PoplarV1, Main, Exploration, bibRecord, 001B20

The Eucalyptus grandis R2R3-MYB transcription factor family: evidence for woody growth-related evolution and function.

Identifieur interne : 001B20 ( Main/Exploration ); précédent : 001B19; suivant : 001B21

The Eucalyptus grandis R2R3-MYB transcription factor family: evidence for woody growth-related evolution and function.

Auteurs : Marçal Soler [France] ; Eduardo Leal Oliveira Camargo [France] ; Victor Carocha [France, Portugal] ; Hua Cassan-Wang [France] ; Hélène San Clemente [France] ; Bruno Savelli [France] ; Charles A. Hefer [Afrique du Sud] ; Jorge A Pinto Paiva [Portugal] ; Alexander A. Myburg [Afrique du Sud] ; Jacqueline Grima-Pettenati [France]

Source :

The New phytologist [ 1469-8137 ] ; 2015.

RBID : pubmed:25250741

Descripteurs français

English descriptors

KwdEn :
- Biological Evolution (MeSH), Computer Simulation (MeSH), Eucalyptus (genetics), Eucalyptus (growth & development), Gene Expression Profiling (MeSH), Gene Expression Regulation, Plant (MeSH), Genes, Plant (MeSH), Microfluidics (MeSH), Models, Genetic (MeSH), Multigene Family (MeSH), Phylogeny (MeSH), Plant Proteins (genetics), RNA, Messenger (genetics), RNA, Messenger (metabolism), Real-Time Polymerase Chain Reaction (MeSH), Sequence Analysis, RNA (MeSH), Species Specificity (MeSH), Transcription Factors (genetics), Transcription Factors (metabolism), Wood (growth & development).
MESH :
- chemical , genetics : Plant Proteins, RNA, Messenger, Transcription Factors.
- genetics : Eucalyptus.
- growth & development : Eucalyptus, Wood.
- chemical , metabolism : RNA, Messenger, Transcription Factors.
- Biological Evolution, Computer Simulation, Gene Expression Profiling, Gene Expression Regulation, Plant, Genes, Plant, Microfluidics, Models, Genetic, Multigene Family, Phylogeny, Real-Time Polymerase Chain Reaction, Sequence Analysis, RNA, Species Specificity.

Abstract

The R2R3-MYB family, one of the largest transcription factor families in higher plants, controls a wide variety of plant-specific processes including, notably, phenylpropanoid metabolism and secondary cell wall formation. We performed a genome-wide analysis of this superfamily in Eucalyptus, one of the most planted hardwood trees world-wide. A total of 141 predicted R2R3-MYB sequences identified in the Eucalyptus grandis genome sequence were subjected to comparative phylogenetic analyses with Arabidopsis thaliana, Oryza sativa, Populus trichocarpa and Vitis vinifera. We analysed features such as gene structure, conserved motifs and genome location. Transcript abundance patterns were assessed by RNAseq and validated by high-throughput quantitative PCR. We found some R2R3-MYB subgroups with expanded membership in E. grandis, V. vinifera and P. trichocarpa, and others preferentially found in woody species, suggesting diversification of specific functions in woody plants. By contrast, subgroups containing key genes regulating lignin biosynthesis and secondary cell wall formation are more conserved across all of the species analysed. In Eucalyptus, R2R3-MYB tandem gene duplications seem to disproportionately affect woody-preferential and woody-expanded subgroups. Interestingly, some of the genes belonging to woody-preferential subgroups show higher expression in the cambial region, suggesting a putative role in the regulation of secondary growth.

DOI: 10.1111/nph.13039
PubMed: 25250741

Affiliations:

Links toward previous steps (curation, corpus...)

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Le document en format XML

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<author><name sortKey="Grima Pettenati, Jacqueline" sort="Grima Pettenati, Jacqueline" uniqKey="Grima Pettenati J" first="Jacqueline" last="Grima-Pettenati">Jacqueline Grima-Pettenati</name>
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<country xml:lang="fr">France</country>
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<series><title level="j">The New phytologist</title>
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<profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Biological Evolution (MeSH)</term>
<term>Computer Simulation (MeSH)</term>
<term>Eucalyptus (genetics)</term>
<term>Eucalyptus (growth & development)</term>
<term>Gene Expression Profiling (MeSH)</term>
<term>Gene Expression Regulation, Plant (MeSH)</term>
<term>Genes, Plant (MeSH)</term>
<term>Microfluidics (MeSH)</term>
<term>Models, Genetic (MeSH)</term>
<term>Multigene Family (MeSH)</term>
<term>Phylogeny (MeSH)</term>
<term>Plant Proteins (genetics)</term>
<term>RNA, Messenger (genetics)</term>
<term>RNA, Messenger (metabolism)</term>
<term>Real-Time Polymerase Chain Reaction (MeSH)</term>
<term>Sequence Analysis, RNA (MeSH)</term>
<term>Species Specificity (MeSH)</term>
<term>Transcription Factors (genetics)</term>
<term>Transcription Factors (metabolism)</term>
<term>Wood (growth & development)</term>
</keywords>
<keywords scheme="KwdFr" xml:lang="fr"><term>ARN messager (génétique)</term>
<term>ARN messager (métabolisme)</term>
<term>Analyse de profil d'expression de gènes (MeSH)</term>
<term>Analyse de séquence d'ARN (MeSH)</term>
<term>Bois (croissance et développement)</term>
<term>Eucalyptus (croissance et développement)</term>
<term>Eucalyptus (génétique)</term>
<term>Facteurs de transcription (génétique)</term>
<term>Facteurs de transcription (métabolisme)</term>
<term>Famille multigénique (MeSH)</term>
<term>Gènes de plante (MeSH)</term>
<term>Microfluidique (MeSH)</term>
<term>Modèles génétiques (MeSH)</term>
<term>Phylogenèse (MeSH)</term>
<term>Protéines végétales (génétique)</term>
<term>Réaction de polymérisation en chaine en temps réel (MeSH)</term>
<term>Régulation de l'expression des gènes végétaux (MeSH)</term>
<term>Simulation numérique (MeSH)</term>
<term>Spécificité d'espèce (MeSH)</term>
<term>Évolution biologique (MeSH)</term>
</keywords>
<keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>Plant Proteins</term>
<term>RNA, Messenger</term>
<term>Transcription Factors</term>
</keywords>
<keywords scheme="MESH" qualifier="croissance et développement" xml:lang="fr"><term>Bois</term>
<term>Eucalyptus</term>
</keywords>
<keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Eucalyptus</term>
</keywords>
<keywords scheme="MESH" qualifier="growth & development" xml:lang="en"><term>Eucalyptus</term>
<term>Wood</term>
</keywords>
<keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>ARN messager</term>
<term>Eucalyptus</term>
<term>Facteurs de transcription</term>
<term>Protéines végétales</term>
</keywords>
<keywords scheme="MESH" type="chemical" qualifier="metabolism" xml:lang="en"><term>RNA, Messenger</term>
<term>Transcription Factors</term>
</keywords>
<keywords scheme="MESH" qualifier="métabolisme" xml:lang="fr"><term>ARN messager</term>
<term>Facteurs de transcription</term>
</keywords>
<keywords scheme="MESH" xml:lang="en"><term>Biological Evolution</term>
<term>Computer Simulation</term>
<term>Gene Expression Profiling</term>
<term>Gene Expression Regulation, Plant</term>
<term>Genes, Plant</term>
<term>Microfluidics</term>
<term>Models, Genetic</term>
<term>Multigene Family</term>
<term>Phylogeny</term>
<term>Real-Time Polymerase Chain Reaction</term>
<term>Sequence Analysis, RNA</term>
<term>Species Specificity</term>
</keywords>
<keywords scheme="MESH" xml:lang="fr"><term>Analyse de profil d'expression de gènes</term>
<term>Analyse de séquence d'ARN</term>
<term>Famille multigénique</term>
<term>Gènes de plante</term>
<term>Microfluidique</term>
<term>Modèles génétiques</term>
<term>Phylogenèse</term>
<term>Réaction de polymérisation en chaine en temps réel</term>
<term>Régulation de l'expression des gènes végétaux</term>
<term>Simulation numérique</term>
<term>Spécificité d'espèce</term>
<term>Évolution biologique</term>
</keywords>
</textClass>
</profileDesc>
</teiHeader>
<front><div type="abstract" xml:lang="en">The R2R3-MYB family, one of the largest transcription factor families in higher plants, controls a wide variety of plant-specific processes including, notably, phenylpropanoid metabolism and secondary cell wall formation. We performed a genome-wide analysis of this superfamily in Eucalyptus, one of the most planted hardwood trees world-wide. A total of 141 predicted R2R3-MYB sequences identified in the Eucalyptus grandis genome sequence were subjected to comparative phylogenetic analyses with Arabidopsis thaliana, Oryza sativa, Populus trichocarpa and Vitis vinifera. We analysed features such as gene structure, conserved motifs and genome location. Transcript abundance patterns were assessed by RNAseq and validated by high-throughput quantitative PCR. We found some R2R3-MYB subgroups with expanded membership in E. grandis, V. vinifera and P. trichocarpa, and others preferentially found in woody species, suggesting diversification of specific functions in woody plants. By contrast, subgroups containing key genes regulating lignin biosynthesis and secondary cell wall formation are more conserved across all of the species analysed. In Eucalyptus, R2R3-MYB tandem gene duplications seem to disproportionately affect woody-preferential and woody-expanded subgroups. Interestingly, some of the genes belonging to woody-preferential subgroups show higher expression in the cambial region, suggesting a putative role in the regulation of secondary growth.</div>
</front>
</TEI>
<pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">25250741</PMID>
<DateCompleted><Year>2016</Year>
<Month>02</Month>
<Day>01</Day>
</DateCompleted>
<DateRevised><Year>2020</Year>
<Month>09</Month>
<Day>30</Day>
</DateRevised>
<Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1469-8137</ISSN>
<JournalIssue CitedMedium="Internet"><Volume>206</Volume>
<Issue>4</Issue>
<PubDate><Year>2015</Year>
<Month>Jun</Month>
</PubDate>
</JournalIssue>
<Title>The New phytologist</Title>
<ISOAbbreviation>New Phytol</ISOAbbreviation>
</Journal>
<ArticleTitle>The Eucalyptus grandis R2R3-MYB transcription factor family: evidence for woody growth-related evolution and function.</ArticleTitle>
<Pagination><MedlinePgn>1364-77</MedlinePgn>
</Pagination>
<ELocationID EIdType="doi" ValidYN="Y">10.1111/nph.13039</ELocationID>
<Abstract><AbstractText>The R2R3-MYB family, one of the largest transcription factor families in higher plants, controls a wide variety of plant-specific processes including, notably, phenylpropanoid metabolism and secondary cell wall formation. We performed a genome-wide analysis of this superfamily in Eucalyptus, one of the most planted hardwood trees world-wide. A total of 141 predicted R2R3-MYB sequences identified in the Eucalyptus grandis genome sequence were subjected to comparative phylogenetic analyses with Arabidopsis thaliana, Oryza sativa, Populus trichocarpa and Vitis vinifera. We analysed features such as gene structure, conserved motifs and genome location. Transcript abundance patterns were assessed by RNAseq and validated by high-throughput quantitative PCR. We found some R2R3-MYB subgroups with expanded membership in E. grandis, V. vinifera and P. trichocarpa, and others preferentially found in woody species, suggesting diversification of specific functions in woody plants. By contrast, subgroups containing key genes regulating lignin biosynthesis and secondary cell wall formation are more conserved across all of the species analysed. In Eucalyptus, R2R3-MYB tandem gene duplications seem to disproportionately affect woody-preferential and woody-expanded subgroups. Interestingly, some of the genes belonging to woody-preferential subgroups show higher expression in the cambial region, suggesting a putative role in the regulation of secondary growth.</AbstractText>
<CopyrightInformation>© 2014 The Authors New Phytologist © 2014 New Phytologist Trust.</CopyrightInformation>
</Abstract>
<AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Soler</LastName>
<ForeName>Marçal</ForeName>
<Initials>M</Initials>
<AffiliationInfo><Affiliation>LRSV Laboratoire de Recherche en Sciences Végétales, UMR5546, Université Toulouse III/CNRS, BP 42617 Auzeville, 31326, Castanet Tolosan, France.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Camargo</LastName>
<ForeName>Eduardo Leal Oliveira</ForeName>
<Initials>EL</Initials>
<AffiliationInfo><Affiliation>LRSV Laboratoire de Recherche en Sciences Végétales, UMR5546, Université Toulouse III/CNRS, BP 42617 Auzeville, 31326, Castanet Tolosan, France.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Carocha</LastName>
<ForeName>Victor</ForeName>
<Initials>V</Initials>
<AffiliationInfo><Affiliation>LRSV Laboratoire de Recherche en Sciences Végétales, UMR5546, Université Toulouse III/CNRS, BP 42617 Auzeville, 31326, Castanet Tolosan, France.</Affiliation>
</AffiliationInfo>
<AffiliationInfo><Affiliation>Instituto de Tecnologia Química e Biológica (ITQB), Universidade Nova de Lisboa, Av. da República, 2780-157, Oeiras, Portugal.</Affiliation>
</AffiliationInfo>
<AffiliationInfo><Affiliation>Instituto de Biologia Experimental e Tecnológica (iBET) Av. da República, Quinta do Marquês, 2781-901, Oeiras, Portugal.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Cassan-Wang</LastName>
<ForeName>Hua</ForeName>
<Initials>H</Initials>
<AffiliationInfo><Affiliation>LRSV Laboratoire de Recherche en Sciences Végétales, UMR5546, Université Toulouse III/CNRS, BP 42617 Auzeville, 31326, Castanet Tolosan, France.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>San Clemente</LastName>
<ForeName>Hélène</ForeName>
<Initials>H</Initials>
<AffiliationInfo><Affiliation>LRSV Laboratoire de Recherche en Sciences Végétales, UMR5546, Université Toulouse III/CNRS, BP 42617 Auzeville, 31326, Castanet Tolosan, France.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Savelli</LastName>
<ForeName>Bruno</ForeName>
<Initials>B</Initials>
<AffiliationInfo><Affiliation>LRSV Laboratoire de Recherche en Sciences Végétales, UMR5546, Université Toulouse III/CNRS, BP 42617 Auzeville, 31326, Castanet Tolosan, France.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Hefer</LastName>
<ForeName>Charles A</ForeName>
<Initials>CA</Initials>
<AffiliationInfo><Affiliation>Bioinformatics and Computational Biology Unit, Department of Biochemistry, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag X20, Pretoria, 0028, South Africa.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Paiva</LastName>
<ForeName>Jorge A Pinto</ForeName>
<Initials>JA</Initials>
<AffiliationInfo><Affiliation>Instituto de Biologia Experimental e Tecnológica (iBET) Av. da República, Quinta do Marquês, 2781-901, Oeiras, Portugal.</Affiliation>
</AffiliationInfo>
<AffiliationInfo><Affiliation>Instituto de Investigaçao Científica e Tropical (IICT/MNE) Palacio Burnay - Rua da Junqueira, 30, 1349-007, Lisboa, Portugal.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Myburg</LastName>
<ForeName>Alexander A</ForeName>
<Initials>AA</Initials>
<AffiliationInfo><Affiliation>Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag X20, Pretoria, 0028, South Africa.</Affiliation>
</AffiliationInfo>
<AffiliationInfo><Affiliation>Genomics Research Institute (GRI), University of Pretoria, Private Bag X20, Pretoria, 0028, South Africa.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Grima-Pettenati</LastName>
<ForeName>Jacqueline</ForeName>
<Initials>J</Initials>
<AffiliationInfo><Affiliation>LRSV Laboratoire de Recherche en Sciences Végétales, UMR5546, Université Toulouse III/CNRS, BP 42617 Auzeville, 31326, Castanet Tolosan, France.</Affiliation>
</AffiliationInfo>
</Author>
</AuthorList>
<Language>eng</Language>
<PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType>
<PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType>
</PublicationTypeList>
<ArticleDate DateType="Electronic"><Year>2014</Year>
<Month>09</Month>
<Day>24</Day>
</ArticleDate>
</Article>
<MedlineJournalInfo><Country>England</Country>
<MedlineTA>New Phytol</MedlineTA>
<NlmUniqueID>9882884</NlmUniqueID>
<ISSNLinking>0028-646X</ISSNLinking>
</MedlineJournalInfo>
<ChemicalList><Chemical><RegistryNumber>0</RegistryNumber>
<NameOfSubstance UI="D010940">Plant Proteins</NameOfSubstance>
</Chemical>
<Chemical><RegistryNumber>0</RegistryNumber>
<NameOfSubstance UI="D012333">RNA, Messenger</NameOfSubstance>
</Chemical>
<Chemical><RegistryNumber>0</RegistryNumber>
<NameOfSubstance UI="D014157">Transcription Factors</NameOfSubstance>
</Chemical>
</ChemicalList>
<CitationSubset>IM</CitationSubset>
<MeshHeadingList><MeshHeading><DescriptorName UI="D005075" MajorTopicYN="Y">Biological Evolution</DescriptorName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D003198" MajorTopicYN="N">Computer Simulation</DescriptorName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D005052" MajorTopicYN="N">Eucalyptus</DescriptorName>
<QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName>
<QualifierName UI="Q000254" MajorTopicYN="Y">growth & development</QualifierName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D020869" MajorTopicYN="N">Gene Expression Profiling</DescriptorName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D018506" MajorTopicYN="N">Gene Expression Regulation, Plant</DescriptorName>
</MeshHeading>
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</MeshHeading>
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</MeshHeading>
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</MeshHeading>
<MeshHeading><DescriptorName UI="D010802" MajorTopicYN="N">Phylogeny</DescriptorName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D010940" MajorTopicYN="N">Plant Proteins</DescriptorName>
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</MeshHeading>
<MeshHeading><DescriptorName UI="D012333" MajorTopicYN="N">RNA, Messenger</DescriptorName>
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<QualifierName UI="Q000378" MajorTopicYN="N">metabolism</QualifierName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D060888" MajorTopicYN="N">Real-Time Polymerase Chain Reaction</DescriptorName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D017423" MajorTopicYN="N">Sequence Analysis, RNA</DescriptorName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D013045" MajorTopicYN="N">Species Specificity</DescriptorName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D014157" MajorTopicYN="N">Transcription Factors</DescriptorName>
<QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName>
<QualifierName UI="Q000378" MajorTopicYN="Y">metabolism</QualifierName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D014934" MajorTopicYN="N">Wood</DescriptorName>
<QualifierName UI="Q000254" MajorTopicYN="Y">growth & development</QualifierName>
</MeshHeading>
</MeshHeadingList>
<KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">Eucalyptus grandis</Keyword>
<Keyword MajorTopicYN="N">R2R3-MYB transcription factors</Keyword>
<Keyword MajorTopicYN="N">cambium</Keyword>
<Keyword MajorTopicYN="N">evolution</Keyword>
<Keyword MajorTopicYN="N">secondary growth</Keyword>
<Keyword MajorTopicYN="N">tandem duplications</Keyword>
<Keyword MajorTopicYN="N">wood formation</Keyword>
</KeywordList>
</MedlineCitation>
<PubmedData><History><PubMedPubDate PubStatus="received"><Year>2014</Year>
<Month>06</Month>
<Day>24</Day>
</PubMedPubDate>
<PubMedPubDate PubStatus="accepted"><Year>2014</Year>
<Month>08</Month>
<Day>05</Day>
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<li>Portugal</li>
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<region><li>Midi-Pyrénées</li>
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<tree><country name="France"><region name="Occitanie (région administrative)"><name sortKey="Soler, Marcal" sort="Soler, Marcal" uniqKey="Soler M" first="Marçal" last="Soler">Marçal Soler</name>
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<name sortKey="Grima Pettenati, Jacqueline" sort="Grima Pettenati, Jacqueline" uniqKey="Grima Pettenati J" first="Jacqueline" last="Grima-Pettenati">Jacqueline Grima-Pettenati</name>
<name sortKey="San Clemente, Helene" sort="San Clemente, Helene" uniqKey="San Clemente H" first="Hélène" last="San Clemente">Hélène San Clemente</name>
<name sortKey="Savelli, Bruno" sort="Savelli, Bruno" uniqKey="Savelli B" first="Bruno" last="Savelli">Bruno Savelli</name>
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<country name="Portugal"><noRegion><name sortKey="Carocha, Victor" sort="Carocha, Victor" uniqKey="Carocha V" first="Victor" last="Carocha">Victor Carocha</name>
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<name sortKey="Paiva, Jorge A Pinto" sort="Paiva, Jorge A Pinto" uniqKey="Paiva J" first="Jorge A Pinto" last="Paiva">Jorge A Pinto Paiva</name>
<name sortKey="Paiva, Jorge A Pinto" sort="Paiva, Jorge A Pinto" uniqKey="Paiva J" first="Jorge A Pinto" last="Paiva">Jorge A Pinto Paiva</name>
</country>
<country name="Afrique du Sud"><noRegion><name sortKey="Hefer, Charles A" sort="Hefer, Charles A" uniqKey="Hefer C" first="Charles A" last="Hefer">Charles A. Hefer</name>
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<name sortKey="Myburg, Alexander A" sort="Myburg, Alexander A" uniqKey="Myburg A" first="Alexander A" last="Myburg">Alexander A. Myburg</name>
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The Eucalyptus grandis R2R3-MYB transcription factor family: evidence for woody growth-related evolution and function.

The Eucalyptus grandis R2R3-MYB transcription factor family: evidence for woody growth-related evolution and function.

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