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Genome-Wide Characterization and Expression Profiling of the AUXIN RESPONSE FACTOR (ARF) Gene Family in Eucalyptus grandis

Identifieur interne : 000211 ( Pmc/Curation ); précédent : 000210; suivant : 000212

Genome-Wide Characterization and Expression Profiling of the AUXIN RESPONSE FACTOR (ARF) Gene Family in Eucalyptus grandis

Auteurs : Hong Yu [France] ; Marçal Soler [France] ; Isabelle Mila [France] ; Hélène San Clemente [France] ; Bruno Savelli [France] ; Christophe Dunand [France] ; Jorge A. P. Paiva [Portugal] ; Alexander A. Myburg [Afrique du Sud] ; Mondher Bouzayen [France] ; Jacqueline Grima-Pettenati [France] ; Hua Cassan-Wang [France]

Source :

RBID : PMC:4182523

Abstract

Auxin is a central hormone involved in a wide range of developmental processes including the specification of vascular stem cells. Auxin Response Factors (ARF) are important actors of the auxin signalling pathway, regulating the transcription of auxin-responsive genes through direct binding to their promoters. The recent availability of the Eucalyptus grandis genome sequence allowed us to examine the characteristics and evolutionary history of this gene family in a woody plant of high economic importance. With 17 members, the E. grandis ARF gene family is slightly contracted, as compared to those of most angiosperms studied hitherto, lacking traces of duplication events. In silico analysis of alternative transcripts and gene truncation suggested that these two mechanisms were preeminent in shaping the functional diversity of the ARF family in Eucalyptus. Comparative phylogenetic analyses with genomes of other taxonomic lineages revealed the presence of a new ARF clade found preferentially in woody and/or perennial plants. High-throughput expression profiling among different organs and tissues and in response to environmental cues highlighted genes expressed in vascular cambium and/or developing xylem, responding dynamically to various environmental stimuli. Finally, this study allowed identification of three ARF candidates potentially involved in the auxin-regulated transcriptional program underlying wood formation.


Url:
DOI: 10.1371/journal.pone.0108906
PubMed: 25269088
PubMed Central: 4182523

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PMC:4182523

Le document en format XML

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<p>Auxin is a central hormone involved in a wide range of developmental processes including the specification of vascular stem cells. Auxin Response Factors (ARF) are important actors of the auxin signalling pathway, regulating the transcription of auxin-responsive genes through direct binding to their promoters. The recent availability of the
<italic>Eucalyptus grandis</italic>
genome sequence allowed us to examine the characteristics and evolutionary history of this gene family in a woody plant of high economic importance. With 17 members, the
<italic>E. grandis ARF</italic>
gene family is slightly contracted, as compared to those of most angiosperms studied hitherto, lacking traces of duplication events.
<italic>In silico</italic>
analysis of alternative transcripts and gene truncation suggested that these two mechanisms were preeminent in shaping the functional diversity of the
<italic>ARF</italic>
family in
<italic>Eucalyptus</italic>
. Comparative phylogenetic analyses with genomes of other taxonomic lineages revealed the presence of a new ARF clade found preferentially in woody and/or perennial plants. High-throughput expression profiling among different organs and tissues and in response to environmental cues highlighted genes expressed in vascular cambium and/or developing xylem, responding dynamically to various environmental stimuli. Finally, this study allowed identification of three
<italic>ARF</italic>
candidates potentially involved in the auxin-regulated transcriptional program underlying wood formation.</p>
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</TEI>
<pmc article-type="research-article">
<pmc-dir>properties open_access</pmc-dir>
<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">25269088</article-id>
<article-id pub-id-type="pmc">4182523</article-id>
<article-id pub-id-type="publisher-id">PONE-D-14-29515</article-id>
<article-id pub-id-type="doi">10.1371/journal.pone.0108906</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>Agroecology</subject>
<subj-group>
<subject>Agroforests</subject>
</subj-group>
</subj-group>
<subj-group>
<subject>Forestry</subject>
</subj-group>
</subj-group>
<subj-group>
<subject>Biochemistry</subject>
<subj-group>
<subject>Hormones</subject>
<subj-group>
<subject>Plant Hormones</subject>
<subj-group>
<subject>Auxins</subject>
</subj-group>
</subj-group>
</subj-group>
<subj-group>
<subject>Plant Biochemistry</subject>
</subj-group>
</subj-group>
<subj-group>
<subject>Computational Biology</subject>
<subj-group>
<subject>Genome Analysis</subject>
<subj-group>
<subject>Gene Prediction</subject>
<subject>Genome-Wide Association Studies</subject>
</subj-group>
</subj-group>
</subj-group>
<subj-group>
<subject>Evolutionary Biology</subject>
<subj-group>
<subject>Evolutionary Systematics</subject>
<subj-group>
<subject>Phylogenetics</subject>
<subj-group>
<subject>Plant Phylogenetics</subject>
</subj-group>
</subj-group>
</subj-group>
<subj-group>
<subject>Molecular Evolution</subject>
<subj-group>
<subject>Gene Duplication</subject>
</subj-group>
</subj-group>
<subj-group>
<subject>Organismal Evolution</subject>
<subj-group>
<subject>Plant Evolution</subject>
</subj-group>
</subj-group>
</subj-group>
<subj-group>
<subject>Genetics</subject>
<subj-group>
<subject>Plant Genetics</subject>
<subj-group>
<subject>Crop Genetics</subject>
</subj-group>
</subj-group>
<subj-group>
<subject>Gene Function</subject>
<subject>Genomics</subject>
</subj-group>
</subj-group>
<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>
<subject>Plant Science</subject>
</subj-group>
</subj-group>
</article-categories>
<title-group>
<article-title>Genome-Wide Characterization and Expression Profiling of the
<italic>AUXIN RESPONSE FACTOR</italic>
(
<italic>ARF</italic>
) Gene Family in
<italic>Eucalyptus grandis</italic>
</article-title>
<alt-title alt-title-type="running-head">The
<italic>Eucalyptus ARF</italic>
Family</alt-title>
</title-group>
<contrib-group>
<contrib contrib-type="author">
<name>
<surname>Yu</surname>
<given-names>Hong</given-names>
</name>
<xref ref-type="aff" rid="aff1">
<sup>1</sup>
</xref>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Soler</surname>
<given-names>Marçal</given-names>
</name>
<xref ref-type="aff" rid="aff1">
<sup>1</sup>
</xref>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Mila</surname>
<given-names>Isabelle</given-names>
</name>
<xref ref-type="aff" rid="aff2">
<sup>2</sup>
</xref>
</contrib>
<contrib contrib-type="author">
<name>
<surname>San Clemente</surname>
<given-names>Hélène</given-names>
</name>
<xref ref-type="aff" rid="aff1">
<sup>1</sup>
</xref>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Savelli</surname>
<given-names>Bruno</given-names>
</name>
<xref ref-type="aff" rid="aff1">
<sup>1</sup>
</xref>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Dunand</surname>
<given-names>Christophe</given-names>
</name>
<xref ref-type="aff" rid="aff1">
<sup>1</sup>
</xref>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Paiva</surname>
<given-names>Jorge A. P.</given-names>
</name>
<xref ref-type="aff" rid="aff3">
<sup>3</sup>
</xref>
<xref ref-type="aff" rid="aff4">
<sup>4</sup>
</xref>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Myburg</surname>
<given-names>Alexander A.</given-names>
</name>
<xref ref-type="aff" rid="aff5">
<sup>5</sup>
</xref>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Bouzayen</surname>
<given-names>Mondher</given-names>
</name>
<xref ref-type="aff" rid="aff2">
<sup>2</sup>
</xref>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Grima-Pettenati</surname>
<given-names>Jacqueline</given-names>
</name>
<xref ref-type="aff" rid="aff1">
<sup>1</sup>
</xref>
<xref ref-type="corresp" rid="cor1">
<sup>*</sup>
</xref>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Cassan-Wang</surname>
<given-names>Hua</given-names>
</name>
<xref ref-type="aff" rid="aff1">
<sup>1</sup>
</xref>
</contrib>
</contrib-group>
<aff id="aff1">
<label>1</label>
<addr-line>LRSV Laboratoire de Recherche en Sciences Végétales, UMR5546, Université Toulouse III/CNRS, Castanet Tolosan, France</addr-line>
</aff>
<aff id="aff2">
<label>2</label>
<addr-line>Université de Toulouse, Institut National Polytechnique-Ecole Nationale Supérieure Agronomique de Toulouse, Laboratoire de Génomique et Biotechnologie des Fruits, Castanet-Tolosan, France</addr-line>
</aff>
<aff id="aff3">
<label>3</label>
<addr-line>Instituto de Investigação Científica e Tropical (IICT/MCTES), Lisboa, Portugal</addr-line>
</aff>
<aff id="aff4">
<label>4</label>
<addr-line>Instituto de Biologia Experimental e Tecnológica (IBET), Oeiras, Portugal</addr-line>
</aff>
<aff id="aff5">
<label>5</label>
<addr-line>Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), Genomics Research Institute (GRI), University of Pretoria, Pretoria, South Africa</addr-line>
</aff>
<contrib-group>
<contrib contrib-type="editor">
<name>
<surname>Quint</surname>
<given-names>Marcel</given-names>
</name>
<role>Editor</role>
<xref ref-type="aff" rid="edit1"></xref>
</contrib>
</contrib-group>
<aff id="edit1">
<addr-line>Leibniz Institute of Plant Biochemistry, Germany</addr-line>
</aff>
<author-notes>
<corresp id="cor1">* E-mail:
<email>yu@lrsv.ups-tlse.fr</email>
</corresp>
<fn fn-type="conflict">
<p>
<bold>Competing Interests: </bold>
The authors declare that no competing interests exist.</p>
</fn>
<fn fn-type="con">
<p>Conceived and designed the experiments: HY HCW MS JGP. Performed the experiments: HY HSC CD IM BS. Analyzed the data: HY HCW MB MS JGP. Contributed reagents/materials/analysis tools: JAPP AAM. Wrote the paper: JGP YH HCW.</p>
</fn>
</author-notes>
<pub-date pub-type="collection">
<year>2014</year>
</pub-date>
<pub-date pub-type="epub">
<day>30</day>
<month>9</month>
<year>2014</year>
</pub-date>
<volume>9</volume>
<issue>9</issue>
<elocation-id>e108906</elocation-id>
<history>
<date date-type="received">
<day>2</day>
<month>7</month>
<year>2014</year>
</date>
<date date-type="accepted">
<day>27</day>
<month>8</month>
<year>2014</year>
</date>
</history>
<permissions>
<copyright-year>2014</copyright-year>
<copyright-holder>Yu 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>Auxin is a central hormone involved in a wide range of developmental processes including the specification of vascular stem cells. Auxin Response Factors (ARF) are important actors of the auxin signalling pathway, regulating the transcription of auxin-responsive genes through direct binding to their promoters. The recent availability of the
<italic>Eucalyptus grandis</italic>
genome sequence allowed us to examine the characteristics and evolutionary history of this gene family in a woody plant of high economic importance. With 17 members, the
<italic>E. grandis ARF</italic>
gene family is slightly contracted, as compared to those of most angiosperms studied hitherto, lacking traces of duplication events.
<italic>In silico</italic>
analysis of alternative transcripts and gene truncation suggested that these two mechanisms were preeminent in shaping the functional diversity of the
<italic>ARF</italic>
family in
<italic>Eucalyptus</italic>
. Comparative phylogenetic analyses with genomes of other taxonomic lineages revealed the presence of a new ARF clade found preferentially in woody and/or perennial plants. High-throughput expression profiling among different organs and tissues and in response to environmental cues highlighted genes expressed in vascular cambium and/or developing xylem, responding dynamically to various environmental stimuli. Finally, this study allowed identification of three
<italic>ARF</italic>
candidates potentially involved in the auxin-regulated transcriptional program underlying wood formation.</p>
</abstract>
<funding-group>
<funding-statement>This work was supported by the Centre National pour la Recherche Scientifique (CNRS), the University Paul Sabatier Toulouse III (UPS), the French Laboratory of Excellence project “TULIP” (ANR-10-LABX-41; ANR-11-IDEX-0002-02) and the Plant KBBE TreeForJoules project (ANR-2010-KBBE-007-01 (FR) and P-KBBE/AGR_GPL/0001/2010 (FCT, PT)). HY was supported by PhD grants from the China Scholarship council. MS was supported by a Postdoc fellowship “Beatriu de Pinós” thanks to the Departament d'Universitats, Recerca i Societat de la Informació de la Generalitat de Catalunya. JAPP acknowledges Fundação para a Ciência e a Tecnologia (FCT, Portugal) and his research contract funded by Programa Ciência 2008 and POPH (QREN). 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="13"></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 Eucalyptus ARF sequences used in this paper are available in phytozome
<ext-link ext-link-type="uri" xlink:href="http://www.phytozome.net/">http://www.phytozome.net/</ext-link>
. E. globulus RNA Seq Illumina reads are provided in File S1.</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 Eucalyptus ARF sequences used in this paper are available in phytozome
<ext-link ext-link-type="uri" xlink:href="http://www.phytozome.net/">http://www.phytozome.net/</ext-link>
. E. globulus RNA Seq Illumina reads are provided in File S1.</p>
</notes>
</front>
</pmc>
</record>

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