NorWood: a gene expression resource for evo-devo studies of conifer wood development.
Identifieur interne : 001286 ( Main/Exploration ); précédent : 001285; suivant : 001287NorWood: a gene expression resource for evo-devo studies of conifer wood development.
Auteurs : Soile Jokipii-Lukkari [Suède] ; David Sundell [Suède] ; Ove Nilsson [Suède] ; Torgeir R. Hvidsten [Suède, Norvège] ; Nathaniel R. Street [Suède] ; Hannele Tuominen [Suède]Source :
- The New phytologist [ 1469-8137 ] ; 2017.
Descripteurs français
- KwdFr :
- Analyse de regroupements (MeSH), Bois (croissance et développement), Bois (génétique), Facteurs de transcription (métabolisme), Gènes de plante (MeSH), Internet (MeSH), Logiciel (MeSH), Paroi cellulaire (génétique), Picea (croissance et développement), Picea (génétique), Protéines végétales (génétique), Protéines végétales (métabolisme), Régulation de l'expression des gènes végétaux (MeSH), Réseaux de régulation génique (MeSH), Évolution biologique (MeSH).
- MESH :
- croissance et développement : Bois, Picea.
- génétique : Bois, Paroi cellulaire, Picea, Protéines végétales.
- métabolisme : Facteurs de transcription, Protéines végétales.
- Analyse de regroupements, Gènes de plante, Internet, Logiciel, Régulation de l'expression des gènes végétaux, Réseaux de régulation génique, Évolution biologique.
English descriptors
- KwdEn :
- Biological Evolution (MeSH), Cell Wall (genetics), Cluster Analysis (MeSH), Gene Expression Regulation, Plant (MeSH), Gene Regulatory Networks (MeSH), Genes, Plant (MeSH), Internet (MeSH), Picea (genetics), Picea (growth & development), Plant Proteins (genetics), Plant Proteins (metabolism), Software (MeSH), Transcription Factors (metabolism), Wood (genetics), Wood (growth & development).
- MESH :
- chemical , genetics : Plant Proteins.
- genetics : Cell Wall, Picea, Wood.
- growth & development : Picea, Wood.
- chemical , metabolism : Plant Proteins, Transcription Factors.
- Biological Evolution, Cluster Analysis, Gene Expression Regulation, Plant, Gene Regulatory Networks, Genes, Plant, Internet, Software.
Abstract
The secondary xylem of conifers is composed mainly of tracheids that differ anatomically and chemically from angiosperm xylem cells. There is currently no high-spatial-resolution data available profiling gene expression during wood formation for any coniferous species, which limits insight into tracheid development. RNA-sequencing data from replicated, high-spatial-resolution section series throughout the cambial and woody tissues of Picea abies were used to generate the NorWood.conGenIE.org web resource, which facilitates exploration of the associated gene expression profiles and co-expression networks. Integration within PlantGenIE.org enabled a comparative regulomics analysis, revealing divergent co-expression networks between P. abies and the two angiosperm species Arabidopsis thaliana and Populus tremula for the secondary cell wall (SCW) master regulator NAC Class IIB transcription factors. The SCW cellulose synthase genes (CesAs) were located in the neighbourhoods of the NAC factors in A. thaliana and P. tremula, but not in P. abies. The NorWood co-expression network enabled identification of potential SCW CesA regulators in P. abies. The NorWood web resource represents a powerful community tool for generating evo-devo insights into the divergence of wood formation between angiosperms and gymnosperms and for advancing understanding of the regulation of wood development in P. abies.
DOI: 10.1111/nph.14458
PubMed: 28186632
PubMed Central: PMC6079643
Affiliations:
Links toward previous steps (curation, corpus...)
Le document en format XML
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Hvidsten</name><affiliation wicri:level="1"><nlm:affiliation>Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, SE-901 87, Umeå, Sweden.</nlm:affiliation><country xml:lang="fr">Suède</country><wicri:regionArea>Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, SE-901 87, Umeå</wicri:regionArea><wicri:noRegion>Umeå</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:affiliation>Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, 1430, Ås, Norway.</nlm:affiliation><country xml:lang="fr">Norvège</country><wicri:regionArea>Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, 1430, Ås</wicri:regionArea><wicri:noRegion>Ås</wicri:noRegion></affiliation></author><author><name sortKey="Street, Nathaniel R" sort="Street, Nathaniel R" uniqKey="Street N" first="Nathaniel R" last="Street">Nathaniel R. Street</name><affiliation wicri:level="1"><nlm:affiliation>Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, SE-901 87, Umeå, Sweden.</nlm:affiliation><country xml:lang="fr">Suède</country><wicri:regionArea>Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, SE-901 87, Umeå</wicri:regionArea><wicri:noRegion>Umeå</wicri:noRegion></affiliation></author><author><name sortKey="Tuominen, Hannele" sort="Tuominen, Hannele" uniqKey="Tuominen H" first="Hannele" last="Tuominen">Hannele Tuominen</name><affiliation wicri:level="1"><nlm:affiliation>Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, SE-901 87, Umeå, Sweden.</nlm:affiliation><country xml:lang="fr">Suède</country><wicri:regionArea>Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, SE-901 87, Umeå</wicri:regionArea><wicri:noRegion>Umeå</wicri:noRegion></affiliation></author></analytic><series><title level="j">The New phytologist</title><idno type="eISSN">1469-8137</idno><imprint><date when="2017" type="published">2017</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Biological Evolution (MeSH)</term><term>Cell Wall (genetics)</term><term>Cluster Analysis (MeSH)</term><term>Gene Expression Regulation, Plant (MeSH)</term><term>Gene Regulatory Networks (MeSH)</term><term>Genes, Plant (MeSH)</term><term>Internet (MeSH)</term><term>Picea (genetics)</term><term>Picea (growth & development)</term><term>Plant Proteins (genetics)</term><term>Plant Proteins (metabolism)</term><term>Software (MeSH)</term><term>Transcription Factors (metabolism)</term><term>Wood (genetics)</term><term>Wood (growth & development)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Analyse de regroupements (MeSH)</term><term>Bois (croissance et développement)</term><term>Bois (génétique)</term><term>Facteurs de transcription (métabolisme)</term><term>Gènes de plante (MeSH)</term><term>Internet (MeSH)</term><term>Logiciel (MeSH)</term><term>Paroi cellulaire (génétique)</term><term>Picea (croissance et développement)</term><term>Picea (génétique)</term><term>Protéines végétales (génétique)</term><term>Protéines végétales (métabolisme)</term><term>Régulation de l'expression des gènes végétaux (MeSH)</term><term>Réseaux de régulation génique (MeSH)</term><term>Évolution biologique (MeSH)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>Plant Proteins</term></keywords><keywords scheme="MESH" qualifier="croissance et développement" xml:lang="fr"><term>Bois</term><term>Picea</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Cell Wall</term><term>Picea</term><term>Wood</term></keywords><keywords scheme="MESH" qualifier="growth & development" xml:lang="en"><term>Picea</term><term>Wood</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Bois</term><term>Paroi cellulaire</term><term>Picea</term><term>Protéines végétales</term></keywords><keywords scheme="MESH" type="chemical" qualifier="metabolism" xml:lang="en"><term>Plant Proteins</term><term>Transcription Factors</term></keywords><keywords scheme="MESH" qualifier="métabolisme" xml:lang="fr"><term>Facteurs de transcription</term><term>Protéines végétales</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Biological Evolution</term><term>Cluster Analysis</term><term>Gene Expression Regulation, Plant</term><term>Gene Regulatory Networks</term><term>Genes, Plant</term><term>Internet</term><term>Software</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Analyse de regroupements</term><term>Gènes de plante</term><term>Internet</term><term>Logiciel</term><term>Régulation de l'expression des gènes végétaux</term><term>Réseaux de régulation génique</term><term>Évolution biologique</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">The secondary xylem of conifers is composed mainly of tracheids that differ anatomically and chemically from angiosperm xylem cells. There is currently no high-spatial-resolution data available profiling gene expression during wood formation for any coniferous species, which limits insight into tracheid development. RNA-sequencing data from replicated, high-spatial-resolution section series throughout the cambial and woody tissues of Picea abies were used to generate the NorWood.conGenIE.org web resource, which facilitates exploration of the associated gene expression profiles and co-expression networks. Integration within PlantGenIE.org enabled a comparative regulomics analysis, revealing divergent co-expression networks between P. abies and the two angiosperm species Arabidopsis thaliana and Populus tremula for the secondary cell wall (SCW) master regulator NAC Class IIB transcription factors. The SCW cellulose synthase genes (CesAs) were located in the neighbourhoods of the NAC factors in A. thaliana and P. tremula, but not in P. abies. The NorWood co-expression network enabled identification of potential SCW CesA regulators in P. abies. The NorWood web resource represents a powerful community tool for generating evo-devo insights into the divergence of wood formation between angiosperms and gymnosperms and for advancing understanding of the regulation of wood development in P. abies.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">28186632</PMID><DateCompleted><Year>2018</Year><Month>05</Month><Day>21</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>216</Volume><Issue>2</Issue><PubDate><Year>2017</Year><Month>Oct</Month></PubDate></JournalIssue><Title>The New phytologist</Title><ISOAbbreviation>New Phytol</ISOAbbreviation></Journal><ArticleTitle>NorWood: a gene expression resource for evo-devo studies of conifer wood development.</ArticleTitle><Pagination><MedlinePgn>482-494</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1111/nph.14458</ELocationID><Abstract><AbstractText>The secondary xylem of conifers is composed mainly of tracheids that differ anatomically and chemically from angiosperm xylem cells. There is currently no high-spatial-resolution data available profiling gene expression during wood formation for any coniferous species, which limits insight into tracheid development. RNA-sequencing data from replicated, high-spatial-resolution section series throughout the cambial and woody tissues of Picea abies were used to generate the NorWood.conGenIE.org web resource, which facilitates exploration of the associated gene expression profiles and co-expression networks. Integration within PlantGenIE.org enabled a comparative regulomics analysis, revealing divergent co-expression networks between P. abies and the two angiosperm species Arabidopsis thaliana and Populus tremula for the secondary cell wall (SCW) master regulator NAC Class IIB transcription factors. The SCW cellulose synthase genes (CesAs) were located in the neighbourhoods of the NAC factors in A. thaliana and P. tremula, but not in P. abies. The NorWood co-expression network enabled identification of potential SCW CesA regulators in P. abies. The NorWood web resource represents a powerful community tool for generating evo-devo insights into the divergence of wood formation between angiosperms and gymnosperms and for advancing understanding of the regulation of wood development in P. abies.</AbstractText><CopyrightInformation>© 2017 The Authors. New Phytologist © 2017 New Phytologist Trust.</CopyrightInformation></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Jokipii-Lukkari</LastName><ForeName>Soile</ForeName><Initials>S</Initials><AffiliationInfo><Affiliation>Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, SE-901 87, Umeå, Sweden.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, SE-901 84, Umeå, Sweden.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Sundell</LastName><ForeName>David</ForeName><Initials>D</Initials><AffiliationInfo><Affiliation>Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, SE-901 87, Umeå, Sweden.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Nilsson</LastName><ForeName>Ove</ForeName><Initials>O</Initials><AffiliationInfo><Affiliation>Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, SE-901 84, Umeå, Sweden.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Hvidsten</LastName><ForeName>Torgeir R</ForeName><Initials>TR</Initials><AffiliationInfo><Affiliation>Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, SE-901 87, Umeå, Sweden.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, 1430, Ås, Norway.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Street</LastName><ForeName>Nathaniel R</ForeName><Initials>NR</Initials><AffiliationInfo><Affiliation>Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, SE-901 87, Umeå, Sweden.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Tuominen</LastName><ForeName>Hannele</ForeName><Initials>H</Initials><AffiliationInfo><Affiliation>Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, SE-901 87, Umeå, Sweden.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2017</Year><Month>02</Month><Day>10</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="D014157">Transcription Factors</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D005075" MajorTopicYN="Y">Biological Evolution</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D002473" MajorTopicYN="N">Cell Wall</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D016000" MajorTopicYN="N">Cluster Analysis</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D018506" MajorTopicYN="Y">Gene Expression Regulation, Plant</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D053263" MajorTopicYN="N">Gene Regulatory Networks</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D017343" MajorTopicYN="N">Genes, Plant</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D020407" MajorTopicYN="N">Internet</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D028222" MajorTopicYN="N">Picea</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName><QualifierName UI="Q000254" MajorTopicYN="Y">growth & development</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D010940" MajorTopicYN="N">Plant Proteins</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName><QualifierName UI="Q000378" MajorTopicYN="N">metabolism</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D012984" MajorTopicYN="Y">Software</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D014157" MajorTopicYN="N">Transcription Factors</DescriptorName><QualifierName UI="Q000378" MajorTopicYN="N">metabolism</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D014934" MajorTopicYN="N">Wood</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName><QualifierName UI="Q000254" MajorTopicYN="Y">growth & development</QualifierName></MeshHeading></MeshHeadingList><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">Norway spruce (Picea abies)</Keyword><Keyword MajorTopicYN="N">RNA-sequencing</Keyword><Keyword MajorTopicYN="N">co-expression network</Keyword><Keyword MajorTopicYN="N">comparative genomics</Keyword><Keyword MajorTopicYN="N">cryosection</Keyword><Keyword MajorTopicYN="N">evo-devo</Keyword><Keyword MajorTopicYN="N">growth ring</Keyword><Keyword MajorTopicYN="N">secondary cell wall</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2016</Year><Month>10</Month><Day>21</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2016</Year><Month>12</Month><Day>22</Day></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2017</Year><Month>2</Month><Day>12</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate 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