Genome-Wide Analysis of the AP2/ERF Gene Family in Physic Nut and Overexpression of the JcERF011 Gene in Rice Increased Its Sensitivity to Salinity Stress
Identifieur interne : 000380 ( Pmc/Curation ); précédent : 000379; suivant : 000381Genome-Wide Analysis of the AP2/ERF Gene Family in Physic Nut and Overexpression of the JcERF011 Gene in Rice Increased Its Sensitivity to Salinity Stress
Auteurs : Yuehui Tang [République populaire de Chine] ; Shanshan Qin [République populaire de Chine] ; Yali Guo [République populaire de Chine] ; Yanbo Chen [République populaire de Chine] ; Pingzhi Wu [République populaire de Chine] ; Yaping Chen [République populaire de Chine] ; Meiru Li [République populaire de Chine] ; Huawu Jiang [République populaire de Chine] ; Guojiang Wu [République populaire de Chine]Source :
- PLoS ONE [ 1932-6203 ] ; 2016.
Abstract
The AP2/ERF transcription factors play crucial roles in plant growth, development and responses to biotic and abiotic stresses. A total of 119 AP2/ERF genes (
Url:
DOI: 10.1371/journal.pone.0150879
PubMed: 26943337
PubMed Central: 4778941
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Gene in Rice Increased Its Sensitivity to Salinity Stress</title>
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Gene in Rice Increased Its Sensitivity to Salinity Stress</title>
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<author><name sortKey="Jiang, Huawu" sort="Jiang, Huawu" uniqKey="Jiang H" first="Huawu" last="Jiang">Huawu Jiang</name>
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<author><name sortKey="Wu, Guojiang" sort="Wu, Guojiang" uniqKey="Wu G" first="Guojiang" last="Wu">Guojiang Wu</name>
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<front><div type="abstract" xml:lang="en"><p>The AP2/ERF transcription factors play crucial roles in plant growth, development and responses to biotic and abiotic stresses. A total of 119 AP2/ERF genes (<italic>JcAP2/ERFs</italic>
) have been identified in the physic nut genome; they include 16 AP2, 4 RAV, 1 Soloist, and 98 ERF genes. Phylogenetic analysis indicated that physic nut AP2 genes could be divided into 3 subgroups, while ERF genes could be classed into 11 groups or 43 subgroups. The AP2/ERF genes are non-randomly distributed across the 11 linkage groups of the physic nut genome and retain many duplicates which arose from ancient duplication events. The expression patterns of several <italic>JcAP2/ERF</italic>
duplicates in the physic nut showed differences among four tissues (root, stem, leaf, and seed), and 38 <italic>JcAP2/ERF</italic>
genes responded to at least one abiotic stressor (drought, salinity, phosphate starvation, and nitrogen starvation) in leaves and/or roots according to analysis of digital gene expression tag data. The expression of <italic>JcERF011</italic>
was downregulated by salinity stress in physic nut roots. Overexpression of the <italic>JcERF011</italic>
gene in rice plants increased its sensitivity to salinity stress. The increased expression levels of several salt tolerance-related genes were impaired in the <italic>JcERF011</italic>
-overexpressing plants under salinity stress.</p>
</div>
</front>
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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">26943337</article-id>
<article-id pub-id-type="pmc">4778941</article-id>
<article-id pub-id-type="doi">10.1371/journal.pone.0150879</article-id>
<article-id pub-id-type="publisher-id">PONE-D-15-53005</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>Plant Science</subject>
<subj-group><subject>Plant Physiology</subject>
<subj-group><subject>Plant Defenses</subject>
<subj-group><subject>Plant Resistance to Abiotic Stress</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 Pathology</subject>
<subj-group><subject>Plant Resistance to Abiotic Stress</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>Ecology</subject>
<subj-group><subject>Plant Ecology</subject>
<subj-group><subject>Plant-Environment Interactions</subject>
<subj-group><subject>Plant Resistance to Abiotic Stress</subject>
</subj-group>
</subj-group>
</subj-group>
</subj-group>
</subj-group>
<subj-group subj-group-type="Discipline-v3"><subject>Ecology and Environmental Sciences</subject>
<subj-group><subject>Ecology</subject>
<subj-group><subject>Plant Ecology</subject>
<subj-group><subject>Plant-Environment Interactions</subject>
<subj-group><subject>Plant Resistance to Abiotic Stress</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 Ecology</subject>
<subj-group><subject>Plant-Environment Interactions</subject>
<subj-group><subject>Plant Resistance to Abiotic Stress</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>Agriculture</subject>
<subj-group><subject>Crop Science</subject>
<subj-group><subject>Crops</subject>
<subj-group><subject>Cereal Crops</subject>
<subj-group><subject>Rice</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>Rice</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>Rice</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 Complexity</subject>
<subj-group><subject>Introns</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 Complexity</subject>
<subj-group><subject>Introns</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>Plant Science</subject>
<subj-group><subject>Plant Anatomy</subject>
<subj-group><subject>Leaves</subject>
</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 Properties</subject>
<subj-group><subject>Salinity</subject>
</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>Physical Chemistry</subject>
<subj-group><subject>Chemical Properties</subject>
<subj-group><subject>Salinity</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>Molecular Biology</subject>
<subj-group><subject>Molecular Biology Techniques</subject>
<subj-group><subject>Molecular Biology Assays and Analysis Techniques</subject>
<subj-group><subject>Phylogenetic Analysis</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>Molecular Biology Techniques</subject>
<subj-group><subject>Molecular Biology Assays and Analysis Techniques</subject>
<subj-group><subject>Phylogenetic Analysis</subject>
</subj-group>
</subj-group>
</subj-group>
</subj-group>
</article-categories>
<title-group><article-title>Genome-Wide Analysis of the AP2/ERF Gene Family in Physic Nut and Overexpression of the <italic>JcERF011</italic>
Gene in Rice Increased Its Sensitivity to Salinity Stress</article-title>
<alt-title alt-title-type="running-head">AP2/ERF Genes in the Physic Nut Genome</alt-title>
</title-group>
<contrib-group><contrib contrib-type="author"><name><surname>Tang</surname>
<given-names>Yuehui</given-names>
</name>
<xref ref-type="aff" rid="aff001"><sup>1</sup>
</xref>
<xref ref-type="aff" rid="aff002"><sup>2</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Qin</surname>
<given-names>Shanshan</given-names>
</name>
<xref ref-type="aff" rid="aff001"><sup>1</sup>
</xref>
<xref ref-type="aff" rid="aff002"><sup>2</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Guo</surname>
<given-names>Yali</given-names>
</name>
<xref ref-type="aff" rid="aff001"><sup>1</sup>
</xref>
<xref ref-type="aff" rid="aff002"><sup>2</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Chen</surname>
<given-names>Yanbo</given-names>
</name>
<xref ref-type="aff" rid="aff001"><sup>1</sup>
</xref>
<xref ref-type="aff" rid="aff002"><sup>2</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Wu</surname>
<given-names>Pingzhi</given-names>
</name>
<xref ref-type="aff" rid="aff001"><sup>1</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Chen</surname>
<given-names>Yaping</given-names>
</name>
<xref ref-type="aff" rid="aff001"><sup>1</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Li</surname>
<given-names>Meiru</given-names>
</name>
<xref ref-type="aff" rid="aff001"><sup>1</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Jiang</surname>
<given-names>Huawu</given-names>
</name>
<xref ref-type="aff" rid="aff001"><sup>1</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Wu</surname>
<given-names>Guojiang</given-names>
</name>
<xref ref-type="aff" rid="aff001"><sup>1</sup>
</xref>
<xref ref-type="corresp" rid="cor001">*</xref>
</contrib>
</contrib-group>
<aff id="aff001"><label>1</label>
<addr-line>Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, PR China</addr-line>
</aff>
<aff id="aff002"><label>2</label>
<addr-line>University of Chinese Academy of Sciences, Beijing, 100049, PR China</addr-line>
</aff>
<contrib-group><contrib contrib-type="editor"><name><surname>Zhang</surname>
<given-names>Jin-Song</given-names>
</name>
<role>Editor</role>
<xref ref-type="aff" rid="edit1"></xref>
</contrib>
</contrib-group>
<aff id="edit1"><addr-line>Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 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: HJ GW ML. Performed the experiments: YT SQ YG YC. Analyzed the data: YT PW YC. Contributed reagents/materials/analysis tools: YT SQ YG YC. Wrote the paper: YT. Designed the software used in analysis, PhyML version 3.0: YT.</p>
</fn>
<corresp id="cor001">* E-mail: <email>wugj@scbg.ac.cn</email>
</corresp>
</author-notes>
<pub-date pub-type="epub"><day>4</day>
<month>3</month>
<year>2016</year>
</pub-date>
<pub-date pub-type="collection"><year>2016</year>
</pub-date>
<volume>11</volume>
<issue>3</issue>
<elocation-id>e0150879</elocation-id>
<history><date date-type="received"><day>7</day>
<month>12</month>
<year>2015</year>
</date>
<date date-type="accepted"><day>19</day>
<month>2</month>
<year>2016</year>
</date>
</history>
<permissions><copyright-statement>© 2016 Tang et al</copyright-statement>
<copyright-year>2016</copyright-year>
<copyright-holder>Tang 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.0150879.pdf"></self-uri>
<abstract><p>The AP2/ERF transcription factors play crucial roles in plant growth, development and responses to biotic and abiotic stresses. A total of 119 AP2/ERF genes (<italic>JcAP2/ERFs</italic>
) have been identified in the physic nut genome; they include 16 AP2, 4 RAV, 1 Soloist, and 98 ERF genes. Phylogenetic analysis indicated that physic nut AP2 genes could be divided into 3 subgroups, while ERF genes could be classed into 11 groups or 43 subgroups. The AP2/ERF genes are non-randomly distributed across the 11 linkage groups of the physic nut genome and retain many duplicates which arose from ancient duplication events. The expression patterns of several <italic>JcAP2/ERF</italic>
duplicates in the physic nut showed differences among four tissues (root, stem, leaf, and seed), and 38 <italic>JcAP2/ERF</italic>
genes responded to at least one abiotic stressor (drought, salinity, phosphate starvation, and nitrogen starvation) in leaves and/or roots according to analysis of digital gene expression tag data. The expression of <italic>JcERF011</italic>
was downregulated by salinity stress in physic nut roots. Overexpression of the <italic>JcERF011</italic>
gene in rice plants increased its sensitivity to salinity stress. The increased expression levels of several salt tolerance-related genes were impaired in the <italic>JcERF011</italic>
-overexpressing plants under salinity stress.</p>
</abstract>
<funding-group><funding-statement>This work was supported by grants from the National Basic Research Program of China (973 Program) (grant no. 2010CB126603) (<ext-link ext-link-type="uri" xlink:href="http://www.973.gov.cn/">http://www.973.gov.cn/</ext-link>
) and the Knowledge Innovation Program of the Chinese Academy of Sciences (grant no. KSCX2-EW-J-28) (<ext-link ext-link-type="uri" xlink:href="http://www.cas.cn/">http://www.cas.cn/</ext-link>
). 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="0"></table-count>
<page-count count="20"></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>
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