Genome-wide identification of sweet orange (Citrus sinensis) histone modification gene families and their expression analysis during the fruit development and fruit-blue mold infection process
Identifieur interne : 000077 ( Pmc/Curation ); précédent : 000076; suivant : 000078Genome-wide identification of sweet orange (Citrus sinensis) histone modification gene families and their expression analysis during the fruit development and fruit-blue mold infection process
Auteurs : Jidi Xu ; Haidan Xu ; Yuanlong Liu ; Xia Wang ; Qiang Xu ; Xiuxin DengSource :
- Frontiers in Plant Science [ 1664-462X ] ; 2015.
Abstract
In eukaryotes, histone acetylation and methylation have been known to be involved in regulating diverse developmental processes and plant defense. These histone modification events are controlled by a series of histone modification gene families. To date, there is no study regarding genome-wide characterization of histone modification related genes in citrus species. Based on the two recent sequenced sweet orange genome databases, a total of 136
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DOI: 10.3389/fpls.2015.00607
PubMed: 26300904
PubMed Central: 4525380
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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Genome-wide identification of sweet orange (<italic>Citrus sinensis</italic>) histone modification gene families and their expression analysis during the fruit development and fruit-blue mold infection process</title><author><name sortKey="Xu, Jidi" sort="Xu, Jidi" uniqKey="Xu J" first="Jidi" last="Xu">Jidi Xu</name></author><author><name sortKey="Xu, Haidan" sort="Xu, Haidan" uniqKey="Xu H" first="Haidan" last="Xu">Haidan Xu</name></author><author><name sortKey="Liu, Yuanlong" sort="Liu, Yuanlong" uniqKey="Liu Y" first="Yuanlong" last="Liu">Yuanlong Liu</name></author><author><name sortKey="Wang, Xia" sort="Wang, Xia" uniqKey="Wang X" first="Xia" last="Wang">Xia Wang</name></author><author><name sortKey="Xu, Qiang" sort="Xu, Qiang" uniqKey="Xu Q" first="Qiang" last="Xu">Qiang Xu</name></author><author><name sortKey="Deng, Xiuxin" sort="Deng, Xiuxin" uniqKey="Deng X" first="Xiuxin" last="Deng">Xiuxin Deng</name></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">26300904</idno><idno type="pmc">4525380</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4525380</idno><idno type="RBID">PMC:4525380</idno><idno type="doi">10.3389/fpls.2015.00607</idno><date when="2015">2015</date><idno type="wicri:Area/Pmc/Corpus">000077</idno><idno type="wicri:Area/Pmc/Curation">000077</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Genome-wide identification of sweet orange (<italic>Citrus sinensis</italic>) histone modification gene families and their expression analysis during the fruit development and fruit-blue mold infection process</title><author><name sortKey="Xu, Jidi" sort="Xu, Jidi" uniqKey="Xu J" first="Jidi" last="Xu">Jidi Xu</name></author><author><name sortKey="Xu, Haidan" sort="Xu, Haidan" uniqKey="Xu H" first="Haidan" last="Xu">Haidan Xu</name></author><author><name sortKey="Liu, Yuanlong" sort="Liu, Yuanlong" uniqKey="Liu Y" first="Yuanlong" last="Liu">Yuanlong Liu</name></author><author><name sortKey="Wang, Xia" sort="Wang, Xia" uniqKey="Wang X" first="Xia" last="Wang">Xia Wang</name></author><author><name sortKey="Xu, Qiang" sort="Xu, Qiang" uniqKey="Xu Q" first="Qiang" last="Xu">Qiang Xu</name></author><author><name sortKey="Deng, Xiuxin" sort="Deng, Xiuxin" uniqKey="Deng X" first="Xiuxin" last="Deng">Xiuxin Deng</name></author></analytic><series><title level="j">Frontiers in Plant Science</title><idno type="eISSN">1664-462X</idno><imprint><date when="2015">2015</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>In eukaryotes, histone acetylation and methylation have been known to be involved in regulating diverse developmental processes and plant defense. These histone modification events are controlled by a series of histone modification gene families. To date, there is no study regarding genome-wide characterization of histone modification related genes in citrus species. Based on the two recent sequenced sweet orange genome databases, a total of 136 <italic>CsHMs</italic> (<italic>Citrus sinensis</italic> histone modification genes), including 47 <italic>CsHMTs</italic> (histone methyltransferase genes), 23 <italic>CsHDMs</italic> (histone demethylase genes), 50 <italic>CsHATs</italic> (histone acetyltransferase genes), and 16 <italic>CsHDACs</italic> (histone deacetylase genes) were identified. These genes were categorized to 11 gene families. A comprehensive analysis of these 11 gene families was performed with chromosome locations, phylogenetic comparison, gene structures, and conserved domain compositions of proteins. In order to gain an insight into the potential roles of these genes in citrus fruit development, 42 <italic>CsHMs</italic> with high mRNA abundance in fruit tissues were selected to further analyze their expression profiles at six stages of fruit development. Interestingly, a numbers of genes were expressed highly in flesh of ripening fruit and some of them showed the increasing expression levels along with the fruit development. Furthermore, we analyzed the expression patterns of all 136 <italic>CsHMs</italic> response to the infection of blue mold (<italic>Penicillium digitatum</italic>), which is the most devastating pathogen in citrus post-harvest process. The results indicated that 20 of them showed the strong alterations of their expression levels during the fruit-pathogen infection. In conclusion, this study presents a comprehensive analysis of the histone modification gene families in sweet orange and further elucidates their behaviors during the fruit development and the blue mold infection responses.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Ahmad, A" uniqKey="Ahmad A">A. Ahmad</name></author><author><name sortKey="Cao, X" uniqKey="Cao X">X. Cao</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Aiese Cigliano, R" uniqKey="Aiese Cigliano R">R. Aiese Cigliano</name></author><author><name sortKey="Sanseverino, W" uniqKey="Sanseverino W">W. Sanseverino</name></author><author><name sortKey="Cremona, G" uniqKey="Cremona G">G. Cremona</name></author><author><name sortKey="Ercolano, M R" uniqKey="Ercolano M">M. R. Ercolano</name></author><author><name sortKey="Conicella, C" uniqKey="Conicella C">C. 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<front><journal-meta><journal-id journal-id-type="nlm-ta">Front Plant Sci</journal-id><journal-id journal-id-type="iso-abbrev">Front Plant Sci</journal-id><journal-id journal-id-type="publisher-id">Front. Plant Sci.</journal-id><journal-title-group><journal-title>Frontiers in Plant Science</journal-title></journal-title-group><issn pub-type="epub">1664-462X</issn><publisher><publisher-name>Frontiers Media S.A.</publisher-name></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">26300904</article-id><article-id pub-id-type="pmc">4525380</article-id><article-id pub-id-type="doi">10.3389/fpls.2015.00607</article-id><article-categories><subj-group subj-group-type="heading"><subject>Plant Science</subject><subj-group><subject>Original Research</subject></subj-group></subj-group></article-categories><title-group><article-title>Genome-wide identification of sweet orange (<italic>Citrus sinensis</italic>) histone modification gene families and their expression analysis during the fruit development and fruit-blue mold infection process</article-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Xu</surname><given-names>Jidi</given-names></name><uri xlink:type="simple" xlink:href="http://loop.frontiersin.org/people/258975"></uri></contrib><contrib contrib-type="author"><name><surname>Xu</surname><given-names>Haidan</given-names></name><uri xlink:type="simple" xlink:href="http://loop.frontiersin.org/people/258970"></uri></contrib><contrib contrib-type="author"><name><surname>Liu</surname><given-names>Yuanlong</given-names></name><uri xlink:type="simple" xlink:href="http://loop.frontiersin.org/people/258983"></uri></contrib><contrib contrib-type="author"><name><surname>Wang</surname><given-names>Xia</given-names></name><uri xlink:type="simple" xlink:href="http://loop.frontiersin.org/people/258987"></uri></contrib><contrib contrib-type="author"><name><surname>Xu</surname><given-names>Qiang</given-names></name><uri xlink:type="simple" xlink:href="http://loop.frontiersin.org/people/258977"></uri></contrib><contrib contrib-type="author"><name><surname>Deng</surname><given-names>Xiuxin</given-names></name><xref ref-type="author-notes" rid="fn001"><sup>*</sup></xref><uri xlink:type="simple" xlink:href="http://loop.frontiersin.org/people/236370"></uri></contrib></contrib-group><aff><institution>Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University</institution><country>Wuhan, China</country></aff><author-notes><fn fn-type="edited-by"><p>Edited by: <italic>Anna Maria Mastrangelo, Centro di Ricerca per la Cerealicoltura, Italy</italic></p></fn><fn fn-type="edited-by"><p>Reviewed by: <italic>Fernando Martinez, University of Seville, Spain; Li-Song Chen, Fujian Agriculture and Forestry University, China</italic></p></fn><corresp id="fn001">*Correspondence: <italic>Xiuxin Deng, Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan 430070, China, <email xlink:type="simple">xxdeng@mail.hzau.edu.cn</email></italic></corresp><fn fn-type="other" id="fn002"><p>This article was submitted to Crop Science and Horticulture, a section of the journal Frontiers in Plant Science</p></fn></author-notes><pub-date pub-type="epub"><day>05</day><month>8</month><year>2015</year></pub-date><pub-date pub-type="collection"><year>2015</year></pub-date><volume>6</volume><elocation-id>607</elocation-id><history><date date-type="received"><day>07</day><month>5</month><year>2015</year></date><date date-type="accepted"><day>23</day><month>7</month><year>2015</year></date></history><permissions><copyright-statement>Copyright © 2015 Xu, Xu, Liu, Wang, Xu and Deng.</copyright-statement><copyright-year>2015</copyright-year><copyright-holder>Xu, Xu, Liu, Wang, Xu and Deng</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 Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.</license-p></license></permissions><abstract><p>In eukaryotes, histone acetylation and methylation have been known to be involved in regulating diverse developmental processes and plant defense. These histone modification events are controlled by a series of histone modification gene families. To date, there is no study regarding genome-wide characterization of histone modification related genes in citrus species. Based on the two recent sequenced sweet orange genome databases, a total of 136 <italic>CsHMs</italic> (<italic>Citrus sinensis</italic> histone modification genes), including 47 <italic>CsHMTs</italic> (histone methyltransferase genes), 23 <italic>CsHDMs</italic> (histone demethylase genes), 50 <italic>CsHATs</italic> (histone acetyltransferase genes), and 16 <italic>CsHDACs</italic> (histone deacetylase genes) were identified. These genes were categorized to 11 gene families. A comprehensive analysis of these 11 gene families was performed with chromosome locations, phylogenetic comparison, gene structures, and conserved domain compositions of proteins. In order to gain an insight into the potential roles of these genes in citrus fruit development, 42 <italic>CsHMs</italic> with high mRNA abundance in fruit tissues were selected to further analyze their expression profiles at six stages of fruit development. Interestingly, a numbers of genes were expressed highly in flesh of ripening fruit and some of them showed the increasing expression levels along with the fruit development. Furthermore, we analyzed the expression patterns of all 136 <italic>CsHMs</italic> response to the infection of blue mold (<italic>Penicillium digitatum</italic>), which is the most devastating pathogen in citrus post-harvest process. The results indicated that 20 of them showed the strong alterations of their expression levels during the fruit-pathogen infection. In conclusion, this study presents a comprehensive analysis of the histone modification gene families in sweet orange and further elucidates their behaviors during the fruit development and the blue mold infection responses.</p></abstract><kwd-group><kwd>histone modifications</kwd><kwd><italic>Citrus sinensis</italic></kwd><kwd>epigenetics</kwd><kwd>fruit development</kwd><kwd>blue mold</kwd></kwd-group><funding-group><award-group><funding-source id="c001">Ministry of Science and Technology of China</funding-source><award-id rid="c001">2011CB100600</award-id></award-group><award-group><funding-source id="c002">National Natural Science Foundation of China</funding-source><award-id rid="c002">31330066</award-id><award-id rid="c002">31221062</award-id></award-group></funding-group><counts><fig-count count="10"></fig-count><table-count count="1"></table-count><equation-count count="0"></equation-count><ref-count count="62"></ref-count><page-count count="16"></page-count><word-count count="0"></word-count></counts></article-meta></front></pmc></record>Pour manipuler ce document sous Unix (Dilib)
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