Genome-Wide Analysis and Characterization of Aux/IAA Family Genes in Brassica rapa
Identifieur interne : 000167 ( Pmc/Checkpoint ); précédent : 000166; suivant : 000168Genome-Wide Analysis and Characterization of Aux/IAA Family Genes in Brassica rapa
Auteurs : Parameswari Paul ; Vignesh Dhandapani ; Jana Jeevan Rameneni ; Xiaonan Li ; Ganesan Sivanandhan ; Su Ryun Choi ; Wenxing Pang ; Subin Im ; Yong Pyo LimSource :
- PLoS ONE [ 1932-6203 ] ; 2016.
Abstract
Auxins are the key players in plant growth development involving leaf formation, phototropism, root, fruit and embryo development. Auxin/Indole-3-Acetic Acid (Aux/IAA) are early auxin response genes noted as transcriptional repressors in plant auxin signaling. However, many studies focus on Aux/ARF gene families and much less is known about the Aux/IAA gene family in
Url:
DOI: 10.1371/journal.pone.0151522
PubMed: 27049520
PubMed Central: 4822780
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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Genome-Wide Analysis and Characterization of Aux/IAA Family Genes in <italic>Brassica rapa</italic></title><author><name sortKey="Paul, Parameswari" sort="Paul, Parameswari" uniqKey="Paul P" first="Parameswari" last="Paul">Parameswari Paul</name><affiliation><nlm:aff id="aff001"></nlm:aff></affiliation></author><author><name sortKey="Dhandapani, Vignesh" sort="Dhandapani, Vignesh" uniqKey="Dhandapani V" first="Vignesh" last="Dhandapani">Vignesh Dhandapani</name><affiliation><nlm:aff id="aff001"></nlm:aff></affiliation></author><author><name sortKey="Rameneni, Jana Jeevan" sort="Rameneni, Jana Jeevan" uniqKey="Rameneni J" first="Jana Jeevan" last="Rameneni">Jana Jeevan Rameneni</name><affiliation><nlm:aff id="aff001"></nlm:aff></affiliation></author><author><name sortKey="Li, Xiaonan" sort="Li, Xiaonan" uniqKey="Li X" first="Xiaonan" last="Li">Xiaonan Li</name><affiliation><nlm:aff id="aff001"></nlm:aff></affiliation></author><author><name sortKey="Sivanandhan, Ganesan" sort="Sivanandhan, Ganesan" uniqKey="Sivanandhan G" first="Ganesan" last="Sivanandhan">Ganesan Sivanandhan</name><affiliation><nlm:aff id="aff001"></nlm:aff></affiliation></author><author><name sortKey="Choi, Su Ryun" sort="Choi, Su Ryun" uniqKey="Choi S" first="Su Ryun" last="Choi">Su Ryun Choi</name><affiliation><nlm:aff id="aff001"></nlm:aff></affiliation></author><author><name sortKey="Pang, Wenxing" sort="Pang, Wenxing" uniqKey="Pang W" first="Wenxing" last="Pang">Wenxing Pang</name><affiliation><nlm:aff id="aff001"></nlm:aff></affiliation></author><author><name sortKey="Im, Subin" sort="Im, Subin" uniqKey="Im S" first="Subin" last="Im">Subin Im</name><affiliation><nlm:aff id="aff001"></nlm:aff></affiliation></author><author><name sortKey="Lim, Yong Pyo" sort="Lim, Yong Pyo" uniqKey="Lim Y" first="Yong Pyo" last="Lim">Yong Pyo Lim</name><affiliation><nlm:aff id="aff001"></nlm:aff></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">27049520</idno><idno type="pmc">4822780</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4822780</idno><idno type="RBID">PMC:4822780</idno><idno type="doi">10.1371/journal.pone.0151522</idno><date when="2016">2016</date><idno type="wicri:Area/Pmc/Corpus">000387</idno><idno type="wicri:Area/Pmc/Curation">000386</idno><idno type="wicri:Area/Pmc/Checkpoint">000167</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Genome-Wide Analysis and Characterization of Aux/IAA Family Genes in <italic>Brassica rapa</italic></title><author><name sortKey="Paul, Parameswari" sort="Paul, Parameswari" uniqKey="Paul P" first="Parameswari" last="Paul">Parameswari Paul</name><affiliation><nlm:aff id="aff001"></nlm:aff></affiliation></author><author><name sortKey="Dhandapani, Vignesh" sort="Dhandapani, Vignesh" uniqKey="Dhandapani V" first="Vignesh" last="Dhandapani">Vignesh Dhandapani</name><affiliation><nlm:aff id="aff001"></nlm:aff></affiliation></author><author><name sortKey="Rameneni, Jana Jeevan" sort="Rameneni, Jana Jeevan" uniqKey="Rameneni J" first="Jana Jeevan" last="Rameneni">Jana Jeevan Rameneni</name><affiliation><nlm:aff id="aff001"></nlm:aff></affiliation></author><author><name sortKey="Li, Xiaonan" sort="Li, Xiaonan" uniqKey="Li X" first="Xiaonan" last="Li">Xiaonan Li</name><affiliation><nlm:aff id="aff001"></nlm:aff></affiliation></author><author><name sortKey="Sivanandhan, Ganesan" sort="Sivanandhan, Ganesan" uniqKey="Sivanandhan G" first="Ganesan" last="Sivanandhan">Ganesan Sivanandhan</name><affiliation><nlm:aff id="aff001"></nlm:aff></affiliation></author><author><name sortKey="Choi, Su Ryun" sort="Choi, Su Ryun" uniqKey="Choi S" first="Su Ryun" last="Choi">Su Ryun Choi</name><affiliation><nlm:aff id="aff001"></nlm:aff></affiliation></author><author><name sortKey="Pang, Wenxing" sort="Pang, Wenxing" uniqKey="Pang W" first="Wenxing" last="Pang">Wenxing Pang</name><affiliation><nlm:aff id="aff001"></nlm:aff></affiliation></author><author><name sortKey="Im, Subin" sort="Im, Subin" uniqKey="Im S" first="Subin" last="Im">Subin Im</name><affiliation><nlm:aff id="aff001"></nlm:aff></affiliation></author><author><name sortKey="Lim, Yong Pyo" sort="Lim, Yong Pyo" uniqKey="Lim Y" first="Yong Pyo" last="Lim">Yong Pyo Lim</name><affiliation><nlm:aff id="aff001"></nlm:aff></affiliation></author></analytic><series><title level="j">PLoS ONE</title><idno type="eISSN">1932-6203</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>Auxins are the key players in plant growth development involving leaf formation, phototropism, root, fruit and embryo development. Auxin/Indole-3-Acetic Acid (Aux/IAA) are early auxin response genes noted as transcriptional repressors in plant auxin signaling. However, many studies focus on Aux/ARF gene families and much less is known about the Aux/IAA gene family in <italic>Brassica rapa</italic> (<italic>B</italic>. <italic>rapa</italic>). Here we performed a comprehensive genome-wide analysis and identified 55 Aux/IAA genes in <italic>B</italic>. <italic>rapa</italic> using four conserved motifs of Aux/IAA family (PF02309). Chromosomal mapping of the <italic>B</italic>. <italic>rapa</italic> Aux/IAA (<italic>BrIAA</italic>) genes facilitated understanding cluster rearrangement of the crucifer building blocks in the genome. Phylogenetic analysis of <italic>BrIAA</italic> with <italic>Arabidopsis thaliana</italic>, <italic>Oryza sativa</italic> and <italic>Zea mays</italic> identified 51 sister pairs including 15 same species (<italic>BrIAA</italic>—<italic>BrIAA</italic>) and 36 cross species (<italic>BrIAA</italic>—<italic>AtIAA</italic>) <italic>IAA</italic> genes. Among the 55 <italic>BrIAA</italic> genes, expression of 43 and 45 genes were verified using Genebank <italic>B</italic>. <italic>rapa</italic> ESTs and in home developed microarray data from mature leaves of Chiifu and RcBr lines. Despite their huge morphological difference, tissue specific expression analysis of <italic>BrIAA</italic> genes between the parental lines Chiifu and RcBr showed that the genes followed a similar pattern of expression during leaf development and a different pattern during bud, flower and siliqua development stages. The response of the <italic>BrIAA</italic> genes to abiotic and auxin stress at different time intervals revealed their involvement in stress response. Single Nucleotide Polymorphisms between <italic>IAA</italic> genes of reference genome Chiifu and RcBr were focused and identified. Our study examines the scope of conservation and divergence of Aux/IAA genes and their structures in <italic>B</italic>. <italic>rapa</italic>. Analyzing the expression and structural variation between two parental lines will significantly contribute to functional genomics of <italic>Brassica</italic> crops and we belive our study would provide a foundation in understanding the Aux/IAA genes in <italic>B</italic>. <italic>rapa</italic>.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Hagen, H" uniqKey="Hagen H">H Hagen</name></author><author><name sortKey="Guilfoyle, T" uniqKey="Guilfoyle T">T Guilfoyle</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Jain, M" uniqKey="Jain M">M Jain</name></author><author><name sortKey="Kaur, N" uniqKey="Kaur N">N Kaur</name></author><author><name sortKey="Tyagi, Ak" uniqKey="Tyagi A">AK Tyagi</name></author><author><name sortKey="Khurana, Jp" uniqKey="Khurana J">JP Khurana</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Szemenyei, H" uniqKey="Szemenyei H">H Szemenyei</name></author><author><name sortKey="Hannon, M" uniqKey="Hannon M">M Hannon</name></author><author><name sortKey="Long, Ja" uniqKey="Long J">JA Long</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Dharmasiri, N" uniqKey="Dharmasiri N">N Dharmasiri</name></author><author><name sortKey="Dharmasiri, S" uniqKey="Dharmasiri S">S Dharmasiri</name></author><author><name sortKey="Estelle, M" uniqKey="Estelle M">M Estelle</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Overvoorde, Pj" uniqKey="Overvoorde P">PJ Overvoorde</name></author><author><name sortKey="Okushimaa, Y" uniqKey="Okushimaa Y">Y Okushimaa</name></author><author><name sortKey="Alonsob, Jm" uniqKey="Alonsob J">JM Alonsob</name></author><author><name sortKey="Chana, A" uniqKey="Chana A">A Chana</name></author><author><name sortKey="Changa, C" uniqKey="Changa C">C Changa</name></author><author><name sortKey="Eckerb, Jr" uniqKey="Eckerb J">JR Eckerb</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Walker, Jc" uniqKey="Walker J">JC Walker</name></author><author><name sortKey="Key, Jl" uniqKey="Key J">JL Key</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Theologis, A" uniqKey="Theologis A">A Theologis</name></author><author><name sortKey="Huynh, Tv" uniqKey="Huynh T">TV Huynh</name></author><author><name sortKey="Davis, Rw" uniqKey="Davis R">RW Davis</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Ainley, Wm" uniqKey="Ainley W">WM Ainley</name></author><author><name sortKey="Walker, Jc" uniqKey="Walker J">JC Walker</name></author><author><name sortKey="Nagao, Rt" uniqKey="Nagao R">RT Nagao</name></author><author><name sortKey="Key, Jl" uniqKey="Key J">JL Key</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Wang, X" uniqKey="Wang X">X Wang</name></author><author><name sortKey="Wang, H" uniqKey="Wang H">H Wang</name></author><author><name sortKey="Wang, J" uniqKey="Wang J">J Wang</name></author><author><name sortKey="Sun, R" uniqKey="Sun R">R Sun</name></author><author><name sortKey="Wu, J" uniqKey="Wu J">J Wu</name></author><author><name sortKey="Liu, S" uniqKey="Liu S">S Liu</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Dhandapani, V" uniqKey="Dhandapani V">V Dhandapani</name></author><author><name sortKey="Choi, Sr" uniqKey="Choi S">SR Choi</name></author><author><name sortKey="Paul, P" uniqKey="Paul P">P Paul</name></author><author><name sortKey="Kim, Yk" uniqKey="Kim Y">YK Kim</name></author><author><name sortKey="Ramchiary, N" uniqKey="Ramchiary N">N Ramchiary</name></author><author><name sortKey="Hur, Y" uniqKey="Hur Y">Y Hur</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Lee, Sc" uniqKey="Lee S">SC Lee</name></author><author><name sortKey="Lim, Mh" uniqKey="Lim M">MH Lim</name></author><author><name sortKey="Kim, Ja" uniqKey="Kim J">JA Kim</name></author><author><name sortKey="Lee, Si" uniqKey="Lee S">SI Lee</name></author><author><name sortKey="Kim, Js" uniqKey="Kim J">JS Kim</name></author><author><name sortKey="Jin, M" uniqKey="Jin M">M Jin</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Schranz, Me" uniqKey="Schranz M">ME Schranz</name></author><author><name sortKey="Lysak, Ma" uniqKey="Lysak M">MA Lysak</name></author><author><name sortKey="Mitchell Olds, T" uniqKey="Mitchell Olds T">T Mitchell-Olds</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Wu, J" uniqKey="Wu J">J Wu</name></author><author><name sortKey="Peng, Z" uniqKey="Peng Z">Z Peng</name></author><author><name sortKey="Liu, S" uniqKey="Liu S">S Liu</name></author><author><name sortKey="He, Y" uniqKey="He Y">Y He</name></author><author><name sortKey="Cheng, L" uniqKey="Cheng L">L Cheng</name></author><author><name sortKey="Kong, F" uniqKey="Kong F">F Kong</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Cakir, B" uniqKey="Cakir B">B Çakir</name></author><author><name sortKey="Kilickaya, O" uniqKey="Kilickaya O">O Kiliçkaya</name></author><author><name sortKey="Olcay, Ac" uniqKey="Olcay A">AC Olcay</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Abel, S" uniqKey="Abel S">S Abel</name></author><author><name sortKey="Oeller, Pw" uniqKey="Oeller P">PW Oeller</name></author><author><name sortKey="Theologis, A" uniqKey="Theologis A">A Theologis</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Muto, H" uniqKey="Muto H">H Muto</name></author><author><name sortKey="Watahiki, Mk" uniqKey="Watahiki M">MK Watahiki</name></author><author><name sortKey="Yamamoto, Kt" uniqKey="Yamamoto K">KT Yamamoto</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Audran Delalande, C" uniqKey="Audran Delalande C">C Audran-Delalande</name></author><author><name sortKey="Bassa, C" uniqKey="Bassa C">C Bassa</name></author><author><name sortKey="Mila, I" uniqKey="Mila I">I Mila</name></author><author><name sortKey="Regad, F" uniqKey="Regad F">F Regad</name></author><author><name sortKey="Zouine, M" uniqKey="Zouine M">M Zouine</name></author><author><name sortKey="Bouzayen, M" uniqKey="Bouzayen M">M Bouzayen</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Wang, Y" uniqKey="Wang Y">Y Wang</name></author><author><name sortKey="Deng, D" uniqKey="Deng D">D Deng</name></author><author><name sortKey="Bian, Y" uniqKey="Bian Y">Y Bian</name></author><author><name sortKey="Lv, Y" uniqKey="Lv Y">Y Lv</name></author><author><name sortKey="Xie, Q" uniqKey="Xie Q">Q Xie</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Ramchiary, N" uniqKey="Ramchiary N">N Ramchiary</name></author><author><name sortKey="Nguyen, Vd" uniqKey="Nguyen V">VD Nguyen</name></author><author><name sortKey="Li, X" uniqKey="Li X">X Li</name></author><author><name sortKey="Hong, Cp" uniqKey="Hong C">CP Hong</name></author><author><name sortKey="Dhandapani, V" uniqKey="Dhandapani V">V Dhandapani</name></author><author><name sortKey="Choi, Sr" uniqKey="Choi S">SR Choi</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Rinaldi, Ma" uniqKey="Rinaldi M">MA Rinaldi</name></author><author><name sortKey="Liu, J" uniqKey="Liu J">J Liu</name></author><author><name sortKey="Enders, Ta" uniqKey="Enders T">TA Enders</name></author><author><name sortKey="Bartel, B" uniqKey="Bartel B">B Bartel</name></author><author><name sortKey="Strader, Lc" uniqKey="Strader L">LC Strader</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Gifford, Ml" uniqKey="Gifford M">ML Gifford</name></author><author><name sortKey="Dean, A" uniqKey="Dean A">A Dean</name></author><author><name sortKey="Gutierrez, Ra" uniqKey="Gutierrez R">RA Gutierrez</name></author><author><name sortKey="Coruzzi, Gm" uniqKey="Coruzzi G">GM Coruzzi</name></author><author><name sortKey="Birnbaum, Kd" uniqKey="Birnbaum K">KD Birnbaum</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Kang, K" uniqKey="Kang K">K Kang</name></author><author><name sortKey="Li, J" uniqKey="Li J">J Li</name></author><author><name sortKey="Zhao, T" uniqKey="Zhao T">T Zhao</name></author><author><name sortKey="Xiao, F" uniqKey="Xiao F">F Xiao</name></author><author><name sortKey="Tang, X" uniqKey="Tang X">X Tang</name></author><author><name sortKey="Thilmony, R" uniqKey="Thilmony R">R Thilmony</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Jain, M" uniqKey="Jain M">M Jain</name></author><author><name sortKey="Kaur, N" uniqKey="Kaur N">N Kaur</name></author><author><name sortKey="Garg, R" uniqKey="Garg R">R Garg</name></author><author><name sortKey="Thakur, Jk" uniqKey="Thakur J">JK Thakur</name></author><author><name sortKey="Tyagi, Ak" uniqKey="Tyagi A">AK Tyagi</name></author><author><name sortKey="Khurana, Jp" uniqKey="Khurana J">JP Khurana</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Li, Sb" uniqKey="Li S">SB Li</name></author><author><name sortKey="Ouyang, Wz" uniqKey="Ouyang W">WZ OuYang</name></author><author><name sortKey="Hou, Xj" uniqKey="Hou X">XJ Hou</name></author><author><name sortKey="Xie, Ll" uniqKey="Xie L">LL Xie</name></author><author><name sortKey="Hu, Gc" uniqKey="Hu G">GC Hu</name></author><author><name sortKey="Zhang, Jz" uniqKey="Zhang J">JZ Zhang</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Dreher, Ka" uniqKey="Dreher K">KA Dreher</name></author><author><name sortKey="Brown, J" uniqKey="Brown J">J Brown</name></author><author><name sortKey="Saw, Re" uniqKey="Saw R">RE Saw</name></author><author><name sortKey="Callis, J" uniqKey="Callis J">J Callis</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Wang, S" uniqKey="Wang S">S Wang</name></author><author><name sortKey="Bai, Y" uniqKey="Bai Y">Y Bai</name></author><author><name sortKey="Shen, C" uniqKey="Shen C">C Shen</name></author><author><name sortKey="Wu, Y" uniqKey="Wu Y">Y Wu</name></author><author><name sortKey="Zhang, S" uniqKey="Zhang S">S Zhang</name></author><author><name sortKey="Jiang, D" uniqKey="Jiang D">D Jiang</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Audran Delalande, C" uniqKey="Audran Delalande C">C Audran-Delalande</name></author><author><name sortKey="Bassa, C" uniqKey="Bassa C">C Bassa</name></author><author><name sortKey="Mila, I" uniqKey="Mila I">I Mila</name></author><author><name sortKey="Regad, F" uniqKey="Regad F">F Regad</name></author><author><name sortKey="Zouine, M" uniqKey="Zouine M">M Zouine</name></author><author><name sortKey="Bouzayen, M" uniqKey="Bouzayen M">M Bouzayen</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Jain, M" uniqKey="Jain M">M Jain</name></author><author><name sortKey="Khurana, Jp" uniqKey="Khurana J">JP Khurana</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">PLoS One</journal-id><journal-id journal-id-type="iso-abbrev">PLoS ONE</journal-id><journal-id journal-id-type="publisher-id">plos</journal-id><journal-id journal-id-type="pmc">plosone</journal-id><journal-title-group><journal-title>PLoS ONE</journal-title></journal-title-group><issn pub-type="epub">1932-6203</issn><publisher><publisher-name>Public Library of Science</publisher-name><publisher-loc>San Francisco, CA USA</publisher-loc></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">27049520</article-id><article-id pub-id-type="pmc">4822780</article-id><article-id pub-id-type="doi">10.1371/journal.pone.0151522</article-id><article-id pub-id-type="publisher-id">PONE-D-15-44791</article-id><article-categories><subj-group subj-group-type="heading"><subject>Research Article</subject></subj-group><subj-group subj-group-type="Discipline-v3"><subject>Biology and Life Sciences</subject><subj-group><subject>Organisms</subject><subj-group><subject>Plants</subject><subj-group><subject>Brassica</subject><subj-group><subject>Arabidopsis Thaliana</subject></subj-group></subj-group></subj-group></subj-group></subj-group><subj-group subj-group-type="Discipline-v3"><subject>Research and Analysis Methods</subject><subj-group><subject>Model Organisms</subject><subj-group><subject>Plant and Algal Models</subject><subj-group><subject>Arabidopsis Thaliana</subject></subj-group></subj-group></subj-group></subj-group><subj-group subj-group-type="Discipline-v3"><subject>Biology and Life Sciences</subject><subj-group><subject>Genetics</subject><subj-group><subject>Gene Expression</subject></subj-group></subj-group></subj-group><subj-group subj-group-type="Discipline-v3"><subject>Biology and Life Sciences</subject><subj-group><subject>Molecular Biology</subject><subj-group><subject>Molecular Biology Techniques</subject><subj-group><subject>Sequencing Techniques</subject><subj-group><subject>Sequence Analysis</subject><subj-group><subject>Sequence Motif Analysis</subject></subj-group></subj-group></subj-group></subj-group></subj-group></subj-group><subj-group subj-group-type="Discipline-v3"><subject>Research and Analysis Methods</subject><subj-group><subject>Molecular Biology Techniques</subject><subj-group><subject>Sequencing Techniques</subject><subj-group><subject>Sequence Analysis</subject><subj-group><subject>Sequence Motif Analysis</subject></subj-group></subj-group></subj-group></subj-group></subj-group><subj-group subj-group-type="Discipline-v3"><subject>Biology and Life Sciences</subject><subj-group><subject>Biochemistry</subject><subj-group><subject>Hormones</subject><subj-group><subject>Plant Hormones</subject><subj-group><subject>Auxins</subject></subj-group></subj-group></subj-group></subj-group></subj-group><subj-group subj-group-type="Discipline-v3"><subject>Biology and Life Sciences</subject><subj-group><subject>Biochemistry</subject><subj-group><subject>Plant Biochemistry</subject><subj-group><subject>Plant Hormones</subject><subj-group><subject>Auxins</subject></subj-group></subj-group></subj-group></subj-group></subj-group><subj-group subj-group-type="Discipline-v3"><subject>Biology and Life Sciences</subject><subj-group><subject>Plant Science</subject><subj-group><subject>Plant Biochemistry</subject><subj-group><subject>Plant Hormones</subject><subj-group><subject>Auxins</subject></subj-group></subj-group></subj-group></subj-group></subj-group><subj-group subj-group-type="Discipline-v3"><subject>Research and Analysis Methods</subject><subj-group><subject>Database and Informatics Methods</subject><subj-group><subject>Biological Databases</subject><subj-group><subject>Genomic Databases</subject></subj-group></subj-group></subj-group></subj-group><subj-group subj-group-type="Discipline-v3"><subject>Biology and Life Sciences</subject><subj-group><subject>Computational Biology</subject><subj-group><subject>Genome Analysis</subject><subj-group><subject>Genomic Databases</subject></subj-group></subj-group></subj-group></subj-group><subj-group subj-group-type="Discipline-v3"><subject>Biology and Life Sciences</subject><subj-group><subject>Genetics</subject><subj-group><subject>Genomics</subject><subj-group><subject>Genome Analysis</subject><subj-group><subject>Genomic Databases</subject></subj-group></subj-group></subj-group></subj-group></subj-group><subj-group subj-group-type="Discipline-v3"><subject>Biology and Life Sciences</subject><subj-group><subject>Genetics</subject><subj-group><subject>Genomics</subject><subj-group><subject>Plant Genomics</subject></subj-group></subj-group></subj-group></subj-group><subj-group subj-group-type="Discipline-v3"><subject>Biology and Life Sciences</subject><subj-group><subject>Biotechnology</subject><subj-group><subject>Plant Biotechnology</subject><subj-group><subject>Plant Genomics</subject></subj-group></subj-group></subj-group></subj-group><subj-group subj-group-type="Discipline-v3"><subject>Biology and Life Sciences</subject><subj-group><subject>Plant Science</subject><subj-group><subject>Plant Biotechnology</subject><subj-group><subject>Plant Genomics</subject></subj-group></subj-group></subj-group></subj-group><subj-group subj-group-type="Discipline-v3"><subject>Biology and Life Sciences</subject><subj-group><subject>Genetics</subject><subj-group><subject>Plant Genetics</subject><subj-group><subject>Plant Genomics</subject></subj-group></subj-group></subj-group></subj-group><subj-group subj-group-type="Discipline-v3"><subject>Biology and Life Sciences</subject><subj-group><subject>Plant Science</subject><subj-group><subject>Plant Genetics</subject><subj-group><subject>Plant Genomics</subject></subj-group></subj-group></subj-group></subj-group><subj-group subj-group-type="Discipline-v3"><subject>Biology and Life Sciences</subject><subj-group><subject>Agriculture</subject><subj-group><subject>Crop Science</subject><subj-group><subject>Crops</subject><subj-group><subject>Cereal Crops</subject><subj-group><subject>Maize</subject></subj-group></subj-group></subj-group></subj-group></subj-group></subj-group><subj-group subj-group-type="Discipline-v3"><subject>Biology and Life Sciences</subject><subj-group><subject>Organisms</subject><subj-group><subject>Plants</subject><subj-group><subject>Grasses</subject><subj-group><subject>Maize</subject></subj-group></subj-group></subj-group></subj-group></subj-group><subj-group subj-group-type="Discipline-v3"><subject>Research and Analysis Methods</subject><subj-group><subject>Model Organisms</subject><subj-group><subject>Plant and Algal Models</subject><subj-group><subject>Maize</subject></subj-group></subj-group></subj-group></subj-group><subj-group subj-group-type="Discipline-v3"><subject>Biology and Life Sciences</subject><subj-group><subject>Biochemistry</subject><subj-group><subject>Proteins</subject><subj-group><subject>Protein Domains</subject></subj-group></subj-group></subj-group></subj-group></article-categories><title-group><article-title>Genome-Wide Analysis and Characterization of Aux/IAA Family Genes in <italic>Brassica rapa</italic></article-title><alt-title alt-title-type="running-head">Aux/IAA Genes in <italic>B</italic>. <italic>rapa</italic></alt-title></title-group><contrib-group><contrib contrib-type="author" equal-contrib="yes"><name><surname>Paul</surname><given-names>Parameswari</given-names></name><xref ref-type="aff" rid="aff001"></xref></contrib><contrib contrib-type="author" equal-contrib="yes"><name><surname>Dhandapani</surname><given-names>Vignesh</given-names></name><xref ref-type="aff" rid="aff001"></xref></contrib><contrib contrib-type="author"><name><surname>Rameneni</surname><given-names>Jana Jeevan</given-names></name><xref ref-type="aff" rid="aff001"></xref></contrib><contrib contrib-type="author"><name><surname>Li</surname><given-names>Xiaonan</given-names></name><xref ref-type="aff" rid="aff001"></xref></contrib><contrib contrib-type="author"><name><surname>Sivanandhan</surname><given-names>Ganesan</given-names></name><xref ref-type="aff" rid="aff001"></xref></contrib><contrib contrib-type="author"><name><surname>Choi</surname><given-names>Su Ryun</given-names></name><xref ref-type="aff" rid="aff001"></xref></contrib><contrib contrib-type="author"><name><surname>Pang</surname><given-names>Wenxing</given-names></name><xref ref-type="aff" rid="aff001"></xref></contrib><contrib contrib-type="author"><name><surname>Im</surname><given-names>Subin</given-names></name><xref ref-type="aff" rid="aff001"></xref></contrib><contrib contrib-type="author"><name><surname>Lim</surname><given-names>Yong Pyo</given-names></name><xref ref-type="corresp" rid="cor001">*</xref><xref ref-type="aff" rid="aff001"></xref></contrib></contrib-group><aff id="aff001"><addr-line>Molecular Genetics and Genomics Laboratory, Department of Horticulture, Chungnam National University, Daejeon, 305764, South Korea</addr-line></aff><contrib-group><contrib contrib-type="editor"><name><surname>Li</surname><given-names>Maoteng</given-names></name><role>Editor</role><xref ref-type="aff" rid="edit1"></xref></contrib></contrib-group><aff id="edit1"><addr-line>Huazhong university of Science and Technology, CHINA</addr-line></aff><author-notes><fn fn-type="conflict" id="coi001"><p><bold>Competing Interests: </bold>The authors have declared that no competing interests exist.</p></fn><fn fn-type="con" id="contrib001"><p>Conceived and designed the experiments: PP VD. Performed the experiments: JJR XL GS WP SI. Analyzed the data: PP VD SRC YPL. Contributed reagents/materials/analysis tools: SRC YPL. Wrote the paper: PP VD.</p></fn><corresp id="cor001">* E-mail: <email>yplim@cnu.ac.kr</email></corresp></author-notes><pub-date pub-type="epub"><day>6</day><month>4</month><year>2016</year></pub-date><pub-date pub-type="collection"><year>2016</year></pub-date><volume>11</volume><issue>4</issue><elocation-id>e0151522</elocation-id><history><date date-type="received"><day>12</day><month>10</month><year>2015</year></date><date date-type="accepted"><day>28</day><month>2</month><year>2016</year></date></history><permissions><copyright-statement>© 2016 Paul et al</copyright-statement><copyright-year>2016</copyright-year><copyright-holder>Paul et al</copyright-holder><license xlink:href="http://creativecommons.org/licenses/by/4.0/"><license-p>This is an open access article distributed under the terms of the <ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/licenses/by/4.0/">Creative Commons Attribution License</ext-link>, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.</license-p></license></permissions><self-uri content-type="pdf" xlink:type="simple" xlink:href="pone.0151522.pdf"></self-uri><abstract><p>Auxins are the key players in plant growth development involving leaf formation, phototropism, root, fruit and embryo development. Auxin/Indole-3-Acetic Acid (Aux/IAA) are early auxin response genes noted as transcriptional repressors in plant auxin signaling. However, many studies focus on Aux/ARF gene families and much less is known about the Aux/IAA gene family in <italic>Brassica rapa</italic> (<italic>B</italic>. <italic>rapa</italic>). Here we performed a comprehensive genome-wide analysis and identified 55 Aux/IAA genes in <italic>B</italic>. <italic>rapa</italic> using four conserved motifs of Aux/IAA family (PF02309). Chromosomal mapping of the <italic>B</italic>. <italic>rapa</italic> Aux/IAA (<italic>BrIAA</italic>) genes facilitated understanding cluster rearrangement of the crucifer building blocks in the genome. Phylogenetic analysis of <italic>BrIAA</italic> with <italic>Arabidopsis thaliana</italic>, <italic>Oryza sativa</italic> and <italic>Zea mays</italic> identified 51 sister pairs including 15 same species (<italic>BrIAA</italic>—<italic>BrIAA</italic>) and 36 cross species (<italic>BrIAA</italic>—<italic>AtIAA</italic>) <italic>IAA</italic> genes. Among the 55 <italic>BrIAA</italic> genes, expression of 43 and 45 genes were verified using Genebank <italic>B</italic>. <italic>rapa</italic> ESTs and in home developed microarray data from mature leaves of Chiifu and RcBr lines. Despite their huge morphological difference, tissue specific expression analysis of <italic>BrIAA</italic> genes between the parental lines Chiifu and RcBr showed that the genes followed a similar pattern of expression during leaf development and a different pattern during bud, flower and siliqua development stages. The response of the <italic>BrIAA</italic> genes to abiotic and auxin stress at different time intervals revealed their involvement in stress response. Single Nucleotide Polymorphisms between <italic>IAA</italic> genes of reference genome Chiifu and RcBr were focused and identified. Our study examines the scope of conservation and divergence of Aux/IAA genes and their structures in <italic>B</italic>. <italic>rapa</italic>. Analyzing the expression and structural variation between two parental lines will significantly contribute to functional genomics of <italic>Brassica</italic> crops and we belive our study would provide a foundation in understanding the Aux/IAA genes in <italic>B</italic>. <italic>rapa</italic>.</p></abstract><funding-group><funding-statement>This research was supported by the Golden Seed Project (No. 213002-04-4-SBI30), Ministry of Agriculture, Food and Rural Affairs (MAFRA), Ministry of Oceans and Fisheries (MOF), Rural Development Administration (RDA) and Korea Forest Service (KFS).</funding-statement></funding-group><counts><fig-count count="5"></fig-count><table-count count="2"></table-count><page-count count="19"></page-count></counts><custom-meta-group><custom-meta id="data-availability"><meta-name>Data Availability</meta-name><meta-value>All relevant data are within the paper and its Supporting Information files.</meta-value></custom-meta></custom-meta-group></article-meta><notes><title>Data Availability</title><p>All relevant data are within the paper and its Supporting Information files.</p></notes></front></pmc><affiliations><list></list><tree><noCountry><name sortKey="Choi, Su Ryun" sort="Choi, Su Ryun" uniqKey="Choi S" first="Su Ryun" last="Choi">Su Ryun Choi</name><name sortKey="Dhandapani, Vignesh" sort="Dhandapani, Vignesh" uniqKey="Dhandapani V" first="Vignesh" last="Dhandapani">Vignesh Dhandapani</name><name sortKey="Im, Subin" sort="Im, Subin" uniqKey="Im S" first="Subin" last="Im">Subin Im</name><name sortKey="Li, Xiaonan" sort="Li, Xiaonan" uniqKey="Li X" first="Xiaonan" last="Li">Xiaonan Li</name><name sortKey="Lim, Yong Pyo" sort="Lim, Yong Pyo" uniqKey="Lim Y" first="Yong Pyo" last="Lim">Yong Pyo Lim</name><name sortKey="Pang, Wenxing" sort="Pang, Wenxing" uniqKey="Pang W" first="Wenxing" last="Pang">Wenxing Pang</name><name sortKey="Paul, Parameswari" sort="Paul, Parameswari" uniqKey="Paul P" first="Parameswari" last="Paul">Parameswari Paul</name><name sortKey="Rameneni, Jana Jeevan" sort="Rameneni, Jana Jeevan" uniqKey="Rameneni J" first="Jana Jeevan" last="Rameneni">Jana Jeevan Rameneni</name><name sortKey="Sivanandhan, Ganesan" sort="Sivanandhan, Ganesan" uniqKey="Sivanandhan G" first="Ganesan" last="Sivanandhan">Ganesan Sivanandhan</name></noCountry></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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