch139</pub-id><pub-id pub-id-type="pmid">15509840</pub-id></element-citation></ref><ref id="CR280"><label>280.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Hasunuma</surname><given-names>T</given-names></name><name><surname>Miyazawa</surname><given-names>SI</given-names></name><name><surname>Yoshimura</surname><given-names>S</given-names></name><name><surname>Shinzaki</surname><given-names>Y</given-names></name><name><surname>Tomizawa</surname><given-names>KI</given-names></name><name><surname>Shindo</surname><given-names>K</given-names></name><etal></etal></person-group><article-title>Biosynthesis of astaxanthin in tobacco leaves by transplastomic engineering</article-title><source>Plant J</source><year>2008</year><volume>55</volume><fpage>857</fpage><lpage>868</lpage><pub-id pub-id-type="doi">10.1111/j.1365-313X.2008.03559.x</pub-id><pub-id pub-id-type="pmid">18494855</pub-id></element-citation></ref><ref id="CR281"><label>281.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Nakahira</surname><given-names>Y</given-names></name><name><surname>Ishikawa</surname><given-names>K</given-names></name><name><surname>Tanaka</surname><given-names>K</given-names></name><name><surname>Tozawa</surname><given-names>Y</given-names></name><name><surname>Shiina</surname><given-names>T</given-names></name></person-group><article-title>Overproduction of hyperthermostable beta-1,4-endoglucanase from the archaeon <italic>Pyrococcus horikoshii</italic> by tobacco chloroplast engineering</article-title><source>Biosci Biotechnol Biochem</source><year>2013</year><volume>77</volume><fpage>2140</fpage><lpage>2143</lpage><pub-id pub-id-type="doi">10.1271/bbb.130413</pub-id><pub-id pub-id-type="pmid">24096651</pub-id></element-citation></ref><ref id="CR282"><label>282.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Sherman</surname><given-names>A</given-names></name><name><surname>Su</surname><given-names>J</given-names></name><name><surname>Lin</surname><given-names>S</given-names></name><name><surname>Wang</surname><given-names>X</given-names></name><name><surname>Herzog</surname><given-names>RW</given-names></name><name><surname>Daniell</surname><given-names>H</given-names></name></person-group><article-title>Suppression of inhibitor formation against FVIII in a murine model of hemophilia A by oral delivery of antigens bioencapsulated in plant cells</article-title><source>Blood</source><year>2014</year><volume>124</volume><fpage>1659</fpage><lpage>1668</lpage><pub-id pub-id-type="doi">10.1182/blood-2013-10-528737</pub-id><pub-id pub-id-type="pmid">24825864</pub-id></element-citation></ref><ref id="CR283"><label>283.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Sanz-Barrio</surname><given-names>R</given-names></name><name><surname>Fernandez-San Millan</surname><given-names>A</given-names></name><name><surname>Corral-Martinez</surname><given-names>P</given-names></name><name><surname>Segui-Simarro</surname><given-names>JM</given-names></name><name><surname>Farran</surname><given-names>I</given-names></name></person-group><article-title>Tobacco plastidial thioredoxins as modulators of recombinant protein production in transgenic chloroplasts</article-title><source>Plant Biotechnol J</source><year>2011</year><volume>9</volume><fpage>639</fpage><lpage>650</lpage><pub-id pub-id-type="doi">10.1111/j.1467-7652.2011.00608.x</pub-id><pub-id pub-id-type="pmid">21426478</pub-id></element-citation></ref><ref id="CR284"><label>284.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Farran</surname><given-names>I</given-names></name><name><surname>McCarthy-Suarez</surname><given-names>I</given-names></name><name><surname>Rio-Manterola</surname><given-names>F</given-names></name><name><surname>Mansilla</surname><given-names>C</given-names></name><name><surname>Lasarte</surname><given-names>JJ</given-names></name><name><surname>Mingo-Castel</surname><given-names>AM</given-names></name></person-group><article-title>The vaccine adjuvant extra domain A from fibronectin retains its proinflammatory properties when expressed in tobacco chloroplasts</article-title><source>Planta</source><year>2010</year><volume>231</volume><fpage>977</fpage><lpage>990</lpage><pub-id pub-id-type="doi">10.1007/s00425-010-1102-4</pub-id><pub-id pub-id-type="pmid">20108000</pub-id></element-citation></ref><ref id="CR285"><label>285.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Boyhan</surname><given-names>D</given-names></name><name><surname>Daniell</surname><given-names>H</given-names></name></person-group><article-title>Low-cost production of proinsulin in tobacco and lettuce chloroplasts for injectable or oral delivery of functional insulin and C-peptide</article-title><source>Plant Biotechnol J</source><year>2011</year><volume>9</volume><fpage>585</fpage><lpage>598</lpage><pub-id pub-id-type="doi">10.1111/j.1467-7652.2010.00582.x</pub-id><pub-id pub-id-type="pmid">21143365</pub-id></element-citation></ref><ref id="CR286"><label>286.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Fernandez-San Millan</surname><given-names>A</given-names></name><name><surname>Mingo-Castel</surname><given-names>A</given-names></name><name><surname>Miller</surname><given-names>M</given-names></name><name><surname>Daniell</surname><given-names>H</given-names></name></person-group><article-title>A chloroplast transgenic approach to hyper-express and purify human serum albumin, a protein highly susceptible to proteolytic degradation</article-title><source>Plant Biotechnol J</source><year>2003</year><volume>1</volume><fpage>71</fpage><lpage>79</lpage><pub-id pub-id-type="doi">10.1046/j.1467-7652.2003.00008.x</pub-id><pub-id pub-id-type="pmid">17147744</pub-id></element-citation></ref><ref id="CR287"><label>287.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Daniell</surname><given-names>H</given-names></name><name><surname>Ruiz</surname><given-names>G</given-names></name><name><surname>Denes</surname><given-names>B</given-names></name><name><surname>Sandberg</surname><given-names>L</given-names></name><name><surname>Langridge</surname><given-names>W</given-names></name></person-group><article-title>Optimization of codon composition and regulatory elements for expression of human insulin like growth factor-1 in transgenic chloroplasts and evaluation of structural identity and function</article-title><source>BMC Biotechnol</source><year>2009</year><volume>9</volume><fpage>33</fpage><pub-id pub-id-type="doi">10.1186/1472-6750-9-33</pub-id><pub-id pub-id-type="pmid">19344517</pub-id></element-citation></ref><ref id="CR288"><label>288.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Wang</surname><given-names>X</given-names></name><name><surname>Su</surname><given-names>J</given-names></name><name><surname>Sherman</surname><given-names>A</given-names></name><name><surname>Rogers</surname><given-names>GL</given-names></name><name><surname>Liao</surname><given-names>G</given-names></name><name><surname>Hoffman</surname><given-names>BE</given-names></name><etal></etal></person-group><article-title>Plant-based oral tolerance to hemophilia therapy employs a complex immune regulatory response including LAP<sup>+</sup>CD4<sup>+</sup> T cells</article-title><source>Blood</source><year>2015</year><volume>125</volume><fpage>2418</fpage><lpage>2427</lpage><pub-id pub-id-type="doi">10.1182/blood-2014-08-597070</pub-id><pub-id pub-id-type="pmid">25700434</pub-id></element-citation></ref><ref id="CR289"><label>289.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Su</surname><given-names>J</given-names></name><name><surname>Sherman</surname><given-names>A</given-names></name><name><surname>Doerfler</surname><given-names>PA</given-names></name><name><surname>Byrne</surname><given-names>BJ</given-names></name><name><surname>Herzog</surname><given-names>RW</given-names></name><name><surname>Daniell</surname><given-names>H</given-names></name></person-group><article-title>Oral delivery of Acid Alpha Glucosidase epitopes expressed in plant chloroplasts suppresses antibody formation in treatment of Pompe mice</article-title><source>Plant Biotechnol J</source><year>2015</year><volume>13</volume><fpage>1023</fpage><lpage>1032</lpage><pub-id pub-id-type="doi">10.1111/pbi.12413</pub-id><pub-id pub-id-type="pmid">26053072</pub-id></element-citation></ref><ref id="CR290"><label>290.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Youm</surname><given-names>JW</given-names></name><name><surname>Jeon</surname><given-names>JH</given-names></name><name><surname>Kim</surname><given-names>H</given-names></name><name><surname>Min</surname><given-names>SR</given-names></name><name><surname>Kim</surname><given-names>MS</given-names></name><name><surname>Joung</surname><given-names>H</given-names></name><etal></etal></person-group><article-title>High-level expression of a human beta-site APP cleaving enzyme in transgenic tobacco chloroplasts and its immunogenicity in mice</article-title><source>Transgenic Res</source><year>2010</year><volume>19</volume><fpage>1099</fpage><lpage>1108</lpage><pub-id pub-id-type="doi">10.1007/s11248-010-9383-8</pub-id><pub-id pub-id-type="pmid">20229285</pub-id></element-citation></ref><ref id="CR291"><label>291.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Arlen</surname><given-names>PA</given-names></name><name><surname>Falconer</surname><given-names>R</given-names></name><name><surname>Cherukumilli</surname><given-names>S</given-names></name><name><surname>Cole</surname><given-names>A</given-names></name><name><surname>Cole</surname><given-names>AM</given-names></name><name><surname>Oishi</surname><given-names>KK</given-names></name><name><surname>Daniell</surname><given-names>H</given-names></name></person-group><article-title>Field production and functional evaluation of chloroplast-derived interferon-alpha2b</article-title><source>Plant Biotechnol J</source><year>2007</year><volume>5</volume><fpage>511</fpage><lpage>525</lpage><pub-id pub-id-type="doi">10.1111/j.1467-7652.2007.00258.x</pub-id><pub-id pub-id-type="pmid">17490449</pub-id></element-citation></ref><ref id="CR292"><label>292.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Ruhlman</surname><given-names>T</given-names></name><name><surname>Ahangari</surname><given-names>R</given-names></name><name><surname>Devine</surname><given-names>A</given-names></name><name><surname>Samsam</surname><given-names>M</given-names></name><name><surname>Daniell</surname><given-names>H</given-names></name></person-group><article-title>Expression of cholera toxin B-proinsulin fusion protein in lettuce and tobacco chloroplasts--oral administration protects against development of insulitis in non-obese diabetic mice</article-title><source>Plant Biotechnol J</source><year>2007</year><volume>5</volume><fpage>495</fpage><lpage>510</lpage><pub-id pub-id-type="doi">10.1111/j.1467-7652.2007.00259.x</pub-id><pub-id pub-id-type="pmid">17490448</pub-id></element-citation></ref><ref id="CR293"><label>293.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Leelavathi</surname><given-names>S</given-names></name><name><surname>Reddy</surname><given-names>VS</given-names></name></person-group><article-title>Chloroplast expression of His-tagged GUS-fusions: a general strategy to overproduce and purify foreign proteins using transplastomic plants as bioreactors</article-title><source>Mol Breeding</source><year>2003</year><volume>11</volume><fpage>49</fpage><lpage>58</lpage><pub-id pub-id-type="doi">10.1023/A:1022114427971</pub-id></element-citation></ref><ref id="CR294"><label>294.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Lim</surname><given-names>S</given-names></name><name><surname>Ashida</surname><given-names>H</given-names></name><name><surname>Watanabe</surname><given-names>R</given-names></name><name><surname>Inai</surname><given-names>K</given-names></name><name><surname>Kim</surname><given-names>YS</given-names></name><name><surname>Mukougawa</surname><given-names>K</given-names></name><etal></etal></person-group><article-title>Production of biologically active human thioredoxin 1 protein in lettuce chloroplasts</article-title><source>Plant Mol Biol</source><year>2011</year><volume>76</volume><fpage>335</fpage><lpage>344</lpage><pub-id pub-id-type="doi">10.1007/s11103-011-9745-5</pub-id><pub-id pub-id-type="pmid">21290168</pub-id></element-citation></ref><ref id="CR295"><label>295.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Nadai</surname><given-names>M</given-names></name><name><surname>Bally</surname><given-names>J</given-names></name><name><surname>Vitel</surname><given-names>M</given-names></name><name><surname>Job</surname><given-names>C</given-names></name><name><surname>Tissot</surname><given-names>G</given-names></name><name><surname>Botterman</surname><given-names>J</given-names></name><name><surname>Dubald</surname><given-names>M</given-names></name></person-group><article-title>High-level expression of active human alpha1-antitrypsin in transgenic tobacco chloroplasts</article-title><source>Transgenic Res</source><year>2009</year><volume>18</volume><fpage>173</fpage><lpage>183</lpage><pub-id pub-id-type="doi">10.1007/s11248-008-9209-0</pub-id><pub-id pub-id-type="pmid">18686007</pub-id></element-citation></ref><ref id="CR296"><label>296.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Gisby</surname><given-names>MF</given-names></name><name><surname>Mellors</surname><given-names>P</given-names></name><name><surname>Madesis</surname><given-names>P</given-names></name><name><surname>Ellin</surname><given-names>M</given-names></name><name><surname>Laverty</surname><given-names>H</given-names></name><name><surname>O'Kane</surname><given-names>S</given-names></name><etal></etal></person-group><article-title>A synthetic gene increases TGF beta 3 accumulation by 75-fold in tobacco chloroplasts enabling rapid purification and folding into a biologically active molecule</article-title><source>Plant Biotechnol J</source><year>2011</year><volume>9</volume><fpage>618</fpage><lpage>628</lpage><pub-id pub-id-type="doi">10.1111/j.1467-7652.2011.00619.x</pub-id><pub-id pub-id-type="pmid">21535357</pub-id></element-citation></ref><ref id="CR297"><label>297.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Farran</surname><given-names>I</given-names></name><name><surname>Rio-Manterola</surname><given-names>F</given-names></name><name><surname>Iniguez</surname><given-names>M</given-names></name><name><surname>Garate</surname><given-names>S</given-names></name><name><surname>Prieto</surname><given-names>J</given-names></name><name><surname>Mingo-Castel</surname><given-names>AM</given-names></name></person-group><article-title>High-density seedling expression system for the production of bioactive human cardiotrophin-1, a potential therapeutic cytokine, in transgenic tobacco chloroplasts</article-title><source>Plant Biotechnol J</source><year>2008</year><volume>6</volume><fpage>516</fpage><lpage>527</lpage><pub-id pub-id-type="doi">10.1111/j.1467-7652.2008.00334.x</pub-id><pub-id pub-id-type="pmid">18384506</pub-id></element-citation></ref><ref id="CR298"><label>298.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Staub</surname><given-names>JM</given-names></name><name><surname>Garcia</surname><given-names>B</given-names></name><name><surname>Graves</surname><given-names>J</given-names></name><name><surname>Hajdukiewicz</surname><given-names>PT</given-names></name><name><surname>Hunter</surname><given-names>P</given-names></name><name><surname>Nehra</surname><given-names>N</given-names></name><etal></etal></person-group><article-title>High-yield production of a human therapeutic protein in tobacco chloroplasts</article-title><source>Nat Biotechnol</source><year>2000</year><volume>18</volume><fpage>333</fpage><lpage>338</lpage><pub-id pub-id-type="doi">10.1038/73796</pub-id><pub-id pub-id-type="pmid">10700152</pub-id></element-citation></ref><ref id="CR299"><label>299.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Oey</surname><given-names>M</given-names></name><name><surname>Lohse</surname><given-names>M</given-names></name><name><surname>Scharff</surname><given-names>LB</given-names></name><name><surname>Kreikemeyer</surname><given-names>B</given-names></name><name><surname>Bock</surname><given-names>R</given-names></name></person-group><article-title>Plastid production of protein antibiotics against pneumonia via a new strategy for high-level expression of antimicrobial proteins</article-title><source>Proc Natl Acad Sci U S A</source><year>2009</year><volume>106</volume><fpage>6579</fpage><lpage>6584</lpage><pub-id pub-id-type="doi">10.1073/pnas.0813146106</pub-id><pub-id pub-id-type="pmid">19332784</pub-id></element-citation></ref><ref id="CR300"><label>300.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Koya</surname><given-names>V</given-names></name><name><surname>Moayeri</surname><given-names>M</given-names></name><name><surname>Leppla</surname><given-names>SH</given-names></name><name><surname>Daniell</surname><given-names>H</given-names></name></person-group><article-title>Plant-based vaccine: mice immunized with chloroplast-derived anthrax protective antigen survive anthrax lethal toxin challenge</article-title><source>Infect Immun</source><year>2005</year><volume>73</volume><fpage>8266</fpage><lpage>8274</lpage><pub-id pub-id-type="doi">10.1128/IAI.73.12.8266-8274.2005</pub-id><pub-id pub-id-type="pmid">16299323</pub-id></element-citation></ref><ref id="CR301"><label>301.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Watson</surname><given-names>J</given-names></name><name><surname>Koya</surname><given-names>V</given-names></name><name><surname>Leppla</surname><given-names>SH</given-names></name><name><surname>Daniell</surname><given-names>H</given-names></name></person-group><article-title>Expression of Bacillus anthracis protective antigen in transgenic chloroplasts of tobacco, a non-food/feed crop</article-title><source>Vaccine</source><year>2004</year><volume>22</volume><fpage>4374</fpage><lpage>4384</lpage><pub-id pub-id-type="doi">10.1016/j.vaccine.2004.01.069</pub-id><pub-id pub-id-type="pmid">15474731</pub-id></element-citation></ref><ref id="CR302"><label>302.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Millan</surname><given-names>AFS</given-names></name><name><surname>Ortigosa</surname><given-names>SM</given-names></name><name><surname>Hervas-Stubbs</surname><given-names>S</given-names></name><name><surname>Corral-Martinez</surname><given-names>P</given-names></name><name><surname>Segui-Simarro</surname><given-names>JM</given-names></name><name><surname>Gaetan</surname><given-names>J</given-names></name><etal></etal></person-group><article-title>Human papillomavirus L1 protein expressed in tobacco chloroplasts self-assembles into virus-like particles that are highly immunogenic</article-title><source>Plant Biotechnol J</source><year>2008</year><volume>6</volume><fpage>427</fpage><lpage>441</lpage><pub-id pub-id-type="doi">10.1111/j.1467-7652.2008.00338.x</pub-id><pub-id pub-id-type="pmid">18422886</pub-id></element-citation></ref><ref id="CR303"><label>303.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Yacono</surname><given-names>MD</given-names></name><name><surname>Farran</surname><given-names>I</given-names></name><name><surname>Becher</surname><given-names>ML</given-names></name><name><surname>Sander</surname><given-names>V</given-names></name><name><surname>Sanchez</surname><given-names>VR</given-names></name><name><surname>Martin</surname><given-names>V</given-names></name><etal></etal></person-group><article-title>A chloroplast-derived <italic>Toxoplasma gondii</italic> GRA4 antigen used as an oral vaccine protects against toxoplasmosis in mice</article-title><source>Plant Biotechnol J</source><year>2012</year><volume>10</volume><fpage>1136</fpage><lpage>1144</lpage><pub-id pub-id-type="doi">10.1111/pbi.12001</pub-id><pub-id pub-id-type="pmid">23020088</pub-id></element-citation></ref><ref id="CR304"><label>304.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Kolotilin</surname><given-names>I</given-names></name><name><surname>Kaldis</surname><given-names>A</given-names></name><name><surname>Devriendt</surname><given-names>B</given-names></name><name><surname>Joensuu</surname><given-names>J</given-names></name><name><surname>Cox</surname><given-names>E</given-names></name><name><surname>Menassa</surname><given-names>R</given-names></name></person-group><article-title>Production of a subunit vaccine candidate against porcine post-weaning diarrhea in high-biomass transplastomic tobacco</article-title><source>Plos One</source><year>2012</year><volume>7</volume><pub-id pub-id-type="doi">10.1371/journal.pone.0042405</pub-id><pub-id pub-id-type="pmid">22879967</pub-id></element-citation></ref><ref id="CR305"><label>305.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Arlen</surname><given-names>PA</given-names></name><name><surname>Singleton</surname><given-names>M</given-names></name><name><surname>Adamovicz</surname><given-names>JJ</given-names></name><name><surname>Ding</surname><given-names>Y</given-names></name><name><surname>Davoodi-Semiromi</surname><given-names>A</given-names></name><name><surname>Daniell</surname><given-names>H</given-names></name></person-group><article-title>Effective plague vaccination via oral delivery of plant cells expressing F1-V antigens in chloroplasts</article-title><source>Infect Immun</source><year>2008</year><volume>76</volume><fpage>3640</fpage><lpage>3650</lpage><pub-id pub-id-type="doi">10.1128/IAI.00050-08</pub-id><pub-id pub-id-type="pmid">18505806</pub-id></element-citation></ref><ref id="CR306"><label>306.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Molina</surname><given-names>A</given-names></name><name><surname>Hervas-Stubbs</surname><given-names>S</given-names></name><name><surname>Daniell</surname><given-names>H</given-names></name><name><surname>Mingo-Castel</surname><given-names>AM</given-names></name><name><surname>Veramendi</surname><given-names>J</given-names></name></person-group><article-title>High-yield expression of a viral peptide animal vaccine in transgenic tobacco chloroplasts</article-title><source>Plant Biotechnol J</source><year>2004</year><volume>2</volume><fpage>141</fpage><lpage>153</lpage><pub-id pub-id-type="doi">10.1046/j.1467-7652.2004.00057.x</pub-id><pub-id pub-id-type="pmid">17147606</pub-id></element-citation></ref><ref id="CR307"><label>307.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Lentz</surname><given-names>EM</given-names></name><name><surname>Mozgovoj</surname><given-names>MV</given-names></name><name><surname>Bellido</surname><given-names>D</given-names></name><name><surname>Santos</surname><given-names>MJD</given-names></name><name><surname>Wigdorovitz</surname><given-names>A</given-names></name><name><surname>Bravo-Almonacid</surname><given-names>FF</given-names></name></person-group><article-title>VP8*antigen produced in tobacco transplastomic plants confers protection against bovine rotavirus infection in a suckling mouse model</article-title><source>J Biotechnol</source><year>2011</year><volume>156</volume><fpage>100</fpage><lpage>107</lpage><pub-id pub-id-type="doi">10.1016/j.jbiotec.2011.08.023</pub-id><pub-id pub-id-type="pmid">21893114</pub-id></element-citation></ref><ref id="CR308"><label>308.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Daniell</surname><given-names>H</given-names></name><name><surname>Lee</surname><given-names>SB</given-names></name><name><surname>Panchal</surname><given-names>T</given-names></name><name><surname>Wiebe</surname><given-names>PO</given-names></name></person-group><article-title>Expression of the native cholera toxin B subunit gene and assembly as functional oligomers in transgenic tobacco chloroplasts</article-title><source>J Mol Biol</source><year>2001</year><volume>311</volume><fpage>1001</fpage><lpage>1009</lpage><pub-id pub-id-type="doi">10.1006/jmbi.2001.4921</pub-id><pub-id pub-id-type="pmid">11531335</pub-id></element-citation></ref><ref id="CR309"><label>309.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Kang</surname><given-names>TJ</given-names></name><name><surname>Loc</surname><given-names>NH</given-names></name><name><surname>Jang</surname><given-names>MO</given-names></name><name><surname>Jang</surname><given-names>YS</given-names></name><name><surname>Kim</surname><given-names>YS</given-names></name><name><surname>Seo</surname><given-names>JE</given-names></name><name><surname>Yang</surname><given-names>MS</given-names></name></person-group><article-title>Expression of the B subunit of <italic>E. coli</italic> heat-labile enterotoxin in the chloroplasts of plants and its characterization</article-title><source>Transgenic Res</source><year>2003</year><volume>12</volume><fpage>683</fpage><lpage>691</lpage><pub-id pub-id-type="doi">10.1023/B:TRAG.0000005114.23991.bc</pub-id><pub-id pub-id-type="pmid">14713197</pub-id></element-citation></ref><ref id="CR310"><label>310.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Chebolu</surname><given-names>S</given-names></name><name><surname>Daniell</surname><given-names>H</given-names></name></person-group><article-title>Stable expression of Gal/GalNAc lectin of <italic>Entamoeba histolytica</italic> in transgenic chloroplasts and immunogenicity in mice towards vaccine development for amoebiasis</article-title><source>Plant Biotechnol J</source><year>2007</year><volume>5</volume><fpage>230</fpage><lpage>239</lpage><pub-id pub-id-type="doi">10.1111/j.1467-7652.2006.00234.x</pub-id><pub-id pub-id-type="pmid">17309678</pub-id></element-citation></ref><ref id="CR311"><label>311.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Glenz</surname><given-names>K</given-names></name><name><surname>Bouchon</surname><given-names>B</given-names></name><name><surname>Stehle</surname><given-names>T</given-names></name><name><surname>Wallich</surname><given-names>R</given-names></name><name><surname>Simon</surname><given-names>MM</given-names></name><name><surname>Warzecha</surname><given-names>H</given-names></name></person-group><article-title>Production of a recombinant bacterial lipoprotein in higher plant chloroplasts</article-title><source>Nat Biotechnol</source><year>2006</year><volume>24</volume><fpage>76</fpage><lpage>77</lpage><pub-id pub-id-type="doi">10.1038/nbt1170</pub-id><pub-id pub-id-type="pmid">16327810</pub-id></element-citation></ref><ref id="CR312"><label>312.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Rosales-Mendoza</surname><given-names>S</given-names></name><name><surname>Alpuche-Solis</surname><given-names>AG</given-names></name><name><surname>Soria-Guerra</surname><given-names>RE</given-names></name><name><surname>Moreno-Fierros</surname><given-names>L</given-names></name><name><surname>Martinez-Gonzalez</surname><given-names>L</given-names></name><name><surname>Herrera-Diaz</surname><given-names>A</given-names></name><name><surname>Korban</surname><given-names>SS</given-names></name></person-group><article-title>Expression of an <italic>Escherichia coli</italic> antigenic fusion protein comprising the heat labile toxin B subunit and the heat stable toxin, and its assembly as a functional oligomer in transplastomic tobacco plants</article-title><source>Plant J</source><year>2009</year><volume>57</volume><fpage>45</fpage><lpage>54</lpage><pub-id pub-id-type="doi">10.1111/j.1365-313X.2008.03666.x</pub-id><pub-id pub-id-type="pmid">18764920</pub-id></element-citation></ref><ref id="CR313"><label>313.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Soria-Guerra</surname><given-names>RE</given-names></name><name><surname>Alpuche-Solis</surname><given-names>AG</given-names></name><name><surname>Rosales-Mendoza</surname><given-names>S</given-names></name><name><surname>Moreno-Fierros</surname><given-names>L</given-names></name><name><surname>Bendik</surname><given-names>EM</given-names></name><name><surname>Martinez-Gonzalez</surname><given-names>L</given-names></name><name><surname>Korban</surname><given-names>SS</given-names></name></person-group><article-title>Expression of a multi-epitope DPT fusion protein in transplastomic tobacco plants retains both antigenicity and immunogenicity of all three components of the functional oligomer</article-title><source>Planta</source><year>2009</year><volume>229</volume><fpage>1293</fpage><lpage>1302</lpage><pub-id pub-id-type="doi">10.1007/s00425-009-0918-2</pub-id><pub-id pub-id-type="pmid">19306020</pub-id></element-citation></ref><ref id="CR314"><label>314.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Rubio-Infante</surname><given-names>N</given-names></name><name><surname>Govea-Alonso</surname><given-names>DO</given-names></name><name><surname>Alpuche-Solis</surname><given-names>AG</given-names></name><name><surname>Garcia-Hernandez</surname><given-names>AL</given-names></name><name><surname>Soria-Guerra</surname><given-names>RE</given-names></name><name><surname>Paz-Maldonado</surname><given-names>LMT</given-names></name><etal></etal></person-group><article-title>A chloroplast-derived C4V3 polypeptide from the human immunodeficiency virus (HIV) is orally immunogenic in mice</article-title><source>Plant Mol Biol</source><year>2012</year><volume>78</volume><fpage>337</fpage><lpage>349</lpage><pub-id pub-id-type="doi">10.1007/s11103-011-9870-1</pub-id><pub-id pub-id-type="pmid">22228408</pub-id></element-citation></ref><ref id="CR315"><label>315.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Waheed</surname><given-names>MT</given-names></name><name><surname>Thones</surname><given-names>N</given-names></name><name><surname>Muller</surname><given-names>M</given-names></name><name><surname>Hassan</surname><given-names>SW</given-names></name><name><surname>Gottschamel</surname><given-names>J</given-names></name><name><surname>Lossl</surname><given-names>E</given-names></name><etal></etal></person-group><article-title>Plastid expression of a double-pentameric vaccine candidate containing human papillomavirus-16 L1 antigen fused with LTB as adjuvant: transplastomic plants show pleiotropic phenotypes</article-title><source>Plant Biotechnol J</source><year>2011</year><volume>9</volume><fpage>651</fpage><lpage>660</lpage><pub-id pub-id-type="doi">10.1111/j.1467-7652.2011.00612.x</pub-id><pub-id pub-id-type="pmid">21447051</pub-id></element-citation></ref><ref id="CR316"><label>316.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Gonzalez-Rabade</surname><given-names>N</given-names></name><name><surname>McGowan</surname><given-names>EG</given-names></name><name><surname>Zhou</surname><given-names>F</given-names></name><name><surname>McCabe</surname><given-names>MS</given-names></name><name><surname>Bock</surname><given-names>R</given-names></name><name><surname>Dix</surname><given-names>PJ</given-names></name><etal></etal></person-group><article-title>Immunogenicity of chloroplast-derived HIV-1 p24 and a p24-Nef fusion protein following subcutaneous and oral administration in mice</article-title><source>Plant Biotechnol J</source><year>2011</year><volume>9</volume><fpage>629</fpage><lpage>638</lpage><pub-id pub-id-type="doi">10.1111/j.1467-7652.2011.00609.x</pub-id><pub-id pub-id-type="pmid">21443546</pub-id></element-citation></ref><ref id="CR317"><label>317.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Zhou</surname><given-names>YX</given-names></name><name><surname>Lee</surname><given-names>MYT</given-names></name><name><surname>Ng</surname><given-names>JMH</given-names></name><name><surname>Chye</surname><given-names>ML</given-names></name><name><surname>Yip</surname><given-names>WK</given-names></name><name><surname>Zee</surname><given-names>SY</given-names></name><name><surname>Lam</surname><given-names>E</given-names></name></person-group><article-title>A truncated hepatitis E virus ORF2 protein expressed in tobacco plastids is immunogenic in mice</article-title><source>World J Gastroenterol</source><year>2006</year><volume>12</volume><fpage>306</fpage><lpage>312</lpage><pub-id pub-id-type="doi">10.3748/wjg.v12.i2.306</pub-id><pub-id pub-id-type="pmid">16482635</pub-id></element-citation></ref><ref id="CR318"><label>318.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Shao</surname><given-names>HB</given-names></name><name><surname>He</surname><given-names>DM</given-names></name><name><surname>Qian</surname><given-names>KX</given-names></name><name><surname>Shen</surname><given-names>GF</given-names></name><name><surname>Su</surname><given-names>ZL</given-names></name></person-group><article-title>The expression of classical swine fever virus structural protein E2 gene in tobacco chloroplasts for applying chloroplasts as bioreactors</article-title><source>C R Biol</source><year>2008</year><volume>331</volume><fpage>179</fpage><lpage>184</lpage><pub-id pub-id-type="doi">10.1016/j.crvi.2007.12.007</pub-id><pub-id pub-id-type="pmid">18280983</pub-id></element-citation></ref><ref id="CR319"><label>319.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Tregoning</surname><given-names>JS</given-names></name><name><surname>Nixon</surname><given-names>P</given-names></name><name><surname>Kuroda</surname><given-names>H</given-names></name><name><surname>Svab</surname><given-names>Z</given-names></name><name><surname>Clare</surname><given-names>S</given-names></name><name><surname>Bowe</surname><given-names>F</given-names></name><etal></etal></person-group><article-title>Expression of tetanus toxin Fragment C in tobacco chloroplasts</article-title><source>Nucleic Acids Res</source><year>2003</year><volume>31</volume><fpage>1174</fpage><lpage>1179</lpage><pub-id pub-id-type="doi">10.1093/nar/gkg221</pub-id><pub-id pub-id-type="pmid">12582236</pub-id></element-citation></ref><ref id="CR320"><label>320.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Morgenfeld</surname><given-names>M</given-names></name><name><surname>Lentz</surname><given-names>E</given-names></name><name><surname>Segretin</surname><given-names>ME</given-names></name><name><surname>Alfano</surname><given-names>EF</given-names></name><name><surname>Bravo-Almonacid</surname><given-names>F</given-names></name></person-group><article-title>Translational fusion and redirection to thylakoid lumen as strategies to enhance accumulation of human papillomavirus E7 antigen in tobacco chloroplasts</article-title><source>Mol Biotechnol</source><year>2014</year><volume>56</volume><fpage>1021</fpage><lpage>1031</lpage><pub-id pub-id-type="doi">10.1007/s12033-014-9781-x</pub-id><pub-id pub-id-type="pmid">24981330</pub-id></element-citation></ref></ref-list></back></pmc></record>Pour manipuler ce document sous Unix (Dilib)
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