Comparative Genomics of Ten Solanaceous Plastomes
Identifieur interne : 000880 ( Pmc/Checkpoint ); précédent : 000879; suivant : 000881Comparative Genomics of Ten Solanaceous Plastomes
Auteurs : Harpreet Kaur [Inde] ; Bhupinder Pal Singh [Inde] ; Harpreet Singh [Inde] ; Avinash Kaur Nagpal [Inde]Source :
- Advances in Bioinformatics [ 1687-8027 ] ; 2014.
Abstract
Availability of complete plastid genomes of ten solanaceous species,
Url:
DOI: 10.1155/2014/424873
PubMed: 25477958
PubMed Central: 4248371
Affiliations:
Links toward previous steps (curation, corpus...)
Links to Exploration step
PMC:4248371Le document en format XML
<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Comparative Genomics of Ten Solanaceous Plastomes</title><author><name sortKey="Kaur, Harpreet" sort="Kaur, Harpreet" uniqKey="Kaur H" first="Harpreet" last="Kaur">Harpreet Kaur</name><affiliation wicri:level="1"><nlm:aff id="I1">Department of Botanical and Environmental Sciences, Guru Nanak Dev University, Amritsar 143005, India</nlm:aff><country xml:lang="fr">Inde</country><wicri:regionArea>Department of Botanical and Environmental Sciences, Guru Nanak Dev University, Amritsar 143005</wicri:regionArea><wicri:noRegion>Amritsar 143005</wicri:noRegion></affiliation></author><author><name sortKey="Singh, Bhupinder Pal" sort="Singh, Bhupinder Pal" uniqKey="Singh B" first="Bhupinder Pal" last="Singh">Bhupinder Pal Singh</name><affiliation wicri:level="1"><nlm:aff id="I1">Department of Botanical and Environmental Sciences, Guru Nanak Dev University, Amritsar 143005, India</nlm:aff><country xml:lang="fr">Inde</country><wicri:regionArea>Department of Botanical and Environmental Sciences, Guru Nanak Dev University, Amritsar 143005</wicri:regionArea><wicri:noRegion>Amritsar 143005</wicri:noRegion></affiliation></author><author><name sortKey="Singh, Harpreet" sort="Singh, Harpreet" uniqKey="Singh H" first="Harpreet" last="Singh">Harpreet Singh</name><affiliation wicri:level="1"><nlm:aff id="I2">Department of Bioinformatics, Hans Raj Mahila Maha Vidyalaya, Jalandhar 144008, India</nlm:aff><country xml:lang="fr">Inde</country><wicri:regionArea>Department of Bioinformatics, Hans Raj Mahila Maha Vidyalaya, Jalandhar 144008</wicri:regionArea><wicri:noRegion>Jalandhar 144008</wicri:noRegion></affiliation></author><author><name sortKey="Nagpal, Avinash Kaur" sort="Nagpal, Avinash Kaur" uniqKey="Nagpal A" first="Avinash Kaur" last="Nagpal">Avinash Kaur Nagpal</name><affiliation wicri:level="1"><nlm:aff id="I1">Department of Botanical and Environmental Sciences, Guru Nanak Dev University, Amritsar 143005, India</nlm:aff><country xml:lang="fr">Inde</country><wicri:regionArea>Department of Botanical and Environmental Sciences, Guru Nanak Dev University, Amritsar 143005</wicri:regionArea><wicri:noRegion>Amritsar 143005</wicri:noRegion></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">25477958</idno><idno type="pmc">4248371</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4248371</idno><idno type="RBID">PMC:4248371</idno><idno type="doi">10.1155/2014/424873</idno><date when="2014">2014</date><idno type="wicri:Area/Pmc/Corpus">000D84</idno><idno type="wicri:Area/Pmc/Curation">000D83</idno><idno type="wicri:Area/Pmc/Checkpoint">000880</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Comparative Genomics of Ten Solanaceous Plastomes</title><author><name sortKey="Kaur, Harpreet" sort="Kaur, Harpreet" uniqKey="Kaur H" first="Harpreet" last="Kaur">Harpreet Kaur</name><affiliation wicri:level="1"><nlm:aff id="I1">Department of Botanical and Environmental Sciences, Guru Nanak Dev University, Amritsar 143005, India</nlm:aff><country xml:lang="fr">Inde</country><wicri:regionArea>Department of Botanical and Environmental Sciences, Guru Nanak Dev University, Amritsar 143005</wicri:regionArea><wicri:noRegion>Amritsar 143005</wicri:noRegion></affiliation></author><author><name sortKey="Singh, Bhupinder Pal" sort="Singh, Bhupinder Pal" uniqKey="Singh B" first="Bhupinder Pal" last="Singh">Bhupinder Pal Singh</name><affiliation wicri:level="1"><nlm:aff id="I1">Department of Botanical and Environmental Sciences, Guru Nanak Dev University, Amritsar 143005, India</nlm:aff><country xml:lang="fr">Inde</country><wicri:regionArea>Department of Botanical and Environmental Sciences, Guru Nanak Dev University, Amritsar 143005</wicri:regionArea><wicri:noRegion>Amritsar 143005</wicri:noRegion></affiliation></author><author><name sortKey="Singh, Harpreet" sort="Singh, Harpreet" uniqKey="Singh H" first="Harpreet" last="Singh">Harpreet Singh</name><affiliation wicri:level="1"><nlm:aff id="I2">Department of Bioinformatics, Hans Raj Mahila Maha Vidyalaya, Jalandhar 144008, India</nlm:aff><country xml:lang="fr">Inde</country><wicri:regionArea>Department of Bioinformatics, Hans Raj Mahila Maha Vidyalaya, Jalandhar 144008</wicri:regionArea><wicri:noRegion>Jalandhar 144008</wicri:noRegion></affiliation></author><author><name sortKey="Nagpal, Avinash Kaur" sort="Nagpal, Avinash Kaur" uniqKey="Nagpal A" first="Avinash Kaur" last="Nagpal">Avinash Kaur Nagpal</name><affiliation wicri:level="1"><nlm:aff id="I1">Department of Botanical and Environmental Sciences, Guru Nanak Dev University, Amritsar 143005, India</nlm:aff><country xml:lang="fr">Inde</country><wicri:regionArea>Department of Botanical and Environmental Sciences, Guru Nanak Dev University, Amritsar 143005</wicri:regionArea><wicri:noRegion>Amritsar 143005</wicri:noRegion></affiliation></author></analytic><series><title level="j">Advances in Bioinformatics</title><idno type="ISSN">1687-8027</idno><idno type="eISSN">1687-8035</idno><imprint><date when="2014">2014</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>Availability of complete plastid genomes of ten solanaceous species, <italic>Atropa belladonna</italic>, <italic>Capsicum annuum</italic>, <italic>Datura stramonium</italic>, <italic>Nicotiana sylvestris</italic>, <italic>Nicotiana tabacum</italic>, <italic>Nicotiana tomentosiformis</italic>, <italic>Nicotiana undulata</italic>, <italic>Solanum bulbocastanum</italic>, <italic>Solanum lycopersicum</italic>, and <italic>Solanum tuberosum</italic> provided us with an opportunity to conduct their <italic>in silico</italic> comparative analysis in depth. The size of complete chloroplast genomes and LSC and SSC regions of three species of <italic>Solanum</italic> is comparatively smaller than that of any other species studied till date (exception: SSC region of <italic>A. belladonna</italic>). AT content of coding regions was found to be less than noncoding regions. A duplicate copy of trnH gene in <italic>C. annuum</italic> and two alternative tRNA genes for proline in <italic>D. stramonium</italic> were observed for the first time in this analysis. Further, homology search revealed the presence of rps19 pseudogene and infA genes in <italic>A. belladonna</italic> and <italic>D. stramonium</italic>, a region identical to rps19 pseudogene in <italic>C. annum</italic> and orthologues of sprA gene in another six species. Among the eighteen intron-containing genes, 3 genes have two introns and 15 genes have one intron. The longest insertion was found in accD gene in <italic>C. annuum</italic>. Phylogenetic analysis using concatenated protein coding sequences gave two clades, one for <italic>Nicotiana</italic> species and another for <italic>Solanum</italic>, <italic>Capsicum</italic>, <italic>Atropa</italic>, and <italic>Datura</italic>.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Bausher, M G" uniqKey="Bausher M">M. G. Bausher</name></author><author><name sortKey="Singh, N D" uniqKey="Singh N">N. D. Singh</name></author><author><name sortKey="Lee, S B" uniqKey="Lee S">S.-B. Lee</name></author><author><name sortKey="Jansen, R K" uniqKey="Jansen R">R. K. Jansen</name></author><author><name sortKey="Daniell, H" uniqKey="Daniell H">H. Daniell</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="Palmer, J D" uniqKey="Palmer J">J. D. Palmer</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Olmstead, R G" uniqKey="Olmstead R">R. G. Olmstead</name></author><author><name sortKey="Palmer, J D" uniqKey="Palmer J">J. D. Palmer</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Bungard, R A" uniqKey="Bungard R">R. A. Bungard</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Raubeson, L A" uniqKey="Raubeson L">L. A. Raubeson</name></author><author><name sortKey="Jansen, R K" uniqKey="Jansen R">R. K. Jansen</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Haberle, R C" uniqKey="Haberle R">R. C. Haberle</name></author><author><name sortKey="Fourcade, H M" uniqKey="Fourcade H">H. M. Fourcade</name></author><author><name sortKey="Boore, J L" uniqKey="Boore J">J. L. Boore</name></author><author><name sortKey="Jansen, R K" uniqKey="Jansen R">R. K. Jansen</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Martin, W" uniqKey="Martin W">W. Martin</name></author><author><name sortKey="Herrmann, R G" uniqKey="Herrmann R">R. G. Herrmann</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Race, H L" uniqKey="Race H">H. L. Race</name></author><author><name sortKey="Herrmann, R G" uniqKey="Herrmann R">R. G. Herrmann</name></author><author><name sortKey="Martin, W" uniqKey="Martin W">W. Martin</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Wakasugi, T" uniqKey="Wakasugi T">T. Wakasugi</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="Kim, Y K" uniqKey="Kim Y">Y.-K. Kim</name></author><author><name sortKey="Park, C W" uniqKey="Park C">C.-W. Park</name></author><author><name sortKey="Kim, K J" uniqKey="Kim K">K.-J. Kim</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Khan, A" uniqKey="Khan A">A. Khan</name></author><author><name sortKey="Khan, I A" uniqKey="Khan I">I. A. Khan</name></author><author><name sortKey="Asif, H" uniqKey="Asif H">H. Asif</name></author><author><name sortKey="Azim, M K" uniqKey="Azim M">M. K. Azim</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Shimada, H" uniqKey="Shimada H">H. Shimada</name></author><author><name sortKey="Sugiura, M" uniqKey="Sugiura M">M. Sugiura</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Sugiura, M" uniqKey="Sugiura M">M. Sugiura</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Cosner, M E" uniqKey="Cosner M">M. E. Cosner</name></author><author><name sortKey="Jansen, R K" uniqKey="Jansen R">R. K. Jansen</name></author><author><name sortKey="Palmer, J D" uniqKey="Palmer J">J. D. Palmer</name></author><author><name sortKey="Downie, S R" uniqKey="Downie S">S. R. Downie</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Gao, L" uniqKey="Gao L">L. Gao</name></author><author><name sortKey="Yi, X" uniqKey="Yi X">X. Yi</name></author><author><name sortKey="Yang, Y X" uniqKey="Yang Y">Y.-X. Yang</name></author><author><name sortKey="Su, Y J" uniqKey="Su Y">Y.-J. Su</name></author><author><name sortKey="Wang, T" uniqKey="Wang T">T. Wang</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="Goffinet, B" uniqKey="Goffinet B">B. Goffinet</name></author><author><name sortKey="Wickett, N J" uniqKey="Wickett N">N. J. Wickett</name></author><author><name sortKey="Werner, O" uniqKey="Werner O">O. Werner</name></author><author><name sortKey="Ros, R M" uniqKey="Ros R">R. M. Ros</name></author><author><name sortKey="Shaw, A J" uniqKey="Shaw A">A. J. Shaw</name></author><author><name sortKey="Cox, C J" uniqKey="Cox C">C. J. Cox</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Palmer, J D" uniqKey="Palmer J">J. D. Palmer</name></author><author><name sortKey="Nugent, J M" uniqKey="Nugent J">J. M. Nugent</name></author><author><name sortKey="Herbon, L A" uniqKey="Herbon L">L. A. Herbon</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Greiner, S" uniqKey="Greiner S">S. Greiner</name></author><author><name sortKey="Wang, X" uniqKey="Wang X">X. Wang</name></author><author><name sortKey="Rauwolf, U" uniqKey="Rauwolf U">U. Rauwolf</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Doyle, J J" uniqKey="Doyle J">J. J. Doyle</name></author><author><name sortKey="Davis, J I" uniqKey="Davis J">J. I. Davis</name></author><author><name sortKey="Soreng, R J" uniqKey="Soreng R">R. J. Soreng</name></author><author><name sortKey="Garvin, D" uniqKey="Garvin D">D. Garvin</name></author><author><name sortKey="Anderson, M J" uniqKey="Anderson M">M. J. Anderson</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Michelangeli, F A" uniqKey="Michelangeli F">F. A. Michelangeli</name></author><author><name sortKey="Davis, J I" uniqKey="Davis J">J. I. Davis</name></author><author><name sortKey="Stevenson, D W" uniqKey="Stevenson D">D. W. Stevenson</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, G R" uniqKey="Lazo G">G. R. Lazo</name></author><author><name sortKey="Anderson, O D" uniqKey="Anderson O">O. D. Anderson</name></author><author><name sortKey="Gu, Y Q" uniqKey="Gu Y">Y. Q. Gu</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Leseberg, C H" uniqKey="Leseberg C">C. H. Leseberg</name></author><author><name sortKey="Duvall, M R" uniqKey="Duvall M">M. R. Duvall</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Chung, H J" uniqKey="Chung H">H. J. Chung</name></author><author><name sortKey="Jung, J D" uniqKey="Jung J">J. D. Jung</name></author><author><name sortKey="Park, H W" uniqKey="Park H">H. W. Park</name></author><author><name sortKey="Kim, J H" uniqKey="Kim J">J. H. Kim</name></author><author><name sortKey="Cha, H W" uniqKey="Cha H">H. W. Cha</name></author><author><name sortKey="Min, S R" uniqKey="Min S">S. R. Min</name></author><author><name sortKey="Jeong, W J" uniqKey="Jeong W">W. J. Jeong</name></author><author><name sortKey="Liu, J R" uniqKey="Liu J">J. R. Liu</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Daniell, H" uniqKey="Daniell H">H. Daniell</name></author><author><name sortKey="Lee, S B" uniqKey="Lee S">S.-B. Lee</name></author><author><name sortKey="Grevich, J" uniqKey="Grevich J">J. Grevich</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Kahlau, S" uniqKey="Kahlau S">S. Kahlau</name></author><author><name sortKey="Aspinall, S" uniqKey="Aspinall S">S. Aspinall</name></author><author><name sortKey="Gray, J C" uniqKey="Gray J">J. C. Gray</name></author><author><name sortKey="Bock, R" uniqKey="Bock R">R. Bock</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Yukawa, M" uniqKey="Yukawa M">M. Yukawa</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="Jo, Y D" uniqKey="Jo Y">Y. D. 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, C G" uniqKey="Hur C">C.-G. Hur</name></author><author><name sortKey="Lee, Y H" uniqKey="Lee Y">Y.-H. Lee</name></author><author><name sortKey="Kang, B C" uniqKey="Kang B">B.-C. Kang</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, T G" uniqKey="Du T">T. G. Du</name></author><author><name sortKey="Hupfer, H" uniqKey="Hupfer H">H. Hupfer</name></author><author><name sortKey="Herrmann, R G" uniqKey="Herrmann R">R. G. Herrmann</name></author><author><name sortKey="Maier, R M" uniqKey="Maier R">R. M. Maier</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Kunnimalaiyaan, M" uniqKey="Kunnimalaiyaan M">M. Kunnimalaiyaan</name></author><author><name sortKey="Nielsen, B L" uniqKey="Nielsen B">B. L. Nielsen</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Thyssen, G" uniqKey="Thyssen G">G. Thyssen</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="Gargano, D" uniqKey="Gargano D">D. Gargano</name></author><author><name sortKey="Vezzi, A" uniqKey="Vezzi A">A. Vezzi</name></author><author><name sortKey="Scotti, N" uniqKey="Scotti N">N. Scotti</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Kim, K J" uniqKey="Kim K">K.-J. Kim</name></author><author><name sortKey="Lee, H L" uniqKey="Lee H">H.-L. Lee</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Steane, D A" uniqKey="Steane D">D. A. Steane</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Palmer, J D" uniqKey="Palmer J">J. D. Palmer</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Sugiura, M" uniqKey="Sugiura M">M. Sugiura</name></author><author><name sortKey="Shinozaki, K" uniqKey="Shinozaki K">K. Shinozaki</name></author><author><name sortKey="Tanaka, M" uniqKey="Tanaka M">M. Tanaka</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Vera, A" uniqKey="Vera A">A. Vera</name></author><author><name sortKey="Sugiura, M" uniqKey="Sugiura M">M. Sugiura</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Sugita, M" uniqKey="Sugita M">M. Sugita</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="Sugiura, M" uniqKey="Sugiura M">M. Sugiura</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Lahaye, R" uniqKey="Lahaye R">R. Lahaye</name></author><author><name sortKey="Van Der Bank, M" uniqKey="Van Der Bank M">M. van der Bank</name></author><author><name sortKey="Bogarin, D" uniqKey="Bogarin D">D. Bogarin</name></author><author><name sortKey="Warner, J" uniqKey="Warner J">J. Warner</name></author><author><name sortKey="Pupulin, F" uniqKey="Pupulin F">F. Pupulin</name></author><author><name sortKey="Gigot, G" uniqKey="Gigot G">G. Gigot</name></author><author><name sortKey="Maurin, O" uniqKey="Maurin O">O. Maurin</name></author><author><name sortKey="Duthoit, S" uniqKey="Duthoit S">S. Duthoit</name></author><author><name sortKey="Barraclough, T G" uniqKey="Barraclough T">T. G. Barraclough</name></author><author><name sortKey="Savolainen, V" uniqKey="Savolainen V">V. Savolainen</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Taberlet, P" uniqKey="Taberlet P">P. Taberlet</name></author><author><name sortKey="Gielly, L" uniqKey="Gielly L">L. Gielly</name></author><author><name sortKey="Pautou, G" uniqKey="Pautou G">G. Pautou</name></author><author><name sortKey="Bouvet, J" uniqKey="Bouvet J">J. Bouvet</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, J L" uniqKey="Fernandez Vazquez J">J. L. Fernández-Vázquez</name></author><author><name sortKey="Santamaria, R" uniqKey="Santamaria R">R. Santamaría</name></author><author><name sortKey="Arellano, J" uniqKey="Arellano J">J. Arellano</name></author><author><name sortKey="Cevallos, M A" uniqKey="Cevallos M">M. A. Cevallos</name></author><author><name sortKey="Davila, G" uniqKey="Davila G">G. Dávila</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Jansen, R K" uniqKey="Jansen R">R. K. 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, S B" uniqKey="Lee S">S.-B. Lee</name></author><author><name sortKey="Tomkins, J" uniqKey="Tomkins J">J. Tomkins</name></author><author><name sortKey="Alverson, A J" uniqKey="Alverson A">A. J. Alverson</name></author><author><name sortKey="Daniell, H" uniqKey="Daniell H">H. Daniell</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Moore, M J" uniqKey="Moore M">M. J. Moore</name></author><author><name sortKey="Soltis, P S" uniqKey="Soltis P">P. S. Soltis</name></author><author><name sortKey="Bell, C D" uniqKey="Bell C">C. D. Bell</name></author><author><name sortKey="Burleigh, J G" uniqKey="Burleigh J">J. G. Burleigh</name></author><author><name sortKey="Soltis, D E" uniqKey="Soltis D">D. E. Soltis</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Jansen, R K" uniqKey="Jansen R">R. K. Jansen</name></author><author><name sortKey="Cai, Z" uniqKey="Cai Z">Z. Cai</name></author><author><name sortKey="Raubeson, L A" uniqKey="Raubeson L">L. A. Raubeson</name></author><author><name sortKey="Daniell, H" uniqKey="Daniell H">H. Daniell</name></author><author><name sortKey="Depamphilis, C W" uniqKey="Depamphilis C">C. W. Depamphilis</name></author><author><name sortKey="Leebens Mack, J" uniqKey="Leebens Mack J">J. Leebens-Mack</name></author><author><name sortKey="Muller, K F" uniqKey="Muller K">K. F. Müller</name></author><author><name sortKey="Guisinger Bellian, M" uniqKey="Guisinger Bellian M">M. Guisinger-Bellian</name></author><author><name sortKey="Haberle, R C" uniqKey="Haberle R">R. C. Haberle</name></author><author><name sortKey="Hansen, A K" uniqKey="Hansen A">A. K. Hansen</name></author><author><name sortKey="Chumley, T W" uniqKey="Chumley T">T. W. Chumley</name></author><author><name sortKey="Lee, S B" uniqKey="Lee S">S.-B. Lee</name></author><author><name sortKey="Peery, R" uniqKey="Peery R">R. Peery</name></author><author><name sortKey="Mcneal, J R" uniqKey="Mcneal J">J. R. McNeal</name></author><author><name sortKey="Kuehl, J V" uniqKey="Kuehl J">J. V. Kuehl</name></author><author><name sortKey="Boore, J L" uniqKey="Boore J">J. L. Boore</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Bohs, L" uniqKey="Bohs L">L. Bohs</name></author><author><name sortKey="Olmstead, R G" uniqKey="Olmstead R">R. G. Olmstead</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Olmstead, R G" uniqKey="Olmstead R">R. G. Olmstead</name></author><author><name sortKey="Bohs, L" uniqKey="Bohs L">L. Bohs</name></author><author><name sortKey="Migid, H A" uniqKey="Migid H">H. A. Migid</name></author><author><name sortKey="Santiago Valentin, E" uniqKey="Santiago Valentin E">E. Santiago-Valentin</name></author><author><name sortKey="Garcia, V F" uniqKey="Garcia V">V. F. Garcia</name></author><author><name sortKey="Collier, S M" uniqKey="Collier S">S. M. Collier</name></author></analytic></biblStruct></listBibl></div1></back></TEI><pmc article-type="research-article"><pmc-dir>properties open_access</pmc-dir>
<front><journal-meta><journal-id journal-id-type="nlm-ta">Adv Bioinformatics</journal-id><journal-id journal-id-type="iso-abbrev">Adv Bioinformatics</journal-id><journal-id journal-id-type="publisher-id">ABI</journal-id><journal-title-group><journal-title>Advances in Bioinformatics</journal-title></journal-title-group><issn pub-type="ppub">1687-8027</issn><issn pub-type="epub">1687-8035</issn><publisher><publisher-name>Hindawi Publishing Corporation</publisher-name></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">25477958</article-id><article-id pub-id-type="pmc">4248371</article-id><article-id pub-id-type="doi">10.1155/2014/424873</article-id><article-categories><subj-group subj-group-type="heading"><subject>Research Article</subject></subj-group></article-categories><title-group><article-title>Comparative Genomics of Ten Solanaceous Plastomes</article-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Kaur</surname><given-names>Harpreet</given-names></name><xref ref-type="aff" rid="I1"><sup>1</sup></xref></contrib><contrib contrib-type="author"><name><surname>Singh</surname><given-names>Bhupinder Pal</given-names></name><xref ref-type="aff" rid="I1"><sup>1</sup></xref></contrib><contrib contrib-type="author"><name><surname>Singh</surname><given-names>Harpreet</given-names></name><xref ref-type="aff" rid="I2"><sup>2</sup></xref></contrib><contrib contrib-type="author"><name><surname>Nagpal</surname><given-names>Avinash Kaur</given-names></name><xref ref-type="aff" rid="I1"><sup>1</sup></xref><xref ref-type="corresp" rid="cor1"><sup>*</sup></xref></contrib></contrib-group><aff id="I1"><sup>1</sup>Department of Botanical and Environmental Sciences, Guru Nanak Dev University, Amritsar 143005, India</aff><aff id="I2"><sup>2</sup>Department of Bioinformatics, Hans Raj Mahila Maha Vidyalaya, Jalandhar 144008, India</aff><author-notes><corresp id="cor1">*Avinash Kaur Nagpal: <email>avnagpal@yahoo.co.in</email></corresp><fn fn-type="other"><p>Academic Editor: Paul Harrison</p></fn></author-notes><pub-date pub-type="ppub"><year>2014</year></pub-date><pub-date pub-type="epub"><day>17</day><month>11</month><year>2014</year></pub-date><volume>2014</volume><elocation-id>424873</elocation-id><history><date date-type="received"><day>26</day><month>8</month><year>2014</year></date><date date-type="accepted"><day>14</day><month>10</month><year>2014</year></date></history><permissions><copyright-statement>Copyright © 2014 Harpreet Kaur et al.</copyright-statement><copyright-year>2014</copyright-year><license license-type="open-access"><license-p>This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.</license-p></license></permissions><abstract><p>Availability of complete plastid genomes of ten solanaceous species, <italic>Atropa belladonna</italic>, <italic>Capsicum annuum</italic>, <italic>Datura stramonium</italic>, <italic>Nicotiana sylvestris</italic>, <italic>Nicotiana tabacum</italic>, <italic>Nicotiana tomentosiformis</italic>, <italic>Nicotiana undulata</italic>, <italic>Solanum bulbocastanum</italic>, <italic>Solanum lycopersicum</italic>, and <italic>Solanum tuberosum</italic> provided us with an opportunity to conduct their <italic>in silico</italic> comparative analysis in depth. The size of complete chloroplast genomes and LSC and SSC regions of three species of <italic>Solanum</italic> is comparatively smaller than that of any other species studied till date (exception: SSC region of <italic>A. belladonna</italic>). AT content of coding regions was found to be less than noncoding regions. A duplicate copy of trnH gene in <italic>C. annuum</italic> and two alternative tRNA genes for proline in <italic>D. stramonium</italic> were observed for the first time in this analysis. Further, homology search revealed the presence of rps19 pseudogene and infA genes in <italic>A. belladonna</italic> and <italic>D. stramonium</italic>, a region identical to rps19 pseudogene in <italic>C. annum</italic> and orthologues of sprA gene in another six species. Among the eighteen intron-containing genes, 3 genes have two introns and 15 genes have one intron. The longest insertion was found in accD gene in <italic>C. annuum</italic>. Phylogenetic analysis using concatenated protein coding sequences gave two clades, one for <italic>Nicotiana</italic> species and another for <italic>Solanum</italic>, <italic>Capsicum</italic>, <italic>Atropa</italic>, and <italic>Datura</italic>.</p></abstract></article-meta></front><floats-group><fig id="fig1" orientation="portrait" position="float"><label>Figure 1</label><caption><p>Partial multiple sequence alignment of accD, clpP, ndhA, rpl32, rps16, sprA, tRNA-Ala (UGC), tRNA-Leu(UAA), and ycf1 gene sequences of ten solanaceous species showing location of InDels indicated by hyphens.</p></caption><graphic xlink:href="ABI2014-424873.001"></graphic></fig><fig id="fig2" orientation="portrait" position="float"><label>Figure 2</label><caption><p>Partial multiple sequence alignment of amino acid sequences of genes, namely, accD, clpP, ndhA, rpl32, rps16, sprA, tRNA-Ala(UGC), tRNA-Leu(UAA), and ycf1, of ten solanaceous species showing location of InDels indicated by hyphens.</p></caption><graphic xlink:href="ABI2014-424873.002"></graphic></fig><fig id="fig3" orientation="portrait" position="float"><label>Figure 3</label><caption><p>Maximum likelihood phylogenetic tree derived using concatenated nucleotide sequences of 75 protein-coding genes of ten solanaceous species and two outgroup species.</p></caption><graphic xlink:href="ABI2014-424873.003"></graphic></fig><table-wrap id="tab1" orientation="portrait" position="float"><label>Table 1</label><caption><p>Properties of the solanaceous chloroplast genomes.</p></caption><table frame="hsides" rules="groups"><thead><tr><th align="left" rowspan="2" colspan="1">Property</th><th align="center" colspan="10" rowspan="1">Name of species</th></tr><tr><th align="center" rowspan="1" colspan="1">ABE</th><th align="center" rowspan="1" colspan="1">CAN</th><th align="center" rowspan="1" colspan="1">DST</th><th align="center" rowspan="1" colspan="1">NSY</th><th align="center" rowspan="1" colspan="1">NTA</th><th align="center" rowspan="1" colspan="1">NTO</th><th align="center" rowspan="1" colspan="1">NUN</th><th align="center" rowspan="1" colspan="1">SBU</th><th align="center" rowspan="1" colspan="1">SLY</th><th align="center" rowspan="1" colspan="1">STU</th></tr></thead><tbody><tr><td align="left" rowspan="1" colspan="1">Genome size (bp)</td><td align="center" rowspan="1" colspan="1">156687</td><td align="center" rowspan="1" colspan="1">156781 </td><td align="center" rowspan="1" colspan="1">155871</td><td align="center" rowspan="1" colspan="1">155941</td><td align="center" rowspan="1" colspan="1">155943</td><td align="center" rowspan="1" colspan="1">155745</td><td align="center" rowspan="1" colspan="1">155863</td><td align="center" rowspan="1" colspan="1">155371</td><td align="center" rowspan="1" colspan="1">155461</td><td align="center" rowspan="1" colspan="1">155296</td></tr><tr><td align="left" rowspan="1" colspan="1">LSC (bp) (coordinates)<sup>*</sup></td><td align="center" rowspan="1" colspan="1">86,869 (1–86869)</td><td align="center" rowspan="1" colspan="1">87366 (1–87366)</td><td align="center" rowspan="1" colspan="1">86297 (1–86297)</td><td align="center" rowspan="1" colspan="1">86684 (1–86684)</td><td align="center" rowspan="1" colspan="1">86,686 (1–86686)</td><td align="center" rowspan="1" colspan="1">86392 (1–86392)</td><td align="center" rowspan="1" colspan="1">86633 (1–86633)</td><td align="center" rowspan="1" colspan="1">85785 (1–85785)</td><td align="center" rowspan="1" colspan="1">85,882 (1–85882)</td><td align="center" rowspan="1" colspan="1">85737 (1–85737)</td></tr><tr><td align="left" rowspan="1" colspan="1">IR<sub>B</sub> (bp) (coordinates)<sup>*</sup></td><td align="center" rowspan="1" colspan="1">25,905 (86870–112774)</td><td align="center" rowspan="1" colspan="1">25783 (87367–113149)</td><td align="center" rowspan="1" colspan="1">25563 (86298–111860)</td><td align="center" rowspan="1" colspan="1">25342 (86685–112026)</td><td align="center" rowspan="1" colspan="1">25,343 (86687–112029)</td><td align="center" rowspan="1" colspan="1">25429 (86393–111821)</td><td align="center" rowspan="1" colspan="1">25331 (86634–111964)</td><td align="center" rowspan="1" colspan="1">25588 (85786–111373)</td><td align="center" rowspan="1" colspan="1">25,608 (85883–111490)</td><td align="center" rowspan="1" colspan="1">25593 (85738–111330)</td></tr><tr><td align="left" rowspan="1" colspan="1">SSC (bp) (coordinates)<sup>*</sup></td><td align="center" rowspan="1" colspan="1">18,008 (112775–130782)</td><td align="center" rowspan="1" colspan="1">17849 (113150–130998)</td><td align="center" rowspan="1" colspan="1">18448 (111861–130308)</td><td align="center" rowspan="1" colspan="1">18573 (112027–130599)</td><td align="center" rowspan="1" colspan="1">18,571 (112030–130600)</td><td align="center" rowspan="1" colspan="1">18495 (111822–130316)</td><td align="center" rowspan="1" colspan="1">18568 (111965–130532)</td><td align="center" rowspan="1" colspan="1">18381 (111374–129754)</td><td align="center" rowspan="1" colspan="1">18,363 (111491–129853)</td><td align="center" rowspan="1" colspan="1">18373 (111331–129703)</td></tr><tr><td align="left" rowspan="1" colspan="1">IR<sub>A</sub> (bp) (coordinates)<sup>*</sup></td><td align="center" rowspan="1" colspan="1">25,905 (130783–156687)</td><td align="center" rowspan="1" colspan="1">25783 (130999–156781)</td><td align="center" rowspan="1" colspan="1">25563 (130309–155871)</td><td align="center" rowspan="1" colspan="1">25342 (130600–155941)</td><td align="center" rowspan="1" colspan="1">25,343 (130601–155943)</td><td align="center" rowspan="1" colspan="1">25429 (130317–155745)</td><td align="center" rowspan="1" colspan="1">25331 (130533–155863)</td><td align="center" rowspan="1" colspan="1">25588 (129755–155342)</td><td align="center" rowspan="1" colspan="1">25,608 (129854–155461)</td><td align="center" rowspan="1" colspan="1">25593 (129704–155296)</td></tr><tr><td align="left" rowspan="1" colspan="1">Coding regions (%)</td><td align="center" rowspan="1" colspan="1">58.89</td><td align="center" rowspan="1" colspan="1">58.50</td><td align="center" rowspan="1" colspan="1">59.19</td><td align="center" rowspan="1" colspan="1">61.49</td><td align="center" rowspan="1" colspan="1">61.12</td><td align="center" rowspan="1" colspan="1">61.58</td><td align="center" rowspan="1" colspan="1">63.12</td><td align="center" rowspan="1" colspan="1">58.52</td><td align="center" rowspan="1" colspan="1">58.91</td><td align="center" rowspan="1" colspan="1">58.45</td></tr><tr><td align="left" rowspan="1" colspan="1">Introns (%)</td><td align="center" rowspan="1" colspan="1">12.51</td><td align="center" rowspan="1" colspan="1">12.71</td><td align="center" rowspan="1" colspan="1">11.62</td><td align="center" rowspan="1" colspan="1">12.70</td><td align="center" rowspan="1" colspan="1">12.70</td><td align="center" rowspan="1" colspan="1">12.68</td><td align="center" rowspan="1" colspan="1">12.69</td><td align="center" rowspan="1" colspan="1">12.82</td><td align="center" rowspan="1" colspan="1">12.47</td><td align="center" rowspan="1" colspan="1">12.49</td></tr><tr><td align="left" rowspan="1" colspan="1">Intergenic regions (%)</td><td align="center" rowspan="1" colspan="1">28.60</td><td align="center" rowspan="1" colspan="1">28.79</td><td align="center" rowspan="1" colspan="1">29.19</td><td align="center" rowspan="1" colspan="1">25.81</td><td align="center" rowspan="1" colspan="1">26.18</td><td align="center" rowspan="1" colspan="1">25.73</td><td align="center" rowspan="1" colspan="1">24.19</td><td align="center" rowspan="1" colspan="1">28.66</td><td align="center" rowspan="1" colspan="1">28.62</td><td align="center" rowspan="1" colspan="1">29.06</td></tr><tr><td align="center" colspan="11" rowspan="1"><hr></hr></td></tr><tr><td align="center" colspan="11" rowspan="1">AT content (%)</td></tr><tr><td align="left" rowspan="1" colspan="1">Overall</td><td align="center" rowspan="1" colspan="1">62.44</td><td align="center" rowspan="1" colspan="1">62.27</td><td align="center" rowspan="1" colspan="1">62.12</td><td align="center" rowspan="1" colspan="1">62.15</td><td align="center" rowspan="1" colspan="1">62.15 </td><td align="center" rowspan="1" colspan="1">62.21</td><td align="center" rowspan="1" colspan="1">62.12</td><td align="center" rowspan="1" colspan="1">62.12</td><td align="center" rowspan="1" colspan="1">62.14</td><td align="center" rowspan="1" colspan="1">62.12</td></tr><tr><td align="left" rowspan="1" colspan="1">Coding regions</td><td align="center" rowspan="1" colspan="1">59.86</td><td align="center" rowspan="1" colspan="1">59.68</td><td align="center" rowspan="1" colspan="1">59.65</td><td align="center" rowspan="1" colspan="1">59.85</td><td align="center" rowspan="1" colspan="1">59.79</td><td align="center" rowspan="1" colspan="1">59.79</td><td align="center" rowspan="1" colspan="1">59.70</td><td align="center" rowspan="1" colspan="1">59.61</td><td align="center" rowspan="1" colspan="1">59.65</td><td align="center" rowspan="1" colspan="1">59.59</td></tr><tr><td align="left" rowspan="1" colspan="1">Noncoding regions</td><td align="center" rowspan="1" colspan="1">66.13</td><td align="center" rowspan="1" colspan="1">65.93</td><td align="center" rowspan="1" colspan="1">65.72</td><td align="center" rowspan="1" colspan="1">65.84</td><td align="center" rowspan="1" colspan="1">65.87</td><td align="center" rowspan="1" colspan="1">66.09</td><td align="center" rowspan="1" colspan="1">66.27</td><td align="center" rowspan="1" colspan="1">65.66</td><td align="center" rowspan="1" colspan="1">65.71</td><td align="center" rowspan="1" colspan="1">65.68</td></tr><tr><td align="left" rowspan="1" colspan="1">tRNAs</td><td align="center" rowspan="1" colspan="1">47.70</td><td align="center" rowspan="1" colspan="1">47.38</td><td align="center" rowspan="1" colspan="1">47.08</td><td align="center" rowspan="1" colspan="1">47.06</td><td align="center" rowspan="1" colspan="1">47.05</td><td align="center" rowspan="1" colspan="1">47.10</td><td align="center" rowspan="1" colspan="1">47.08</td><td align="center" rowspan="1" colspan="1">47.12</td><td align="center" rowspan="1" colspan="1">47.01</td><td align="center" rowspan="1" colspan="1">47.06</td></tr><tr><td align="left" rowspan="1" colspan="1">rRNAs</td><td align="center" rowspan="1" colspan="1">44.64</td><td align="center" rowspan="1" colspan="1">44.73</td><td align="center" rowspan="1" colspan="1">44.63</td><td align="center" rowspan="1" colspan="1">44.64</td><td align="center" rowspan="1" colspan="1">44.64</td><td align="center" rowspan="1" colspan="1">44.64</td><td align="center" rowspan="1" colspan="1">44.64</td><td align="center" rowspan="1" colspan="1">44.66</td><td align="center" rowspan="1" colspan="1">44.66</td><td align="center" rowspan="1" colspan="1">44.65</td></tr><tr><td align="left" rowspan="1" colspan="1">Protein-coding genes</td><td align="center" rowspan="1" colspan="1">62.01</td><td align="center" rowspan="1" colspan="1">61.83</td><td align="center" rowspan="1" colspan="1">61.79</td><td align="center" rowspan="1" colspan="1">61.91</td><td align="center" rowspan="1" colspan="1">61.86</td><td align="center" rowspan="1" colspan="1">61.84</td><td align="center" rowspan="1" colspan="1">61.68</td><td align="center" rowspan="1" colspan="1">61.76</td><td align="center" rowspan="1" colspan="1">61.80</td><td align="center" rowspan="1" colspan="1">61.74</td></tr><tr><td align="left" rowspan="1" colspan="1">LSC</td><td align="center" rowspan="1" colspan="1">64.37</td><td align="center" rowspan="1" colspan="1">64.25</td><td align="center" rowspan="1" colspan="1">64.04</td><td align="center" rowspan="1" colspan="1">64.05</td><td align="center" rowspan="1" colspan="1">64.05</td><td align="center" rowspan="1" colspan="1">64.12</td><td align="center" rowspan="1" colspan="1">64.01</td><td align="center" rowspan="1" colspan="1">63.99</td><td align="center" rowspan="1" colspan="1">64.01</td><td align="center" rowspan="1" colspan="1">63.99</td></tr><tr><td align="left" rowspan="1" colspan="1">SSC</td><td align="center" rowspan="1" colspan="1">68.35</td><td align="center" rowspan="1" colspan="1">67.99</td><td align="center" rowspan="1" colspan="1">67.72</td><td align="center" rowspan="1" colspan="1">67.94</td><td align="center" rowspan="1" colspan="1">67.93</td><td align="center" rowspan="1" colspan="1">68.03</td><td align="center" rowspan="1" colspan="1">67.87</td><td align="center" rowspan="1" colspan="1">67.87</td><td align="center" rowspan="1" colspan="1">67.97</td><td align="center" rowspan="1" colspan="1">67.91</td></tr><tr><td align="left" rowspan="1" colspan="1">IR</td><td align="center" rowspan="1" colspan="1">57.14</td><td align="center" rowspan="1" colspan="1">56.94</td><td align="center" rowspan="1" colspan="1">56.87</td><td align="center" rowspan="1" colspan="1">56.78</td><td align="center" rowspan="1" colspan="1">56.78</td><td align="center" rowspan="1" colspan="1">56.84</td><td align="center" rowspan="1" colspan="1">56.78</td><td align="center" rowspan="1" colspan="1">56.93</td><td align="center" rowspan="1" colspan="1">56.91</td><td align="center" rowspan="1" colspan="1">56.90</td></tr></tbody></table><table-wrap-foot><fn><p>ABE: <italic>Atropa belladonna</italic>, CAN: <italic>Capsicum annuum</italic>, DST: <italic>Datura stramonium</italic>, NSY: <italic>Nicotiana sylvestris</italic>, NTA: <italic>Nicotiana tabacum</italic>, NTO: <italic>Nicotiana tomentosiformis</italic>, NUN: <italic>Nicotiana undulata</italic>, SBU: <italic>Solanum bulbocastanum</italic>, SLY: <italic>Solanum lycopersicum</italic>, STU: <italic>Solanum tuberosum</italic>, LSC: large single copy region, SSC: small single copy region, and IR: inverted repeat region.</p></fn><fn><p><sup>*</sup>Start and end position of nucleotide in the genome. </p></fn></table-wrap-foot></table-wrap><table-wrap id="tab2" orientation="portrait" position="float"><label>Table 2</label><caption><p>The lengths of introns and exons for the split genes of ten solanaceous species.</p></caption><table frame="hsides" rules="groups"><thead><tr><th align="left" rowspan="1" colspan="1">Gene (region)</th><th align="center" rowspan="1" colspan="1">Exon/intron</th><th align="center" rowspan="1" colspan="1">ABE</th><th align="center" rowspan="1" colspan="1">CAN</th><th align="center" rowspan="1" colspan="1">DST</th><th align="center" rowspan="1" colspan="1">NSY</th><th align="center" rowspan="1" colspan="1">NTA</th><th align="center" rowspan="1" colspan="1">NTO</th><th align="center" rowspan="1" colspan="1">NUN</th><th align="center" rowspan="1" colspan="1">SBU</th><th align="center" rowspan="1" colspan="1">SLY</th><th align="center" rowspan="1" colspan="1">STU</th></tr></thead><tbody><tr><td align="left" rowspan="3" colspan="1">trnK-UUU (LSC)</td><td align="center" rowspan="1" colspan="1">Exon I</td><td align="center" rowspan="1" colspan="1">37</td><td align="center" rowspan="1" colspan="1">37</td><td align="center" rowspan="1" colspan="1">37</td><td align="center" rowspan="1" colspan="1">37</td><td align="center" rowspan="1" colspan="1">37</td><td align="center" rowspan="1" colspan="1">37</td><td align="center" rowspan="1" colspan="1">37</td><td align="center" rowspan="1" colspan="1">37</td><td align="center" rowspan="1" colspan="1">37</td><td align="center" rowspan="1" colspan="1">37</td></tr><tr><td align="center" rowspan="1" colspan="1">Intron I</td><td align="center" rowspan="1" colspan="1">2519</td><td align="center" rowspan="1" colspan="1">2500</td><td align="center" rowspan="1" colspan="1">2506</td><td align="center" rowspan="1" colspan="1">2526</td><td align="center" rowspan="1" colspan="1">2526</td><td align="center" rowspan="1" colspan="1">2526</td><td align="center" rowspan="1" colspan="1">2521</td><td align="center" rowspan="1" colspan="1">2501</td><td align="center" rowspan="1" colspan="1">2514</td><td align="center" rowspan="1" colspan="1">2512</td></tr><tr><td align="center" rowspan="1" colspan="1">Exon II</td><td align="center" rowspan="1" colspan="1">36</td><td align="center" rowspan="1" colspan="1">35</td><td align="center" rowspan="1" colspan="1">35</td><td align="center" rowspan="1" colspan="1">35</td><td align="center" rowspan="1" colspan="1">35</td><td align="center" rowspan="1" colspan="1">35</td><td align="center" rowspan="1" colspan="1">35</td><td align="center" rowspan="1" colspan="1">35</td><td align="center" rowspan="1" colspan="1">35</td><td align="center" rowspan="1" colspan="1">35</td></tr><tr><td align="center" colspan="12" rowspan="1"><hr></hr></td></tr><tr><td align="left" rowspan="3" colspan="1">rps16 (LSC)</td><td align="center" rowspan="1" colspan="1">Exon I</td><td align="center" rowspan="1" colspan="1">40</td><td align="center" rowspan="1" colspan="1">40</td><td align="center" rowspan="1" colspan="1">40</td><td align="center" rowspan="1" colspan="1">40</td><td align="center" rowspan="1" colspan="1">40</td><td align="center" rowspan="1" colspan="1">40</td><td align="center" rowspan="1" colspan="1">40</td><td align="center" rowspan="1" colspan="1">40</td><td align="center" rowspan="1" colspan="1">40</td><td align="center" rowspan="1" colspan="1">40</td></tr><tr><td align="center" rowspan="1" colspan="1">Intron I</td><td align="center" rowspan="1" colspan="1">822</td><td align="center" rowspan="1" colspan="1">865</td><td align="center" rowspan="1" colspan="1">866</td><td align="center" rowspan="1" colspan="1">860</td><td align="center" rowspan="1" colspan="1">860</td><td align="center" rowspan="1" colspan="1">860</td><td align="center" rowspan="1" colspan="1">859</td><td align="center" rowspan="1" colspan="1">855</td><td align="center" rowspan="1" colspan="1">864</td><td align="center" rowspan="1" colspan="1">855</td></tr><tr><td align="center" rowspan="1" colspan="1">Exon II</td><td align="center" rowspan="1" colspan="1">227</td><td align="center" rowspan="1" colspan="1">227</td><td align="center" rowspan="1" colspan="1">227</td><td align="center" rowspan="1" colspan="1">218</td><td align="center" rowspan="1" colspan="1">218</td><td align="center" rowspan="1" colspan="1">218</td><td align="center" rowspan="1" colspan="1">218</td><td align="center" rowspan="1" colspan="1">227</td><td align="center" rowspan="1" colspan="1">227</td><td align="center" rowspan="1" colspan="1">227</td></tr><tr><td align="center" colspan="12" rowspan="1"><hr></hr></td></tr><tr><td align="left" rowspan="3" colspan="1">trnG-UCC (LSC)</td><td align="center" rowspan="1" colspan="1">Exon I</td><td align="center" rowspan="1" colspan="1">23</td><td align="center" rowspan="1" colspan="1">23</td><td align="center" rowspan="1" colspan="1">23</td><td align="center" rowspan="1" colspan="1">23</td><td align="center" rowspan="1" colspan="1">23</td><td align="center" rowspan="1" colspan="1">23</td><td align="center" rowspan="1" colspan="1">23</td><td align="center" rowspan="1" colspan="1">23</td><td align="center" rowspan="1" colspan="1">23</td><td align="center" rowspan="1" colspan="1">23</td></tr><tr><td align="center" rowspan="1" colspan="1">Intron I</td><td align="center" rowspan="1" colspan="1">692</td><td align="center" rowspan="1" colspan="1">692</td><td align="center" rowspan="1" colspan="1">694</td><td align="center" rowspan="1" colspan="1">692</td><td align="center" rowspan="1" colspan="1">692</td><td align="center" rowspan="1" colspan="1">690</td><td align="center" rowspan="1" colspan="1">691</td><td align="center" rowspan="1" colspan="1">701</td><td align="center" rowspan="1" colspan="1">695</td><td align="center" rowspan="1" colspan="1">692</td></tr><tr><td align="center" rowspan="1" colspan="1">Exon II</td><td align="center" rowspan="1" colspan="1">48</td><td align="center" rowspan="1" colspan="1">48</td><td align="center" rowspan="1" colspan="1">48</td><td align="center" rowspan="1" colspan="1">48</td><td align="center" rowspan="1" colspan="1">48</td><td align="center" rowspan="1" colspan="1">48</td><td align="center" rowspan="1" colspan="1">48</td><td align="center" rowspan="1" colspan="1">37</td><td align="center" rowspan="1" colspan="1">48</td><td align="center" rowspan="1" colspan="1">48</td></tr><tr><td align="center" colspan="12" rowspan="1"><hr></hr></td></tr><tr><td align="left" rowspan="3" colspan="1">atpF (LSC)</td><td align="center" rowspan="1" colspan="1">Exon I</td><td align="center" rowspan="1" colspan="1">145</td><td align="center" rowspan="1" colspan="1">145</td><td align="center" rowspan="1" colspan="1">145</td><td align="center" rowspan="1" colspan="1">145</td><td align="center" rowspan="1" colspan="1">145</td><td align="center" rowspan="1" colspan="1">145</td><td align="center" rowspan="1" colspan="1">145</td><td align="center" rowspan="1" colspan="1">144</td><td align="center" rowspan="1" colspan="1">144</td><td align="center" rowspan="1" colspan="1">145</td></tr><tr><td align="center" rowspan="1" colspan="1">Intron I</td><td align="center" rowspan="1" colspan="1">715</td><td align="center" rowspan="1" colspan="1">693</td><td align="center" rowspan="1" colspan="1">700</td><td align="center" rowspan="1" colspan="1">695</td><td align="center" rowspan="1" colspan="1">695</td><td align="center" rowspan="1" colspan="1">692</td><td align="center" rowspan="1" colspan="1">692</td><td align="center" rowspan="1" colspan="1">693</td><td align="center" rowspan="1" colspan="1">686</td><td align="center" rowspan="1" colspan="1">693</td></tr><tr><td align="center" rowspan="1" colspan="1">Exon II</td><td align="center" rowspan="1" colspan="1">410</td><td align="center" rowspan="1" colspan="1">410</td><td align="center" rowspan="1" colspan="1">410</td><td align="center" rowspan="1" colspan="1">410</td><td align="center" rowspan="1" colspan="1">410</td><td align="center" rowspan="1" colspan="1">410</td><td align="center" rowspan="1" colspan="1">410</td><td align="center" rowspan="1" colspan="1">411</td><td align="center" rowspan="1" colspan="1">411</td><td align="center" rowspan="1" colspan="1">410</td></tr><tr><td align="center" colspan="12" rowspan="1"><hr></hr></td></tr><tr><td align="left" rowspan="3" colspan="1">rpoC1 (LSC)</td><td align="center" rowspan="1" colspan="1">Exon I</td><td align="center" rowspan="1" colspan="1">432</td><td align="center" rowspan="1" colspan="1">453</td><td align="center" rowspan="1" colspan="1">453</td><td align="center" rowspan="1" colspan="1">453</td><td align="center" rowspan="1" colspan="1">453</td><td align="center" rowspan="1" colspan="1">432</td><td align="center" rowspan="1" colspan="1">453</td><td align="center" rowspan="1" colspan="1">453</td><td align="center" rowspan="1" colspan="1">453</td><td align="center" rowspan="1" colspan="1">453</td></tr><tr><td align="center" rowspan="1" colspan="1">Intron I</td><td align="center" rowspan="1" colspan="1">737</td><td align="center" rowspan="1" colspan="1">742</td><td align="center" rowspan="1" colspan="1">737</td><td align="center" rowspan="1" colspan="1">737</td><td align="center" rowspan="1" colspan="1">737</td><td align="center" rowspan="1" colspan="1">709</td><td align="center" rowspan="1" colspan="1">733</td><td align="center" rowspan="1" colspan="1">737</td><td align="center" rowspan="1" colspan="1">737</td><td align="center" rowspan="1" colspan="1">737</td></tr><tr><td align="center" rowspan="1" colspan="1">Exon II</td><td align="center" rowspan="1" colspan="1">1614</td><td align="center" rowspan="1" colspan="1">1614</td><td align="center" rowspan="1" colspan="1">1614</td><td align="center" rowspan="1" colspan="1">1614</td><td align="center" rowspan="1" colspan="1">1614</td><td align="center" rowspan="1" colspan="1">1614</td><td align="center" rowspan="1" colspan="1">1623</td><td align="center" rowspan="1" colspan="1">1614</td><td align="center" rowspan="1" colspan="1">1614</td><td align="center" rowspan="1" colspan="1">1614</td></tr><tr><td align="center" colspan="12" rowspan="1"><hr></hr></td></tr><tr><td align="left" rowspan="5" colspan="1">ycf3 (LSC)</td><td align="center" rowspan="1" colspan="1">Exon I</td><td align="center" rowspan="1" colspan="1">124</td><td align="center" rowspan="1" colspan="1">124</td><td align="center" rowspan="1" colspan="1">124</td><td align="center" rowspan="1" colspan="1">124</td><td align="center" rowspan="1" colspan="1">124</td><td align="center" rowspan="1" colspan="1">124</td><td align="center" rowspan="1" colspan="1">124</td><td align="center" rowspan="1" colspan="1">124</td><td align="center" rowspan="1" colspan="1">124</td><td align="center" rowspan="1" colspan="1">124</td></tr><tr><td align="center" rowspan="1" colspan="1">Intron I</td><td align="center" rowspan="1" colspan="1">739</td><td align="center" rowspan="1" colspan="1">742</td><td align="center" rowspan="1" colspan="1">740</td><td align="center" rowspan="1" colspan="1">739</td><td align="center" rowspan="1" colspan="1">738</td><td align="center" rowspan="1" colspan="1">731</td><td align="center" rowspan="1" colspan="1">735</td><td align="center" rowspan="1" colspan="1">730</td><td align="center" rowspan="1" colspan="1">729</td><td align="center" rowspan="1" colspan="1">727</td></tr><tr><td align="center" rowspan="1" colspan="1">Exon II</td><td align="center" rowspan="1" colspan="1">230</td><td align="center" rowspan="1" colspan="1">230</td><td align="center" rowspan="1" colspan="1">230</td><td align="center" rowspan="1" colspan="1">230</td><td align="center" rowspan="1" colspan="1">230</td><td align="center" rowspan="1" colspan="1">230</td><td align="center" rowspan="1" colspan="1">230</td><td align="center" rowspan="1" colspan="1">230</td><td align="center" rowspan="1" colspan="1">230</td><td align="center" rowspan="1" colspan="1">230</td></tr><tr><td align="center" rowspan="1" colspan="1">Intron II</td><td align="center" rowspan="1" colspan="1">763</td><td align="center" rowspan="1" colspan="1">744</td><td align="center" rowspan="1" colspan="1">753</td><td align="center" rowspan="1" colspan="1">783</td><td align="center" rowspan="1" colspan="1">783</td><td align="center" rowspan="1" colspan="1">779</td><td align="center" rowspan="1" colspan="1">781</td><td align="center" rowspan="1" colspan="1">750</td><td align="center" rowspan="1" colspan="1">750</td><td align="center" rowspan="1" colspan="1">750</td></tr><tr><td align="center" rowspan="1" colspan="1">Exon III</td><td align="center" rowspan="1" colspan="1">153</td><td align="center" rowspan="1" colspan="1">153</td><td align="center" rowspan="1" colspan="1">159</td><td align="center" rowspan="1" colspan="1">153</td><td align="center" rowspan="1" colspan="1">153</td><td align="center" rowspan="1" colspan="1">153</td><td align="center" rowspan="1" colspan="1">153</td><td align="center" rowspan="1" colspan="1">153</td><td align="center" rowspan="1" colspan="1">153</td><td align="center" rowspan="1" colspan="1">153</td></tr><tr><td align="center" colspan="12" rowspan="1"><hr></hr></td></tr><tr><td align="left" rowspan="3" colspan="1">trnL-UAA (LSC)</td><td align="center" rowspan="1" colspan="1">Exon I</td><td align="center" rowspan="1" colspan="1">35</td><td align="center" rowspan="1" colspan="1">35</td><td align="center" rowspan="1" colspan="1">35</td><td align="center" rowspan="1" colspan="1">35</td><td align="center" rowspan="1" colspan="1">35</td><td align="center" rowspan="1" colspan="1">35</td><td align="center" rowspan="1" colspan="1">35</td><td align="center" rowspan="1" colspan="1">37</td><td align="center" rowspan="1" colspan="1">35</td><td align="center" rowspan="1" colspan="1">35</td></tr><tr><td align="center" rowspan="1" colspan="1">Intron I</td><td align="center" rowspan="1" colspan="1">497</td><td align="center" rowspan="1" colspan="1">426</td><td align="center" rowspan="1" colspan="1">501</td><td align="center" rowspan="1" colspan="1">503</td><td align="center" rowspan="1" colspan="1">503</td><td align="center" rowspan="1" colspan="1">497</td><td align="center" rowspan="1" colspan="1">498</td><td align="center" rowspan="1" colspan="1">502</td><td align="center" rowspan="1" colspan="1">497</td><td align="center" rowspan="1" colspan="1">497</td></tr><tr><td align="center" rowspan="1" colspan="1">Exon II</td><td align="center" rowspan="1" colspan="1">50</td><td align="center" rowspan="1" colspan="1">50</td><td align="center" rowspan="1" colspan="1">50</td><td align="center" rowspan="1" colspan="1">50</td><td align="center" rowspan="1" colspan="1">50</td><td align="center" rowspan="1" colspan="1">50</td><td align="center" rowspan="1" colspan="1">50</td><td align="center" rowspan="1" colspan="1">50</td><td align="center" rowspan="1" colspan="1">50</td><td align="center" rowspan="1" colspan="1">50</td></tr><tr><td align="center" colspan="12" rowspan="1"><hr></hr></td></tr><tr><td align="left" rowspan="3" colspan="1">trnV-UAC (LSC)</td><td align="center" rowspan="1" colspan="1">Exon I</td><td align="center" rowspan="1" colspan="1">38</td><td align="center" rowspan="1" colspan="1">38</td><td align="center" rowspan="1" colspan="1">38</td><td align="center" rowspan="1" colspan="1">38</td><td align="center" rowspan="1" colspan="1">38</td><td align="center" rowspan="1" colspan="1">38</td><td align="center" rowspan="1" colspan="1">38</td><td align="center" rowspan="1" colspan="1">38</td><td align="center" rowspan="1" colspan="1">38</td><td align="center" rowspan="1" colspan="1">38</td></tr><tr><td align="center" rowspan="1" colspan="1">Intron I</td><td align="center" rowspan="1" colspan="1">572</td><td align="center" rowspan="1" colspan="1">575</td><td align="center" rowspan="1" colspan="1">569</td><td align="center" rowspan="1" colspan="1">571</td><td align="center" rowspan="1" colspan="1">571</td><td align="center" rowspan="1" colspan="1">572</td><td align="center" rowspan="1" colspan="1">573</td><td align="center" rowspan="1" colspan="1">569</td><td align="center" rowspan="1" colspan="1">571</td><td align="center" rowspan="1" colspan="1">571</td></tr><tr><td align="center" rowspan="1" colspan="1">Exon II</td><td align="center" rowspan="1" colspan="1">35</td><td align="center" rowspan="1" colspan="1">35</td><td align="center" rowspan="1" colspan="1">37</td><td align="center" rowspan="1" colspan="1">35</td><td align="center" rowspan="1" colspan="1">35</td><td align="center" rowspan="1" colspan="1">35</td><td align="center" rowspan="1" colspan="1">35</td><td align="center" rowspan="1" colspan="1">37</td><td align="center" rowspan="1" colspan="1">35</td><td align="center" rowspan="1" colspan="1">35</td></tr><tr><td align="center" colspan="12" rowspan="1"><hr></hr></td></tr><tr><td align="left" rowspan="5" colspan="1">rps12<sup>*</sup></td><td align="center" rowspan="1" colspan="1">Exon I</td><td align="center" rowspan="1" colspan="1">114</td><td align="center" rowspan="1" colspan="1">114</td><td align="center" rowspan="1" colspan="1">114</td><td align="center" rowspan="1" colspan="1">114</td><td align="center" rowspan="1" colspan="1">114</td><td align="center" rowspan="1" colspan="1">114</td><td align="center" rowspan="1" colspan="1">114</td><td align="center" rowspan="1" colspan="1">114</td><td align="center" rowspan="1" colspan="1">114</td><td align="center" rowspan="1" colspan="1">114</td></tr><tr><td align="center" rowspan="1" colspan="1">Intron I</td><td align="center" rowspan="1" colspan="1">—</td><td align="center" rowspan="1" colspan="1">—</td><td align="center" rowspan="1" colspan="1">—</td><td align="center" rowspan="1" colspan="1">—</td><td align="center" rowspan="1" colspan="1">—</td><td align="center" rowspan="1" colspan="1">—</td><td align="center" rowspan="1" colspan="1">—</td><td align="center" rowspan="1" colspan="1">—</td><td align="center" rowspan="1" colspan="1">—</td><td align="center" rowspan="1" colspan="1">—</td></tr><tr><td align="center" rowspan="1" colspan="1">Exon II</td><td align="center" rowspan="1" colspan="1">232</td><td align="center" rowspan="1" colspan="1">232</td><td align="center" rowspan="1" colspan="1">232</td><td align="center" rowspan="1" colspan="1">232</td><td align="center" rowspan="1" colspan="1">232</td><td align="center" rowspan="1" colspan="1">232</td><td align="center" rowspan="1" colspan="1">232</td><td align="center" rowspan="1" colspan="1">232</td><td align="center" rowspan="1" colspan="1">232</td><td align="center" rowspan="1" colspan="1">232</td></tr><tr><td align="center" rowspan="1" colspan="1">Intron II</td><td align="center" rowspan="1" colspan="1">535</td><td align="center" rowspan="1" colspan="1">536</td><td align="center" rowspan="1" colspan="1">536</td><td align="center" rowspan="1" colspan="1">536</td><td align="center" rowspan="1" colspan="1">536</td><td align="center" rowspan="1" colspan="1">536</td><td align="center" rowspan="1" colspan="1">536</td><td align="center" rowspan="1" colspan="1">536</td><td align="center" rowspan="1" colspan="1">536</td><td align="center" rowspan="1" colspan="1">536</td></tr><tr><td align="center" rowspan="1" colspan="1">Exon III</td><td align="center" rowspan="1" colspan="1">26</td><td align="center" rowspan="1" colspan="1">26</td><td align="center" rowspan="1" colspan="1">26</td><td align="center" rowspan="1" colspan="1">26</td><td align="center" rowspan="1" colspan="1">26</td><td align="center" rowspan="1" colspan="1">26</td><td align="center" rowspan="1" colspan="1">26</td><td align="center" rowspan="1" colspan="1">26</td><td align="center" rowspan="1" colspan="1">26</td><td align="center" rowspan="1" colspan="1">26</td></tr><tr><td align="center" colspan="12" rowspan="1"><hr></hr></td></tr><tr><td align="left" rowspan="5" colspan="1">clpP (LSC)</td><td align="center" rowspan="1" colspan="1">Exon I</td><td align="center" rowspan="1" colspan="1">71</td><td align="center" rowspan="1" colspan="1">71</td><td align="center" rowspan="1" colspan="1">71</td><td align="center" rowspan="1" colspan="1">71</td><td align="center" rowspan="1" colspan="1">71</td><td align="center" rowspan="1" colspan="1">71</td><td align="center" rowspan="1" colspan="1">71</td><td align="center" rowspan="1" colspan="1">71</td><td align="center" rowspan="1" colspan="1">71</td><td align="center" rowspan="1" colspan="1">71</td></tr><tr><td align="center" rowspan="1" colspan="1">Intron I</td><td align="center" rowspan="1" colspan="1">799</td><td align="center" rowspan="1" colspan="1">811</td><td align="center" rowspan="1" colspan="1">792</td><td align="center" rowspan="1" colspan="1">807</td><td align="center" rowspan="1" colspan="1">807</td><td align="center" rowspan="1" colspan="1">789</td><td align="center" rowspan="1" colspan="1">789</td><td align="center" rowspan="1" colspan="1">789</td><td align="center" rowspan="1" colspan="1">798</td><td align="center" rowspan="1" colspan="1">789</td></tr><tr><td align="center" rowspan="1" colspan="1">Exon II</td><td align="center" rowspan="1" colspan="1">292</td><td align="center" rowspan="1" colspan="1">292</td><td align="center" rowspan="1" colspan="1">292</td><td align="center" rowspan="1" colspan="1">292</td><td align="center" rowspan="1" colspan="1">292</td><td align="center" rowspan="1" colspan="1">292</td><td align="center" rowspan="1" colspan="1">292</td><td align="center" rowspan="1" colspan="1">292</td><td align="center" rowspan="1" colspan="1">292</td><td align="center" rowspan="1" colspan="1">292</td></tr><tr><td align="center" rowspan="1" colspan="1">Intron II</td><td align="center" rowspan="1" colspan="1">622</td><td align="center" rowspan="1" colspan="1">626</td><td align="center" rowspan="1" colspan="1">624</td><td align="center" rowspan="1" colspan="1">637</td><td align="center" rowspan="1" colspan="1">637</td><td align="center" rowspan="1" colspan="1">634</td><td align="center" rowspan="1" colspan="1">631</td><td align="center" rowspan="1" colspan="1">625</td><td align="center" rowspan="1" colspan="1">617</td><td align="center" rowspan="1" colspan="1">620</td></tr><tr><td align="center" rowspan="1" colspan="1">Exon III</td><td align="center" rowspan="1" colspan="1">228</td><td align="center" rowspan="1" colspan="1">228</td><td align="center" rowspan="1" colspan="1">234</td><td align="center" rowspan="1" colspan="1">228</td><td align="center" rowspan="1" colspan="1">228</td><td align="center" rowspan="1" colspan="1">228</td><td align="center" rowspan="1" colspan="1">228</td><td align="center" rowspan="1" colspan="1">234</td><td align="center" rowspan="1" colspan="1">258</td><td align="center" rowspan="1" colspan="1">234</td></tr><tr><td align="center" colspan="12" rowspan="1"><hr></hr></td></tr><tr><td align="left" rowspan="3" colspan="1">petB (LSC)</td><td align="center" rowspan="1" colspan="1">Exon I</td><td align="center" rowspan="1" colspan="1">6</td><td align="center" rowspan="1" colspan="1">6</td><td align="center" rowspan="1" colspan="1">6</td><td align="center" rowspan="1" colspan="1">6</td><td align="center" rowspan="1" colspan="1">6</td><td align="center" rowspan="1" colspan="1">6</td><td align="center" rowspan="1" colspan="1">6</td><td align="center" rowspan="1" colspan="1">6</td><td align="center" rowspan="1" colspan="1">6</td><td align="center" rowspan="1" colspan="1">6</td></tr><tr><td align="center" rowspan="1" colspan="1">Intron I</td><td align="center" rowspan="1" colspan="1">759</td><td align="center" rowspan="1" colspan="1">755</td><td align="center" rowspan="1" colspan="1">746</td><td align="center" rowspan="1" colspan="1">753</td><td align="center" rowspan="1" colspan="1">753</td><td align="center" rowspan="1" colspan="1">753</td><td align="center" rowspan="1" colspan="1">753</td><td align="center" rowspan="1" colspan="1">747</td><td align="center" rowspan="1" colspan="1">747</td><td align="center" rowspan="1" colspan="1">747</td></tr><tr><td align="center" rowspan="1" colspan="1">Exon II</td><td align="center" rowspan="1" colspan="1">642</td><td align="center" rowspan="1" colspan="1">642</td><td align="center" rowspan="1" colspan="1">642</td><td align="center" rowspan="1" colspan="1">642</td><td align="center" rowspan="1" colspan="1">642</td><td align="center" rowspan="1" colspan="1">642</td><td align="center" rowspan="1" colspan="1">642</td><td align="center" rowspan="1" colspan="1">642</td><td align="center" rowspan="1" colspan="1">642</td><td align="center" rowspan="1" colspan="1">642</td></tr><tr><td align="center" colspan="12" rowspan="1"><hr></hr></td></tr><tr><td align="left" rowspan="3" colspan="1">petD (LSC)</td><td align="center" rowspan="1" colspan="1">Exon I</td><td align="center" rowspan="1" colspan="1">8</td><td align="center" rowspan="1" colspan="1">8</td><td align="center" rowspan="1" colspan="1">9</td><td align="center" rowspan="1" colspan="1">8</td><td align="center" rowspan="1" colspan="1">8</td><td align="center" rowspan="1" colspan="1">8</td><td align="center" rowspan="1" colspan="1">8</td><td align="center" rowspan="1" colspan="1">6</td><td align="center" rowspan="1" colspan="1">8</td><td align="center" rowspan="1" colspan="1">8</td></tr><tr><td align="center" rowspan="1" colspan="1">Intron I</td><td align="center" rowspan="1" colspan="1">742</td><td align="center" rowspan="1" colspan="1">742</td><td align="center" rowspan="1" colspan="1">748</td><td align="center" rowspan="1" colspan="1">742</td><td align="center" rowspan="1" colspan="1">742</td><td align="center" rowspan="1" colspan="1">742</td><td align="center" rowspan="1" colspan="1">742</td><td align="center" rowspan="1" colspan="1">739</td><td align="center" rowspan="1" colspan="1">738</td><td align="center" rowspan="1" colspan="1">739</td></tr><tr><td align="center" rowspan="1" colspan="1">Exon II</td><td align="center" rowspan="1" colspan="1">475</td><td align="center" rowspan="1" colspan="1">475</td><td align="center" rowspan="1" colspan="1">474</td><td align="center" rowspan="1" colspan="1">475</td><td align="center" rowspan="1" colspan="1">475</td><td align="center" rowspan="1" colspan="1">475</td><td align="center" rowspan="1" colspan="1">475</td><td align="center" rowspan="1" colspan="1">477</td><td align="center" rowspan="1" colspan="1">475</td><td align="center" rowspan="1" colspan="1">475</td></tr><tr><td align="center" colspan="12" rowspan="1"><hr></hr></td></tr><tr><td align="left" rowspan="3" colspan="1">rpl16 (LSC)</td><td align="center" rowspan="1" colspan="1">Exon I</td><td align="center" rowspan="1" colspan="1">9</td><td align="center" rowspan="1" colspan="1">9</td><td align="center" rowspan="1" colspan="1">9</td><td align="center" rowspan="1" colspan="1">9</td><td align="center" rowspan="1" colspan="1">9</td><td align="center" rowspan="1" colspan="1">9</td><td align="center" rowspan="1" colspan="1">9</td><td align="center" rowspan="1" colspan="1">9</td><td align="center" rowspan="1" colspan="1">9</td><td align="center" rowspan="1" colspan="1">9</td></tr><tr><td align="center" rowspan="1" colspan="1">Intron I</td><td align="center" rowspan="1" colspan="1">1019</td><td align="center" rowspan="1" colspan="1">1026</td><td align="center" rowspan="1" colspan="1">1025</td><td align="center" rowspan="1" colspan="1">1020</td><td align="center" rowspan="1" colspan="1">1020</td><td align="center" rowspan="1" colspan="1">1021</td><td align="center" rowspan="1" colspan="1">1020</td><td align="center" rowspan="1" colspan="1">1014</td><td align="center" rowspan="1" colspan="1">1018</td><td align="center" rowspan="1" colspan="1">1014</td></tr><tr><td align="center" rowspan="1" colspan="1">Exon II</td><td align="center" rowspan="1" colspan="1">396</td><td align="center" rowspan="1" colspan="1">396</td><td align="center" rowspan="1" colspan="1">396</td><td align="center" rowspan="1" colspan="1">396</td><td align="center" rowspan="1" colspan="1">396</td><td align="center" rowspan="1" colspan="1">396</td><td align="center" rowspan="1" colspan="1">396</td><td align="center" rowspan="1" colspan="1">396</td><td align="center" rowspan="1" colspan="1">396</td><td align="center" rowspan="1" colspan="1">396</td></tr><tr><td align="center" colspan="12" rowspan="1"><hr></hr></td></tr><tr><td align="left" rowspan="3" colspan="1">rpl2 (IR)</td><td align="center" rowspan="1" colspan="1">Exon I</td><td align="center" rowspan="1" colspan="1">391</td><td align="center" rowspan="1" colspan="1">391</td><td align="center" rowspan="1" colspan="1">393</td><td align="center" rowspan="1" colspan="1">391</td><td align="center" rowspan="1" colspan="1">391</td><td align="center" rowspan="1" colspan="1">391</td><td align="center" rowspan="1" colspan="1">391</td><td align="center" rowspan="1" colspan="1">390</td><td align="center" rowspan="1" colspan="1">391</td><td align="center" rowspan="1" colspan="1">391</td></tr><tr><td align="center" rowspan="1" colspan="1">Intron I</td><td align="center" rowspan="1" colspan="1">664</td><td align="center" rowspan="1" colspan="1">665</td><td align="center" rowspan="1" colspan="1">669</td><td align="center" rowspan="1" colspan="1">666</td><td align="center" rowspan="1" colspan="1">666</td><td align="center" rowspan="1" colspan="1">666</td><td align="center" rowspan="1" colspan="1">666</td><td align="center" rowspan="1" colspan="1">666</td><td align="center" rowspan="1" colspan="1">666</td><td align="center" rowspan="1" colspan="1">666</td></tr><tr><td align="center" rowspan="1" colspan="1">Exon II</td><td align="center" rowspan="1" colspan="1">434</td><td align="center" rowspan="1" colspan="1">434</td><td align="center" rowspan="1" colspan="1">429</td><td align="center" rowspan="1" colspan="1">434</td><td align="center" rowspan="1" colspan="1">434</td><td align="center" rowspan="1" colspan="1">434</td><td align="center" rowspan="1" colspan="1">434</td><td align="center" rowspan="1" colspan="1">435</td><td align="center" rowspan="1" colspan="1">434</td><td align="center" rowspan="1" colspan="1">434</td></tr><tr><td align="center" colspan="12" rowspan="1"><hr></hr></td></tr><tr><td align="left" rowspan="3" colspan="1">ndhB (IR)</td><td align="center" rowspan="1" colspan="1">Exon I</td><td align="center" rowspan="1" colspan="1">777</td><td align="center" rowspan="1" colspan="1">777</td><td align="center" rowspan="1" colspan="1">777</td><td align="center" rowspan="1" colspan="1">777</td><td align="center" rowspan="1" colspan="1">777</td><td align="center" rowspan="1" colspan="1">777</td><td align="center" rowspan="1" colspan="1">777</td><td align="center" rowspan="1" colspan="1">777</td><td align="center" rowspan="1" colspan="1">777</td><td align="center" rowspan="1" colspan="1">777</td></tr><tr><td align="center" rowspan="1" colspan="1">Intron I</td><td align="center" rowspan="1" colspan="1">679</td><td align="center" rowspan="1" colspan="1">679</td><td align="center" rowspan="1" colspan="1">679</td><td align="center" rowspan="1" colspan="1">679</td><td align="center" rowspan="1" colspan="1">679</td><td align="center" rowspan="1" colspan="1">679</td><td align="center" rowspan="1" colspan="1">679</td><td align="center" rowspan="1" colspan="1">679</td><td align="center" rowspan="1" colspan="1">679</td><td align="center" rowspan="1" colspan="1">679</td></tr><tr><td align="center" rowspan="1" colspan="1">Exon II</td><td align="center" rowspan="1" colspan="1">756</td><td align="center" rowspan="1" colspan="1">756</td><td align="center" rowspan="1" colspan="1">756</td><td align="center" rowspan="1" colspan="1">756</td><td align="center" rowspan="1" colspan="1">756</td><td align="center" rowspan="1" colspan="1">756</td><td align="center" rowspan="1" colspan="1">756</td><td align="center" rowspan="1" colspan="1">756</td><td align="center" rowspan="1" colspan="1">756</td><td align="center" rowspan="1" colspan="1">756</td></tr><tr><td align="center" colspan="12" rowspan="1"><hr></hr></td></tr><tr><td align="left" rowspan="3" colspan="1">trnI-GAU (IR)</td><td align="center" rowspan="1" colspan="1">Exon I</td><td align="center" rowspan="1" colspan="1">37</td><td align="center" rowspan="1" colspan="1">37</td><td align="center" rowspan="1" colspan="1">42</td><td align="center" rowspan="1" colspan="1">37</td><td align="center" rowspan="1" colspan="1">37</td><td align="center" rowspan="1" colspan="1">37</td><td align="center" rowspan="1" colspan="1">37</td><td align="center" rowspan="1" colspan="1">42</td><td align="center" rowspan="1" colspan="1">37</td><td align="center" rowspan="1" colspan="1">37</td></tr><tr><td align="center" rowspan="1" colspan="1">Intron I</td><td align="center" rowspan="1" colspan="1">717</td><td align="center" rowspan="1" colspan="1">722</td><td align="center" rowspan="1" colspan="1">717</td><td align="center" rowspan="1" colspan="1">707</td><td align="center" rowspan="1" colspan="1">707</td><td align="center" rowspan="1" colspan="1">716</td><td align="center" rowspan="1" colspan="1">716</td><td align="center" rowspan="1" colspan="1">717</td><td align="center" rowspan="1" colspan="1">722</td><td align="center" rowspan="1" colspan="1">722</td></tr><tr><td align="center" rowspan="1" colspan="1">Exon II</td><td align="center" rowspan="1" colspan="1">34</td><td align="center" rowspan="1" colspan="1">35</td><td align="center" rowspan="1" colspan="1">35</td><td align="center" rowspan="1" colspan="1">35</td><td align="center" rowspan="1" colspan="1">35</td><td align="center" rowspan="1" colspan="1">35</td><td align="center" rowspan="1" colspan="1">35</td><td align="center" rowspan="1" colspan="1">35</td><td align="center" rowspan="1" colspan="1">35</td><td align="center" rowspan="1" colspan="1">35</td></tr><tr><td align="center" colspan="12" rowspan="1"><hr></hr></td></tr><tr><td align="left" rowspan="3" colspan="1">trnA-UGC (IR)</td><td align="center" rowspan="1" colspan="1">Exon I</td><td align="center" rowspan="1" colspan="1">38</td><td align="center" rowspan="1" colspan="1">38</td><td align="center" rowspan="1" colspan="1">38</td><td align="center" rowspan="1" colspan="1">38</td><td align="center" rowspan="1" colspan="1">38</td><td align="center" rowspan="1" colspan="1">38</td><td align="center" rowspan="1" colspan="1">38</td><td align="center" rowspan="1" colspan="1">38</td><td align="center" rowspan="1" colspan="1">38</td><td align="center" rowspan="1" colspan="1">38</td></tr><tr><td align="center" rowspan="1" colspan="1">Intron I</td><td align="center" rowspan="1" colspan="1">681</td><td align="center" rowspan="1" colspan="1">811</td><td align="center" rowspan="1" colspan="1">811</td><td align="center" rowspan="1" colspan="1">709</td><td align="center" rowspan="1" colspan="1">709</td><td align="center" rowspan="1" colspan="1">709</td><td align="center" rowspan="1" colspan="1">709</td><td align="center" rowspan="1" colspan="1">811</td><td align="center" rowspan="1" colspan="1">811</td><td align="center" rowspan="1" colspan="1">811</td></tr><tr><td align="center" rowspan="1" colspan="1">Exon II</td><td align="center" rowspan="1" colspan="1">35</td><td align="center" rowspan="1" colspan="1">35</td><td align="center" rowspan="1" colspan="1">35</td><td align="center" rowspan="1" colspan="1">35</td><td align="center" rowspan="1" colspan="1">35</td><td align="center" rowspan="1" colspan="1">35</td><td align="center" rowspan="1" colspan="1">35</td><td align="center" rowspan="1" colspan="1">35</td><td align="center" rowspan="1" colspan="1">35</td><td align="center" rowspan="1" colspan="1">35</td></tr><tr><td align="center" colspan="12" rowspan="1"><hr></hr></td></tr><tr><td align="left" rowspan="3" colspan="1">ndhA (SSC)</td><td align="center" rowspan="1" colspan="1">Exon I</td><td align="center" rowspan="1" colspan="1">553</td><td align="center" rowspan="1" colspan="1">553</td><td align="center" rowspan="1" colspan="1">552</td><td align="center" rowspan="1" colspan="1">553</td><td align="center" rowspan="1" colspan="1">553</td><td align="center" rowspan="1" colspan="1">553</td><td align="center" rowspan="1" colspan="1">553</td><td align="center" rowspan="1" colspan="1">552</td><td align="center" rowspan="1" colspan="1">553</td><td align="center" rowspan="1" colspan="1">553</td></tr><tr><td align="center" rowspan="1" colspan="1">Intron I</td><td align="center" rowspan="1" colspan="1">1150</td><td align="center" rowspan="1" colspan="1">1157</td><td align="center" rowspan="1" colspan="1">1154</td><td align="center" rowspan="1" colspan="1">1148</td><td align="center" rowspan="1" colspan="1">1148</td><td align="center" rowspan="1" colspan="1">1149</td><td align="center" rowspan="1" colspan="1">1148</td><td align="center" rowspan="1" colspan="1">1158</td><td align="center" rowspan="1" colspan="1">1133</td><td align="center" rowspan="1" colspan="1">1158</td></tr><tr><td align="center" rowspan="1" colspan="1">Exon II</td><td align="center" rowspan="1" colspan="1">539</td><td align="center" rowspan="1" colspan="1">539</td><td align="center" rowspan="1" colspan="1">537</td><td align="center" rowspan="1" colspan="1">539</td><td align="center" rowspan="1" colspan="1">539</td><td align="center" rowspan="1" colspan="1">539</td><td align="center" rowspan="1" colspan="1">539</td><td align="center" rowspan="1" colspan="1">540</td><td align="center" rowspan="1" colspan="1">539</td><td align="center" rowspan="1" colspan="1">539</td></tr></tbody></table><table-wrap-foot><fn><p><sup>*</sup>rps12 gene is dividing gene. The 3′-rps12 locates on the IR-region, while the 5′-rps12 locates on the LSC region.</p></fn><fn><p>ABE: <italic>Atropa belladonna</italic>, CAN: <italic>Capsicum annuum</italic>, DST: <italic>Datura stramonium</italic>, NSY: <italic>Nicotiana sylvestris</italic>, NTA: <italic>Nicotiana tabacum</italic>, NTO: <italic>Nicotiana tomentosiformis</italic>, NUN: <italic>Nicotiana undulata</italic>, SBU: <italic>Solanum bulbocastanum</italic>, SLY: <italic>Solanum lycopersicum</italic>, and STU: <italic>Solanum tuberosum. </italic></p></fn></table-wrap-foot></table-wrap><table-wrap id="tab3" orientation="portrait" position="float"><label>Table 3</label><caption><p>InDels in nucleotide sequences of 9 genes of ten solanaceous plastid genomes.</p></caption><table frame="hsides" rules="groups"><thead><tr><th align="left" rowspan="1" colspan="1">S. number</th><th align="center" rowspan="1" colspan="1">Gene<sup>abc</sup></th><th align="center" rowspan="1" colspan="1">Total number of InDels</th><th align="left" rowspan="1" colspan="1">InDel length (bp)</th></tr></thead><tbody><tr><td align="left" rowspan="1" colspan="1">1</td><td align="center" rowspan="1" colspan="1">accD<sup>a</sup></td><td align="center" rowspan="1" colspan="1">4</td><td align="left" rowspan="1" colspan="1">24, 9, 141, 6</td></tr><tr><td align="left" rowspan="1" colspan="1">2</td><td align="center" rowspan="1" colspan="1">clpP<sup>a</sup></td><td align="center" rowspan="1" colspan="1">24</td><td align="left" rowspan="1" colspan="1">8(I), 14(I), 13(I), 7(I), 1(I), 2-3(I), 7(I), 1–7(I), 3(I), 2(I), 3(I), 1–7(I), 1–3(I), 1(I), 1(I), 1(I), 1–5(I), 4–7(I), 1(I), 9(I), 1-2(I), 3(I), 5(I), 24–30</td></tr><tr><td align="left" rowspan="1" colspan="1">3</td><td align="center" rowspan="1" colspan="1">ndhA<sup>b</sup></td><td align="center" rowspan="1" colspan="1">14</td><td align="left" rowspan="1" colspan="1">9(I), 5-6(I), 3(I), 1(I), 9(I), 3(I), 4(I), 1–4(I), 1-2(I), 1–23(I), 1-2(I), 2(I), 1(I), 3(I)</td></tr><tr><td align="left" rowspan="1" colspan="1">4</td><td align="center" rowspan="1" colspan="1">rpl32<sup>b</sup></td><td align="center" rowspan="1" colspan="1">2</td><td align="left" rowspan="1" colspan="1"> 2-3, 4</td></tr><tr><td align="left" rowspan="1" colspan="1">5</td><td align="center" rowspan="1" colspan="1">rps16<sup>a</sup></td><td align="center" rowspan="1" colspan="1">11</td><td align="left" rowspan="1" colspan="1">1–38, 9(I), 1(I), 1(I), 5(I), 1-2(I), 5(I), 4(I), 6(I), 1(I), 9</td></tr><tr><td align="left" rowspan="1" colspan="1">6</td><td align="center" rowspan="1" colspan="1">sprA<sup>b</sup></td><td align="center" rowspan="1" colspan="1">2</td><td align="left" rowspan="1" colspan="1">109, 7</td></tr><tr><td align="left" rowspan="1" colspan="1">7</td><td align="center" rowspan="1" colspan="1">trnA-UGC<sup>c</sup></td><td align="center" rowspan="1" colspan="1">1</td><td align="left" rowspan="1" colspan="1">102–130</td></tr><tr><td align="left" rowspan="1" colspan="1">8</td><td align="center" rowspan="1" colspan="1">trnL-UAA<sup>a</sup></td><td align="center" rowspan="1" colspan="1">4</td><td align="left" rowspan="1" colspan="1">1, 6, 71, 4</td></tr><tr><td align="left" rowspan="1" colspan="1">9</td><td align="center" rowspan="1" colspan="1">ycf1<sup>b</sup></td><td align="center" rowspan="1" colspan="1">31</td><td align="left" rowspan="1" colspan="1">3, 18, 18, 21, 6, 6, 48, 9, 6, 6, 42, 3, 6, 30, 3, 15, 12–39, 18, 6, 9–36, 6, 6, 6, 9, 9, 12, 6, 6, 6, 57, 6</td></tr></tbody></table><table-wrap-foot><fn><p><sup>abc</sup>Location in different regions; <sup>a</sup>LSC, <sup>b</sup>SSC, and <sup>c</sup>IR; I: InDels present in introns.</p></fn></table-wrap-foot></table-wrap><table-wrap id="tab4" orientation="portrait" position="float"><label>Table 4</label><caption><p>InDels in amino acid sequences of 5 proteins of ten solanaceous plastid genomes.</p></caption><table frame="hsides" rules="groups"><thead><tr><th align="left" rowspan="1" colspan="1">S. number</th><th align="center" rowspan="1" colspan="1">Protein</th><th align="center" rowspan="1" colspan="1">Total number of InDels</th><th align="left" rowspan="1" colspan="1">InDel length (bp)</th></tr></thead><tbody><tr><td align="left" rowspan="1" colspan="1">1</td><td align="center" rowspan="1" colspan="1">accD</td><td align="center" rowspan="1" colspan="1">4</td><td align="left" rowspan="1" colspan="1">8, 3, 47, 2</td></tr><tr><td align="left" rowspan="1" colspan="1">2</td><td align="center" rowspan="1" colspan="1">clpP</td><td align="center" rowspan="1" colspan="1">2</td><td align="left" rowspan="1" colspan="1">2, 10</td></tr><tr><td align="left" rowspan="1" colspan="1">3</td><td align="center" rowspan="1" colspan="1">rpl32 </td><td align="center" rowspan="1" colspan="1">1</td><td align="left" rowspan="1" colspan="1">1-2</td></tr><tr><td align="left" rowspan="1" colspan="1">4</td><td align="center" rowspan="1" colspan="1">rps16</td><td align="center" rowspan="1" colspan="1">1</td><td align="left" rowspan="1" colspan="1">3</td></tr><tr><td align="left" rowspan="1" colspan="1">5</td><td align="center" rowspan="1" colspan="1">ycf1</td><td align="center" rowspan="1" colspan="1">29</td><td align="left" rowspan="1" colspan="1">1, 6, 6, 7, 2, 2, 7, 3, 2, 2, 14, 1–10, 1, 5, 4–13, 6, 2, 3–12, 2, 2, 2, 3, 3, 4, 2, 2, 2, 19, 2</td></tr></tbody></table></table-wrap></floats-group></pmc><affiliations><list><country><li>Inde</li></country></list><tree><country name="Inde"><noRegion><name sortKey="Kaur, Harpreet" sort="Kaur, Harpreet" uniqKey="Kaur H" first="Harpreet" last="Kaur">Harpreet Kaur</name></noRegion><name sortKey="Nagpal, Avinash Kaur" sort="Nagpal, Avinash Kaur" uniqKey="Nagpal A" first="Avinash Kaur" last="Nagpal">Avinash Kaur Nagpal</name><name sortKey="Singh, Bhupinder Pal" sort="Singh, Bhupinder Pal" uniqKey="Singh B" first="Bhupinder Pal" last="Singh">Bhupinder Pal Singh</name><name sortKey="Singh, Harpreet" sort="Singh, Harpreet" uniqKey="Singh H" first="Harpreet" last="Singh">Harpreet Singh</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
EXPLOR_STEP=$WICRI_ROOT/Wicri/Bois/explor/OrangerV1/Data/Pmc/Checkpoint
HfdSelect -h $EXPLOR_STEP/biblio.hfd -nk 000880 | SxmlIndent | more
Ou
HfdSelect -h $EXPLOR_AREA/Data/Pmc/Checkpoint/biblio.hfd -nk 000880 | SxmlIndent | more
Pour mettre un lien sur cette page dans le réseau Wicri
{{Explor lien
|wiki= Wicri/Bois
|area= OrangerV1
|flux= Pmc
|étape= Checkpoint
|type= RBID
|clé= PMC:4248371
|texte= Comparative Genomics of Ten Solanaceous Plastomes
}}
Pour générer des pages wiki
HfdIndexSelect -h $EXPLOR_AREA/Data/Pmc/Checkpoint/RBID.i -Sk "pubmed:25477958" \
| HfdSelect -Kh $EXPLOR_AREA/Data/Pmc/Checkpoint/biblio.hfd \
| NlmPubMed2Wicri -a OrangerV1
| This area was generated with Dilib version V0.6.25. |  |