Genome-Wide Identification of the Transcription Factors Involved in Citrus Fruit Ripening from the Transcriptomes of a Late-Ripening Sweet Orange Mutant and Its Wild Type
Identifieur interne : 000164 ( Pmc/Checkpoint ); précédent : 000163; suivant : 000165Genome-Wide Identification of the Transcription Factors Involved in Citrus Fruit Ripening from the Transcriptomes of a Late-Ripening Sweet Orange Mutant and Its Wild Type
Auteurs : Juxun Wu ; Lili Fu ; Hualin YiSource :
- PLoS ONE [ 1932-6203 ] ; 2016.
Abstract
Fruit ripening is a genetically programmed process. Transcription factors (TFs) play key roles in plant development and ripening by temporarily and spatially regulating the transcription of their target genes. In this study, a total of 159 TFs were identified from a spontaneous late-ripening mutant 'Fengwan' (
Url:
DOI: 10.1371/journal.pone.0154330
PubMed: 27104786
PubMed Central: 4841598
Affiliations:
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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Genome-Wide Identification of the Transcription Factors Involved in <italic>Citrus</italic> Fruit Ripening from the Transcriptomes of a Late-Ripening Sweet Orange Mutant and Its Wild Type</title><author><name sortKey="Wu, Juxun" sort="Wu, Juxun" uniqKey="Wu J" first="Juxun" last="Wu">Juxun Wu</name><affiliation><nlm:aff id="aff001"></nlm:aff></affiliation></author><author><name sortKey="Fu, Lili" sort="Fu, Lili" uniqKey="Fu L" first="Lili" last="Fu">Lili Fu</name><affiliation><nlm:aff id="aff001"></nlm:aff></affiliation></author><author><name sortKey="Yi, Hualin" sort="Yi, Hualin" uniqKey="Yi H" first="Hualin" last="Yi">Hualin Yi</name><affiliation><nlm:aff id="aff001"></nlm:aff></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">27104786</idno><idno type="pmc">4841598</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4841598</idno><idno type="RBID">PMC:4841598</idno><idno type="doi">10.1371/journal.pone.0154330</idno><date when="2016">2016</date><idno type="wicri:Area/Pmc/Corpus">000389</idno><idno type="wicri:Area/Pmc/Curation">000388</idno><idno type="wicri:Area/Pmc/Checkpoint">000164</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Genome-Wide Identification of the Transcription Factors Involved in <italic>Citrus</italic> Fruit Ripening from the Transcriptomes of a Late-Ripening Sweet Orange Mutant and Its Wild Type</title><author><name sortKey="Wu, Juxun" sort="Wu, Juxun" uniqKey="Wu J" first="Juxun" last="Wu">Juxun Wu</name><affiliation><nlm:aff id="aff001"></nlm:aff></affiliation></author><author><name sortKey="Fu, Lili" sort="Fu, Lili" uniqKey="Fu L" first="Lili" last="Fu">Lili Fu</name><affiliation><nlm:aff id="aff001"></nlm:aff></affiliation></author><author><name sortKey="Yi, Hualin" sort="Yi, Hualin" uniqKey="Yi H" first="Hualin" last="Yi">Hualin Yi</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>Fruit ripening is a genetically programmed process. Transcription factors (TFs) play key roles in plant development and ripening by temporarily and spatially regulating the transcription of their target genes. In this study, a total of 159 TFs were identified from a spontaneous late-ripening mutant 'Fengwan' (<italic>C</italic>. <italic>sinensis</italic> L. Osbeck) sweet orange (MT) and its wild-type counterpart ('Fengjie 72–1', WT) along the ripening period via the Transcription Factor Prediction of PlantTFDB 3.0. Fifty-two differentially expressed TFs were identified between MT and WT; 92 and 120 differentially expressed TFs were identified in WT and MT, respectively. The Venn diagram analysis showed that 16 differentially expressed TFs were identified between MT and WT and during the ripening of WT and MT. These TFs were primarily assigned to the families of C2H2, Dof, bHLH, ERF, MYB, NAC and LBD. Particularly, the number of TFs of the ERF family was the greatest between MT and WT. According to the results of the WGCNA analysis, a weighted correlation network analysis tool, several important TFs correlated to abscisic acid (ABA), citric acid, fructose, glucose and sucrose were identified, such as <italic>RD26</italic>, <italic>NTT</italic>, <italic>GATA7</italic> and <italic>MYB21/62/77</italic>. Hierarchical cluster analysis and the expression analysis conducted at five fruit ripening stages further validated the pivotal TFs that potentially function during orange fruit development and ripening.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Jin, J" uniqKey="Jin J">J Jin</name></author><author><name sortKey="Zhang, H" uniqKey="Zhang H">H Zhang</name></author><author><name sortKey="Kong, L" uniqKey="Kong L">L Kong</name></author><author><name sortKey="Gao, G" uniqKey="Gao G">G Gao</name></author><author><name sortKey="Luo, J" uniqKey="Luo J">J Luo</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Klee, Hj" uniqKey="Klee H">HJ Klee</name></author><author><name sortKey="Giovannoni, Jj" uniqKey="Giovannoni J">JJ Giovannoni</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Giovannoni, Jj" uniqKey="Giovannoni J">JJ 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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, CA USA</publisher-loc></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">27104786</article-id><article-id pub-id-type="pmc">4841598</article-id><article-id pub-id-type="doi">10.1371/journal.pone.0154330</article-id><article-id pub-id-type="publisher-id">PONE-D-16-01586</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>Agriculture</subject><subj-group><subject>Crop Science</subject><subj-group><subject>Crops</subject><subj-group><subject>Fruits</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>Organisms</subject><subj-group><subject>Plants</subject><subj-group><subject>Fruits</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>DNA-binding proteins</subject><subj-group><subject>Transcription Factors</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>Gene Expression</subject><subj-group><subject>Gene Regulation</subject><subj-group><subject>Transcription Factors</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>Proteins</subject><subj-group><subject>Regulatory Proteins</subject><subj-group><subject>Transcription Factors</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>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>Biochemistry</subject><subj-group><subject>Proteins</subject><subj-group><subject>DNA-binding proteins</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><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>Fruits</subject><subj-group><subject>Citrus</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>Fruits</subject><subj-group><subject>Citrus</subject></subj-group></subj-group></subj-group></subj-group></subj-group><subj-group subj-group-type="Discipline-v3"><subject>Physical Sciences</subject><subj-group><subject>Chemistry</subject><subj-group><subject>Chemical Compounds</subject><subj-group><subject>Organic Compounds</subject><subj-group><subject>Ethylene</subject></subj-group></subj-group></subj-group></subj-group></subj-group><subj-group subj-group-type="Discipline-v3"><subject>Physical Sciences</subject><subj-group><subject>Chemistry</subject><subj-group><subject>Organic Chemistry</subject><subj-group><subject>Organic Compounds</subject><subj-group><subject>Ethylene</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>Ethylene</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>Ethylene</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>Ethylene</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>Gene Types</subject><subj-group><subject>Regulator Genes</subject></subj-group></subj-group></subj-group></subj-group></article-categories><title-group><article-title>Genome-Wide Identification of the Transcription Factors Involved in <italic>Citrus</italic> Fruit Ripening from the Transcriptomes of a Late-Ripening Sweet Orange Mutant and Its Wild Type</article-title><alt-title alt-title-type="running-head">Identification of Transcription Factors during <italic>Citrus</italic> Fruit Ripening</alt-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Wu</surname><given-names>Juxun</given-names></name><xref ref-type="aff" rid="aff001"></xref></contrib><contrib contrib-type="author"><name><surname>Fu</surname><given-names>Lili</given-names></name><xref ref-type="aff" rid="aff001"></xref></contrib><contrib contrib-type="author"><name><surname>Yi</surname><given-names>Hualin</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>Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan, 430070, China</addr-line></aff><contrib-group><contrib contrib-type="editor"><name><surname>Liu</surname><given-names>Ji-Hong</given-names></name><role>Editor</role><xref ref-type="aff" rid="edit1"></xref></contrib></contrib-group><aff id="edit1"><addr-line>Key Laboratory of Horticultural Plant Biology (MOE), 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: HLY JXW. Performed the experiments: JXW LLF. Analyzed the data: JXW. Contributed reagents/materials/analysis tools: HLY. Wrote the paper: JXW HLY.</p></fn><corresp id="cor001">* E-mail: <email>yihualin@mail.hzau.edu.cn</email></corresp></author-notes><pub-date pub-type="epub"><day>22</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>e0154330</elocation-id><history><date date-type="received"><day>13</day><month>1</month><year>2016</year></date><date date-type="accepted"><day>12</day><month>4</month><year>2016</year></date></history><permissions><copyright-statement>© 2016 Wu et al</copyright-statement><copyright-year>2016</copyright-year><copyright-holder>Wu 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:href="pone.0154330.pdf"></self-uri><abstract><p>Fruit ripening is a genetically programmed process. Transcription factors (TFs) play key roles in plant development and ripening by temporarily and spatially regulating the transcription of their target genes. In this study, a total of 159 TFs were identified from a spontaneous late-ripening mutant 'Fengwan' (<italic>C</italic>. <italic>sinensis</italic> L. Osbeck) sweet orange (MT) and its wild-type counterpart ('Fengjie 72–1', WT) along the ripening period via the Transcription Factor Prediction of PlantTFDB 3.0. Fifty-two differentially expressed TFs were identified between MT and WT; 92 and 120 differentially expressed TFs were identified in WT and MT, respectively. The Venn diagram analysis showed that 16 differentially expressed TFs were identified between MT and WT and during the ripening of WT and MT. These TFs were primarily assigned to the families of C2H2, Dof, bHLH, ERF, MYB, NAC and LBD. Particularly, the number of TFs of the ERF family was the greatest between MT and WT. According to the results of the WGCNA analysis, a weighted correlation network analysis tool, several important TFs correlated to abscisic acid (ABA), citric acid, fructose, glucose and sucrose were identified, such as <italic>RD26</italic>, <italic>NTT</italic>, <italic>GATA7</italic> and <italic>MYB21/62/77</italic>. Hierarchical cluster analysis and the expression analysis conducted at five fruit ripening stages further validated the pivotal TFs that potentially function during orange fruit development and ripening.</p></abstract><funding-group><award-group id="award001"><funding-source><institution>National Modern Citrus Industry System</institution></funding-source><award-id>CARS-27</award-id><principal-award-recipient><name><surname>Yi</surname><given-names>Hualin</given-names></name></principal-award-recipient></award-group><award-group id="award002"><funding-source><institution>Ministry of Education Innovation Team</institution></funding-source><award-id>IRT13065</award-id><principal-award-recipient><name><surname>Yi</surname><given-names>Hualin</given-names></name></principal-award-recipient></award-group><award-group id="award003"><funding-source><institution>National Science and Technology Support Project</institution></funding-source><award-id>2013BAD021302</award-id><principal-award-recipient><name><surname>Yi</surname><given-names>Hualin</given-names></name></principal-award-recipient></award-group><award-group id="award004"><funding-source><institution>the Special Project on the Integration of Industry, Education and Research of Guangdong Province</institution></funding-source><award-id>2012B091100169</award-id><principal-award-recipient><name><surname>Yi</surname><given-names>Hualin</given-names></name></principal-award-recipient></award-group><award-group id="award005"><funding-source><institution>the China Postdoctoral Science Foundation</institution></funding-source><award-id>2015M582242</award-id><principal-award-recipient><name><surname>Wu</surname><given-names>Juxun</given-names></name></principal-award-recipient></award-group><funding-statement>This research was supported by the National Modern Citrus Industry System (CARS-27), the Ministry of Education Innovation Team (IRT13065), the National Science and Technology Support Project (2013BAD021302), the China Postdoctoral Science Foundation (2015M582242) and the Special Project on the Integration of Industry, Education and Research of Guangdong Province (2012B091100169). 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><fig-count count="6"></fig-count><table-count count="2"></table-count><page-count count="22"></page-count></counts><custom-meta-group><custom-meta id="data-availability"><meta-name>Data Availability</meta-name><meta-value>All RNA-seq data are available from the Gene Expression Omnibus database (accession number GSE69432).</meta-value></custom-meta></custom-meta-group></article-meta><notes><title>Data Availability</title><p>All RNA-seq data are available from the Gene Expression Omnibus database (accession number GSE69432).</p></notes></front></pmc><affiliations><list></list><tree><noCountry><name sortKey="Fu, Lili" sort="Fu, Lili" uniqKey="Fu L" first="Lili" last="Fu">Lili Fu</name><name sortKey="Wu, Juxun" sort="Wu, Juxun" uniqKey="Wu J" first="Juxun" last="Wu">Juxun Wu</name><name sortKey="Yi, Hualin" sort="Yi, Hualin" uniqKey="Yi H" first="Hualin" last="Yi">Hualin Yi</name></noCountry></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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