Genome-Wide Classification and Evolutionary and Expression Analyses of Citrus MYB Transcription Factor Families in Sweet Orange
Identifieur interne : 000807 ( Pmc/Checkpoint ); précédent : 000806; suivant : 000808Genome-Wide Classification and Evolutionary and Expression Analyses of Citrus MYB Transcription Factor Families in Sweet Orange
Auteurs : Xiao-Jin Hou ; Si-Bei Li ; Sheng-Rui Liu ; Chun-Gen Hu ; Jin-Zhi ZhangSource :
- PLoS ONE [ 1932-6203 ] ; 2014.
Abstract
Url:
DOI: 10.1371/journal.pone.0112375
PubMed: 25375352
PubMed Central: 4223058
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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Genome-Wide Classification and Evolutionary and Expression Analyses of Citrus <italic>MYB</italic> Transcription Factor Families in Sweet Orange</title><author><name sortKey="Hou, Xiao Jin" sort="Hou, Xiao Jin" uniqKey="Hou X" first="Xiao-Jin" last="Hou">Xiao-Jin Hou</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author><author><name sortKey="Li, Si Bei" sort="Li, Si Bei" uniqKey="Li S" first="Si-Bei" last="Li">Si-Bei Li</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author><author><name sortKey="Liu, Sheng Rui" sort="Liu, Sheng Rui" uniqKey="Liu S" first="Sheng-Rui" last="Liu">Sheng-Rui Liu</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author><author><name sortKey="Hu, Chun Gen" sort="Hu, Chun Gen" uniqKey="Hu C" first="Chun-Gen" last="Hu">Chun-Gen Hu</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author><author><name sortKey="Zhang, Jin Zhi" sort="Zhang, Jin Zhi" uniqKey="Zhang J" first="Jin-Zhi" last="Zhang">Jin-Zhi Zhang</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">25375352</idno><idno type="pmc">4223058</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4223058</idno><idno type="RBID">PMC:4223058</idno><idno type="doi">10.1371/journal.pone.0112375</idno><date when="2014">2014</date><idno type="wicri:Area/Pmc/Corpus">000217</idno><idno type="wicri:Area/Pmc/Curation">000217</idno><idno type="wicri:Area/Pmc/Checkpoint">000807</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Genome-Wide Classification and Evolutionary and Expression Analyses of Citrus <italic>MYB</italic> Transcription Factor Families in Sweet Orange</title><author><name sortKey="Hou, Xiao Jin" sort="Hou, Xiao Jin" uniqKey="Hou X" first="Xiao-Jin" last="Hou">Xiao-Jin Hou</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author><author><name sortKey="Li, Si Bei" sort="Li, Si Bei" uniqKey="Li S" first="Si-Bei" last="Li">Si-Bei Li</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author><author><name sortKey="Liu, Sheng Rui" sort="Liu, Sheng Rui" uniqKey="Liu S" first="Sheng-Rui" last="Liu">Sheng-Rui Liu</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author><author><name sortKey="Hu, Chun Gen" sort="Hu, Chun Gen" uniqKey="Hu C" first="Chun-Gen" last="Hu">Chun-Gen Hu</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author><author><name sortKey="Zhang, Jin Zhi" sort="Zhang, Jin Zhi" uniqKey="Zhang J" first="Jin-Zhi" last="Zhang">Jin-Zhi Zhang</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author></analytic><series><title level="j">PLoS ONE</title><idno type="eISSN">1932-6203</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><italic>MYB</italic> family genes are widely distributed in plants and comprise one of the largest transcription factors involved in various developmental processes and defense responses of plants. To date, few <italic>MYB</italic> genes and little expression profiling have been reported for citrus. Here, we describe and classify 177 members of the sweet orange <italic>MYB</italic> gene (<italic>CsMYB</italic>) family in terms of their genomic gene structures and similarity to their putative <italic>Arabidopsis</italic> orthologs. According to these analyses, these <italic>CsMYBs</italic> were categorized into four groups (4R-MYB, 3R-MYB, 2R-MYB and 1R-MYB). Gene structure analysis revealed that 1R-MYB genes possess relatively more introns as compared with 2R-MYB genes. Investigation of their chromosomal localizations revealed that these <italic>CsMYBs</italic> are distributed across nine chromosomes. Sweet orange includes a relatively small number of <italic>MYB</italic> genes compared with the 198 members in <italic>Arabidopsis</italic>, presumably due to a paralog reduction related to repetitive sequence insertion into promoter and non-coding transcribed region of the genes. Comparative studies of <italic>CsMYBs</italic> and <italic>Arabidopsis</italic> showed that <italic>CsMYBs</italic> had fewer gene duplication events. Expression analysis revealed that the <italic>MYB</italic> gene family has a wide expression profile in sweet orange development and plays important roles in development and stress responses. In addition, 337 new putative microsatellites with flanking sequences sufficient for primer design were also identified from the 177 <italic>CsMYBs</italic>. These results provide a useful reference for the selection of candidate <italic>MYB</italic> genes for cloning and further functional analysis forcitrus.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Feller, A" uniqKey="Feller A">A Feller</name></author><author><name sortKey="Machemer, K" uniqKey="Machemer K">K Machemer</name></author><author><name sortKey="Braun, El" uniqKey="Braun E">EL Braun</name></author><author><name sortKey="Grotewold, E" uniqKey="Grotewold E">E Grotewold</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Du, H" uniqKey="Du H">H Du</name></author><author><name sortKey="Zhang, L" uniqKey="Zhang L">L Zhang</name></author><author><name sortKey="Liu, L" uniqKey="Liu L">L Liu</name></author><author><name sortKey="Tang, X F" uniqKey="Tang X">X-F Tang</name></author><author><name sortKey="Yang, W J" uniqKey="Yang W">W-J 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<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, USA</publisher-loc></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">25375352</article-id><article-id pub-id-type="pmc">4223058</article-id><article-id pub-id-type="publisher-id">PONE-D-14-31501</article-id><article-id pub-id-type="doi">10.1371/journal.pone.0112375</article-id><article-categories><subj-group subj-group-type="heading"><subject>Research Article</subject></subj-group><subj-group subj-group-type="Discipline-v2"><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>Fruits</subject><subj-group><subject>Citrus</subject></subj-group></subj-group></subj-group></subj-group></subj-group><subj-group><subject>Biotechnology</subject><subj-group><subject>Plant Biotechnology</subject><subj-group><subject>Plant Genomics</subject><subj-group><subject>Plant Genomes</subject></subj-group></subj-group></subj-group></subj-group><subj-group><subject>Computational Biology</subject><subj-group><subject>Genome Analysis</subject><subj-group><subject>Genome-Wide Association Studies</subject><subj-group><subject>Family-Based Association Studies</subject></subj-group></subj-group></subj-group></subj-group><subj-group><subject>Genetics</subject><subj-group><subject>Gene expression</subject><subj-group><subject>DNA transcription</subject><subject>Gene regulation</subject></subj-group></subj-group><subj-group><subject>Genomics</subject></subj-group></subj-group></subj-group></article-categories><title-group><article-title>Genome-Wide Classification and Evolutionary and Expression Analyses of Citrus <italic>MYB</italic> Transcription Factor Families in Sweet Orange</article-title><alt-title alt-title-type="running-head">Identification and Expression Analysis of <italic>MYB</italic> Gene Family in Citrus</alt-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Hou</surname><given-names>Xiao-Jin</given-names></name><xref ref-type="aff" rid="aff1"></xref></contrib><contrib contrib-type="author"><name><surname>Li</surname><given-names>Si-Bei</given-names></name><xref ref-type="aff" rid="aff1"></xref></contrib><contrib contrib-type="author"><name><surname>Liu</surname><given-names>Sheng-Rui</given-names></name><xref ref-type="aff" rid="aff1"></xref></contrib><contrib contrib-type="author"><name><surname>Hu</surname><given-names>Chun-Gen</given-names></name><xref ref-type="aff" rid="aff1"></xref><xref ref-type="corresp" rid="cor1"><sup>*</sup></xref></contrib><contrib contrib-type="author"><name><surname>Zhang</surname><given-names>Jin-Zhi</given-names></name><xref ref-type="aff" rid="aff1"></xref><xref ref-type="corresp" rid="cor1"><sup>*</sup></xref></contrib></contrib-group><aff id="aff1"><addr-line>Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan, China</addr-line></aff><contrib-group><contrib contrib-type="editor"><name><surname>Moriguchi</surname><given-names>Takaya</given-names></name><role>Editor</role><xref ref-type="aff" rid="edit1"></xref></contrib></contrib-group><aff id="edit1"><addr-line>NARO Institute of Fruit Tree Science, Japan</addr-line></aff><author-notes><corresp id="cor1">* E-mail: <email>chungen@mail.hzau.edu.cn</email> (CGH); <email>jinzhizhang@mail.hzau.edu.cn</email> (JZZ)</corresp><fn fn-type="conflict"><p><bold>Competing Interests: </bold>The authors have declared that no competing interests exist.</p></fn><fn fn-type="con"><p>Conceived and designed the experiments: JZZ CGH. Performed the experiments: XJH SBL. Analyzed the data: JZZ CGH SRL. Contributed reagents/materials/analysis tools: XJH. Wrote the paper: JZZ.</p></fn></author-notes><pub-date pub-type="collection"><year>2014</year></pub-date><pub-date pub-type="epub"><day>6</day><month>11</month><year>2014</year></pub-date><volume>9</volume><issue>11</issue><elocation-id>e112375</elocation-id><history><date date-type="received"><day>14</day><month>7</month><year>2014</year></date><date date-type="accepted"><day>2</day><month>10</month><year>2014</year></date></history><permissions><copyright-year>2014</copyright-year><copyright-holder>Hou et al</copyright-holder><license><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><abstract><p><italic>MYB</italic> family genes are widely distributed in plants and comprise one of the largest transcription factors involved in various developmental processes and defense responses of plants. To date, few <italic>MYB</italic> genes and little expression profiling have been reported for citrus. Here, we describe and classify 177 members of the sweet orange <italic>MYB</italic> gene (<italic>CsMYB</italic>) family in terms of their genomic gene structures and similarity to their putative <italic>Arabidopsis</italic> orthologs. According to these analyses, these <italic>CsMYBs</italic> were categorized into four groups (4R-MYB, 3R-MYB, 2R-MYB and 1R-MYB). Gene structure analysis revealed that 1R-MYB genes possess relatively more introns as compared with 2R-MYB genes. Investigation of their chromosomal localizations revealed that these <italic>CsMYBs</italic> are distributed across nine chromosomes. Sweet orange includes a relatively small number of <italic>MYB</italic> genes compared with the 198 members in <italic>Arabidopsis</italic>, presumably due to a paralog reduction related to repetitive sequence insertion into promoter and non-coding transcribed region of the genes. Comparative studies of <italic>CsMYBs</italic> and <italic>Arabidopsis</italic> showed that <italic>CsMYBs</italic> had fewer gene duplication events. Expression analysis revealed that the <italic>MYB</italic> gene family has a wide expression profile in sweet orange development and plays important roles in development and stress responses. In addition, 337 new putative microsatellites with flanking sequences sufficient for primer design were also identified from the 177 <italic>CsMYBs</italic>. These results provide a useful reference for the selection of candidate <italic>MYB</italic> genes for cloning and further functional analysis forcitrus.</p></abstract><funding-group><funding-statement>This research was supported financially by the National Natural Science Foundation of China (grant nos. 31130046, 31372046, 31221062, 31471863 and 31360469) and the Fundamental Research Funds for the Central Universities (2013PY083). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.</funding-statement></funding-group><counts><page-count count="16"></page-count></counts><custom-meta-group><custom-meta id="data-availability"><meta-name>Data Availability</meta-name><meta-value>The authors confirm that all data underlying the findings are fully available without restriction. 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>The authors confirm that all data underlying the findings are fully available without restriction. All relevant data are within the paper and its Supporting Information files.</p></notes></front></pmc><affiliations><list></list><tree><noCountry><name sortKey="Hou, Xiao Jin" sort="Hou, Xiao Jin" uniqKey="Hou X" first="Xiao-Jin" last="Hou">Xiao-Jin Hou</name><name sortKey="Hu, Chun Gen" sort="Hu, Chun Gen" uniqKey="Hu C" first="Chun-Gen" last="Hu">Chun-Gen Hu</name><name sortKey="Li, Si Bei" sort="Li, Si Bei" uniqKey="Li S" first="Si-Bei" last="Li">Si-Bei Li</name><name sortKey="Liu, Sheng Rui" sort="Liu, Sheng Rui" uniqKey="Liu S" first="Sheng-Rui" last="Liu">Sheng-Rui Liu</name><name sortKey="Zhang, Jin Zhi" sort="Zhang, Jin Zhi" uniqKey="Zhang J" first="Jin-Zhi" last="Zhang">Jin-Zhi Zhang</name></noCountry></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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