The auxin response factor gene family in banana: genome-wide identification and expression analyses during development, ripening, and abiotic stress
Identifieur interne : 000082 ( Pmc/Curation ); précédent : 000081; suivant : 000083The auxin response factor gene family in banana: genome-wide identification and expression analyses during development, ripening, and abiotic stress
Auteurs : Wei Hu [République populaire de Chine] ; Jiao Zuo [République populaire de Chine] ; Xiaowan Hou [République populaire de Chine] ; Yan Yan [République populaire de Chine] ; Yunxie Wei [République populaire de Chine] ; Juhua Liu [République populaire de Chine] ; Meiying Li [République populaire de Chine] ; Biyu Xu [République populaire de Chine] ; Zhiqiang Jin [République populaire de Chine]Source :
- Frontiers in Plant Science [ 1664-462X ] ; 2015.
Abstract
Auxin signaling regulates various auxin-responsive genes via two types of transcriptional regulators, Auxin Response Factors (ARF) and Aux/IAA. ARF transcription factors act as critical components of auxin signaling that play important roles in modulating various biological processes. However, limited information about this gene family in fruit crops is currently available. Herein, 47
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DOI: 10.3389/fpls.2015.00742
PubMed: 26442055
PubMed Central: 4569978
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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">The auxin response factor gene family in banana: genome-wide identification and expression analyses during development, ripening, and abiotic stress</title><author><name sortKey="Hu, Wei" sort="Hu, Wei" uniqKey="Hu W" first="Wei" last="Hu">Wei Hu</name><affiliation wicri:level="1"><nlm:aff id="aff1"><institution>Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences</institution><country>Haikou, China</country></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea></wicri:regionArea></affiliation></author><author><name sortKey="Zuo, Jiao" sort="Zuo, Jiao" uniqKey="Zuo J" first="Jiao" last="Zuo">Jiao Zuo</name><affiliation wicri:level="1"><nlm:aff id="aff1"><institution>Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences</institution><country>Haikou, China</country></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea></wicri:regionArea></affiliation></author><author><name sortKey="Hou, Xiaowan" sort="Hou, Xiaowan" uniqKey="Hou X" first="Xiaowan" last="Hou">Xiaowan Hou</name><affiliation wicri:level="1"><nlm:aff id="aff1"><institution>Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences</institution><country>Haikou, China</country></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea></wicri:regionArea></affiliation></author><author><name sortKey="Yan, Yan" sort="Yan, Yan" uniqKey="Yan Y" first="Yan" last="Yan">Yan Yan</name><affiliation wicri:level="1"><nlm:aff id="aff1"><institution>Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences</institution><country>Haikou, China</country></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea></wicri:regionArea></affiliation></author><author><name sortKey="Wei, Yunxie" sort="Wei, Yunxie" uniqKey="Wei Y" first="Yunxie" last="Wei">Yunxie Wei</name><affiliation wicri:level="1"><nlm:aff id="aff1"><institution>Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences</institution><country>Haikou, China</country></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea></wicri:regionArea></affiliation></author><author><name sortKey="Liu, Juhua" sort="Liu, Juhua" uniqKey="Liu J" first="Juhua" last="Liu">Juhua Liu</name><affiliation wicri:level="1"><nlm:aff id="aff1"><institution>Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences</institution><country>Haikou, China</country></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea></wicri:regionArea></affiliation></author><author><name sortKey="Li, Meiying" sort="Li, Meiying" uniqKey="Li M" first="Meiying" last="Li">Meiying Li</name><affiliation wicri:level="1"><nlm:aff id="aff1"><institution>Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences</institution><country>Haikou, China</country></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea></wicri:regionArea></affiliation></author><author><name sortKey="Xu, Biyu" sort="Xu, Biyu" uniqKey="Xu B" first="Biyu" last="Xu">Biyu Xu</name><affiliation wicri:level="1"><nlm:aff id="aff1"><institution>Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences</institution><country>Haikou, China</country></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea></wicri:regionArea></affiliation></author><author><name sortKey="Jin, Zhiqiang" sort="Jin, Zhiqiang" uniqKey="Jin Z" first="Zhiqiang" last="Jin">Zhiqiang Jin</name><affiliation wicri:level="1"><nlm:aff id="aff1"><institution>Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences</institution><country>Haikou, China</country></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea></wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="aff2"><institution>Key Laboratory of Genetic Improvement of Bananas, Haikou Experimental Station, Chinese Academy of Tropical Agricultural Sciences</institution><country>Haikou, China</country></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea></wicri:regionArea></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">26442055</idno><idno type="pmc">4569978</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4569978</idno><idno type="RBID">PMC:4569978</idno><idno type="doi">10.3389/fpls.2015.00742</idno><date when="2015">2015</date><idno type="wicri:Area/Pmc/Corpus">000082</idno><idno type="wicri:Area/Pmc/Curation">000082</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">The auxin response factor gene family in banana: genome-wide identification and expression analyses during development, ripening, and abiotic stress</title><author><name sortKey="Hu, Wei" sort="Hu, Wei" uniqKey="Hu W" first="Wei" last="Hu">Wei Hu</name><affiliation wicri:level="1"><nlm:aff id="aff1"><institution>Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences</institution><country>Haikou, China</country></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea></wicri:regionArea></affiliation></author><author><name sortKey="Zuo, Jiao" sort="Zuo, Jiao" uniqKey="Zuo J" first="Jiao" last="Zuo">Jiao Zuo</name><affiliation wicri:level="1"><nlm:aff id="aff1"><institution>Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences</institution><country>Haikou, China</country></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea></wicri:regionArea></affiliation></author><author><name sortKey="Hou, Xiaowan" sort="Hou, Xiaowan" uniqKey="Hou X" first="Xiaowan" last="Hou">Xiaowan Hou</name><affiliation wicri:level="1"><nlm:aff id="aff1"><institution>Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences</institution><country>Haikou, China</country></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea></wicri:regionArea></affiliation></author><author><name sortKey="Yan, Yan" sort="Yan, Yan" uniqKey="Yan Y" first="Yan" last="Yan">Yan Yan</name><affiliation wicri:level="1"><nlm:aff id="aff1"><institution>Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences</institution><country>Haikou, China</country></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea></wicri:regionArea></affiliation></author><author><name sortKey="Wei, Yunxie" sort="Wei, Yunxie" uniqKey="Wei Y" first="Yunxie" last="Wei">Yunxie Wei</name><affiliation wicri:level="1"><nlm:aff id="aff1"><institution>Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences</institution><country>Haikou, China</country></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea></wicri:regionArea></affiliation></author><author><name sortKey="Liu, Juhua" sort="Liu, Juhua" uniqKey="Liu J" first="Juhua" last="Liu">Juhua Liu</name><affiliation wicri:level="1"><nlm:aff id="aff1"><institution>Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences</institution><country>Haikou, China</country></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea></wicri:regionArea></affiliation></author><author><name sortKey="Li, Meiying" sort="Li, Meiying" uniqKey="Li M" first="Meiying" last="Li">Meiying Li</name><affiliation wicri:level="1"><nlm:aff id="aff1"><institution>Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences</institution><country>Haikou, China</country></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea></wicri:regionArea></affiliation></author><author><name sortKey="Xu, Biyu" sort="Xu, Biyu" uniqKey="Xu B" first="Biyu" last="Xu">Biyu Xu</name><affiliation wicri:level="1"><nlm:aff id="aff1"><institution>Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences</institution><country>Haikou, China</country></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea></wicri:regionArea></affiliation></author><author><name sortKey="Jin, Zhiqiang" sort="Jin, Zhiqiang" uniqKey="Jin Z" first="Zhiqiang" last="Jin">Zhiqiang Jin</name><affiliation wicri:level="1"><nlm:aff id="aff1"><institution>Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences</institution><country>Haikou, China</country></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea></wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="aff2"><institution>Key Laboratory of Genetic Improvement of Bananas, Haikou Experimental Station, Chinese Academy of Tropical Agricultural Sciences</institution><country>Haikou, China</country></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea></wicri:regionArea></affiliation></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>Auxin signaling regulates various auxin-responsive genes via two types of transcriptional regulators, Auxin Response Factors (ARF) and Aux/IAA. ARF transcription factors act as critical components of auxin signaling that play important roles in modulating various biological processes. However, limited information about this gene family in fruit crops is currently available. Herein, 47 <italic>ARF</italic> genes were identified in banana based on its genome sequence. Phylogenetic analysis of the ARFs from banana, rice, and <italic>Arabidopsis</italic> suggested that the ARFs could be divided into four subgroups, among which most ARFs from the banana showed a closer relationship with those from rice than those from <italic>Arabidopsis</italic>. Conserved motif analysis showed that all identified MaARFs had typical DNA-binding and ARF domains, but 12 members lacked the dimerization domain. Gene structure analysis showed that the number of exons in <italic>MaARF</italic> genes ranged from 5 to 21, suggesting large variation amongst banana <italic>ARF</italic> genes. The comprehensive expression profiles of <italic>MaARF</italic> genes yielded useful information about their involvement in diverse tissues, different stages of fruit development and ripening, and responses to abiotic stresses in different varieties. Interaction networks and co-expression assays indicated the strong transcriptional response of banana ARFs and ARF-mediated networks in early fruit development for different varieties. Our systematic analysis of MaARFs revealed robust tissue-specific, development-dependent, and abiotic stress-responsive candidate <italic>MaARF</italic> genes for further functional assays <italic>in planta</italic>. These findings could lead to potential applications in the genetic improvement of banana cultivars, and yield new insights into the complexity of the control of <italic>MaARF</italic> gene expression at the transcriptional level. Finally, they support the hypothesis that ARFs are a crucial component of the auxin signaling pathway, which regulates a wide range of physiological processes.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Asif, M H" uniqKey="Asif M">M. H. Asif</name></author><author><name sortKey="Lakhwani, D" uniqKey="Lakhwani D">D. Lakhwani</name></author><author><name sortKey="Pathak, S" uniqKey="Pathak S">S. Pathak</name></author><author><name sortKey="Bhambhani, S" uniqKey="Bhambhani S">S. Bhambhani</name></author><author><name sortKey="Bag, S K" uniqKey="Bag S">S. K. Bag</name></author><author><name sortKey="Trivedi, P K" uniqKey="Trivedi P">P. K. Trivedi</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Backiyarani, S" uniqKey="Backiyarani S">S. Backiyarani</name></author><author><name sortKey="Uma, S" uniqKey="Uma S">S. Uma</name></author><author><name sortKey="Nithya, S" uniqKey="Nithya S">S. 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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">26442055</article-id><article-id pub-id-type="pmc">4569978</article-id><article-id pub-id-type="doi">10.3389/fpls.2015.00742</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>The auxin response factor gene family in banana: genome-wide identification and expression analyses during development, ripening, and abiotic stress</article-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Hu</surname><given-names>Wei</given-names></name><xref ref-type="aff" rid="aff1"><sup>1</sup></xref><xref ref-type="author-notes" rid="fn004"><sup>†</sup></xref><uri xlink:type="simple" xlink:href="http://loop.frontiersin.org/people/223670/overview"></uri></contrib><contrib contrib-type="author"><name><surname>Zuo</surname><given-names>Jiao</given-names></name><xref ref-type="aff" rid="aff1"><sup>1</sup></xref><xref ref-type="author-notes" rid="fn004"><sup>†</sup></xref></contrib><contrib contrib-type="author"><name><surname>Hou</surname><given-names>Xiaowan</given-names></name><xref ref-type="aff" rid="aff1"><sup>1</sup></xref><xref ref-type="author-notes" rid="fn004"><sup>†</sup></xref></contrib><contrib contrib-type="author"><name><surname>Yan</surname><given-names>Yan</given-names></name><xref ref-type="aff" rid="aff1"><sup>1</sup></xref></contrib><contrib contrib-type="author"><name><surname>Wei</surname><given-names>Yunxie</given-names></name><xref ref-type="aff" rid="aff1"><sup>1</sup></xref></contrib><contrib contrib-type="author"><name><surname>Liu</surname><given-names>Juhua</given-names></name><xref ref-type="aff" rid="aff1"><sup>1</sup></xref></contrib><contrib contrib-type="author"><name><surname>Li</surname><given-names>Meiying</given-names></name><xref ref-type="aff" rid="aff1"><sup>1</sup></xref></contrib><contrib contrib-type="author"><name><surname>Xu</surname><given-names>Biyu</given-names></name><xref ref-type="aff" rid="aff1"><sup>1</sup></xref><xref ref-type="author-notes" rid="fn001"><sup>*</sup></xref></contrib><contrib contrib-type="author"><name><surname>Jin</surname><given-names>Zhiqiang</given-names></name><xref ref-type="aff" rid="aff1"><sup>1</sup></xref><xref ref-type="aff" rid="aff2"><sup>2</sup></xref><xref ref-type="author-notes" rid="fn002"><sup>*</sup></xref></contrib></contrib-group><aff id="aff1"><sup>1</sup><institution>Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences</institution><country>Haikou, China</country></aff><aff id="aff2"><sup>2</sup><institution>Key Laboratory of Genetic Improvement of Bananas, Haikou Experimental Station, Chinese Academy of Tropical Agricultural Sciences</institution><country>Haikou, China</country></aff><author-notes><fn fn-type="edited-by"><p>Edited by: Vasileios Fotopoulos, Cyprus University of Technology, Cyprus</p></fn><fn fn-type="edited-by"><p>Reviewed by: Cankui Zhang, Purdue University, USA; Rachid Lahlali, Canadian Light Source, Canada</p></fn><corresp id="fn001">*Correspondence: Biyu Xu, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Xueyuan Road 4, Longhua County, Haikou City, Hainan Province 571101, China <email xlink:type="simple">biyuxu@126.com</email>;</corresp><corresp id="fn002">Zhiqiang Jin, Haikou Experimental Station, Chinese Academy of Tropical Agricultural Sciences, Yilong W Road 2, Longhua County, Haikou City, Hainan Province 570102, China <email xlink:type="simple">18689846976@163.com</email></corresp><fn fn-type="other" id="fn003"><p>This article was submitted to Crop Science and Horticulture, a section of the journal Frontiers in Plant Science</p></fn><fn fn-type="present-address" id="fn004"><p>†These authors have contributed equally to this work.</p></fn></author-notes><pub-date pub-type="epub"><day>15</day><month>9</month><year>2015</year></pub-date><pub-date pub-type="collection"><year>2015</year></pub-date><volume>6</volume><elocation-id>742</elocation-id><history><date date-type="received"><day>08</day><month>5</month><year>2015</year></date><date date-type="accepted"><day>31</day><month>8</month><year>2015</year></date></history><permissions><copyright-statement>Copyright © 2015 Hu, Zuo, Hou, Yan, Wei, Liu, Li, Xu and Jin.</copyright-statement><copyright-year>2015</copyright-year><copyright-holder>Hu, Zuo, Hou, Yan, Wei, Liu, Li, Xu and Jin</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>Auxin signaling regulates various auxin-responsive genes via two types of transcriptional regulators, Auxin Response Factors (ARF) and Aux/IAA. ARF transcription factors act as critical components of auxin signaling that play important roles in modulating various biological processes. However, limited information about this gene family in fruit crops is currently available. Herein, 47 <italic>ARF</italic> genes were identified in banana based on its genome sequence. Phylogenetic analysis of the ARFs from banana, rice, and <italic>Arabidopsis</italic> suggested that the ARFs could be divided into four subgroups, among which most ARFs from the banana showed a closer relationship with those from rice than those from <italic>Arabidopsis</italic>. Conserved motif analysis showed that all identified MaARFs had typical DNA-binding and ARF domains, but 12 members lacked the dimerization domain. Gene structure analysis showed that the number of exons in <italic>MaARF</italic> genes ranged from 5 to 21, suggesting large variation amongst banana <italic>ARF</italic> genes. The comprehensive expression profiles of <italic>MaARF</italic> genes yielded useful information about their involvement in diverse tissues, different stages of fruit development and ripening, and responses to abiotic stresses in different varieties. Interaction networks and co-expression assays indicated the strong transcriptional response of banana ARFs and ARF-mediated networks in early fruit development for different varieties. Our systematic analysis of MaARFs revealed robust tissue-specific, development-dependent, and abiotic stress-responsive candidate <italic>MaARF</italic> genes for further functional assays <italic>in planta</italic>. These findings could lead to potential applications in the genetic improvement of banana cultivars, and yield new insights into the complexity of the control of <italic>MaARF</italic> gene expression at the transcriptional level. Finally, they support the hypothesis that ARFs are a crucial component of the auxin signaling pathway, which regulates a wide range of physiological processes.</p></abstract><kwd-group><kwd>auxin response factors (ARF) transcription factor</kwd><kwd>abiotic stresses</kwd><kwd>banana</kwd><kwd>development</kwd><kwd>expression analysis</kwd><kwd>ripening</kwd></kwd-group><counts><fig-count count="8"></fig-count><table-count count="0"></table-count><equation-count count="0"></equation-count><ref-count count="66"></ref-count><page-count count="16"></page-count><word-count count="9529"></word-count></counts></article-meta></front></pmc></record>Pour manipuler ce document sous Unix (Dilib)
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