Genome-wide identification, classification and expression analysis of the PHD-finger protein family in Populus trichocarpa.
Identifieur interne : 001849 ( Main/Exploration ); précédent : 001848; suivant : 001850Genome-wide identification, classification and expression analysis of the PHD-finger protein family in Populus trichocarpa.
Auteurs : Shengnan Wu [République populaire de Chine] ; Min Wu [République populaire de Chine] ; Qing Dong [République populaire de Chine] ; Haiyang Jiang [République populaire de Chine] ; Ronghao Cai [République populaire de Chine] ; Yan Xiang [République populaire de Chine]Source :
- Gene [ 1879-0038 ] ; 2016.
Descripteurs français
- KwdFr :
- Chromosomes de plante (génétique), Chromosomes de plante (métabolisme), Populus (génétique), Populus (métabolisme), Protéines du groupe Polycomb (biosynthèse), Protéines du groupe Polycomb (classification), Protéines du groupe Polycomb (génétique), Protéines végétales (biosynthèse), Protéines végétales (classification), Protéines végétales (génétique), Régulation de l'expression des gènes végétaux (physiologie), Étude d'association pangénomique (MeSH).
- MESH :
- biosynthèse : Protéines du groupe Polycomb, Protéines végétales.
- classification : Protéines du groupe Polycomb, Protéines végétales.
- génétique : Chromosomes de plante, Populus, Protéines du groupe Polycomb, Protéines végétales.
- métabolisme : Chromosomes de plante, Populus.
- physiologie : Régulation de l'expression des gènes végétaux.
- Étude d'association pangénomique.
English descriptors
- KwdEn :
- Chromosomes, Plant (genetics), Chromosomes, Plant (metabolism), Gene Expression Regulation, Plant (physiology), Genome-Wide Association Study (MeSH), Plant Proteins (biosynthesis), Plant Proteins (classification), Plant Proteins (genetics), Polycomb-Group Proteins (biosynthesis), Polycomb-Group Proteins (classification), Polycomb-Group Proteins (genetics), Populus (genetics), Populus (metabolism).
- MESH :
- chemical , biosynthesis : Plant Proteins, Polycomb-Group Proteins.
- chemical , classification : Plant Proteins, Polycomb-Group Proteins.
- genetics : Chromosomes, Plant, Plant Proteins, Polycomb-Group Proteins, Populus.
- metabolism : Chromosomes, Plant, Populus.
- physiology : Gene Expression Regulation, Plant.
- Genome-Wide Association Study.
Abstract
The plant homeobox domain (PHD) proteins are widespread in eukaryotes, and play important roles in regulating chromatin and transcription. Comprehensive analyses of PHD-finger proteins have been performed in animals, but few plant PHD-finger proteins involved in growth and development have been characterized functionally. In this study, we conducted a genome-wide survey of PHD-finger proteins in Populus trichocarpa by describing the phylogenetic relationship, gene structure, and chromosomal location and microarray analyses of each predicted PHD-finger family member. We identified 73 PHD-finger genes (PtPHD1-73) and classified them into eleven subfamilies (A-K) by phylogenetic analysis. Seventy-two of the 73 genes were unevenly distributed on all 19 chromosomes, with seven segmental duplication events. Analysis of the Ka (non-synonymous substitution rate)/Ks (synonymous substitution rate) ratios suggested that the duplicated genes of the PHD-finger family mainly underwent purifying selection with restrictive functional divergence after the duplication events. Expression profiles analysis indicated that 67 PHD-finger genes were differentially expressed in various tissues. Quantitative real-time RT-PCR (qRT-PCR) analyses of nine selected PtPHD genes under high salinity, drought and cold stresses were also performed to explore their stress-related expression patterns. The results of this study provide a thorough overview of poplar PHD-finger proteins and will be valuable for further functional research of poplar PHD-finger genes to unravel their biological roles.
DOI: 10.1016/j.gene.2015.08.042
PubMed: 26314912
Affiliations:
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Key Laboratory of Biomass Improvement and Conversion of Anhui Province, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, China; Key Laboratory of Biomass Improvement and Conversion of Anhui Province</wicri:regionArea><wicri:noRegion>China; Key Laboratory of Biomass Improvement and Conversion of Anhui Province</wicri:noRegion></affiliation></author><author><name sortKey="Wu, Min" sort="Wu, Min" uniqKey="Wu M" first="Min" last="Wu">Min Wu</name><affiliation wicri:level="3"><nlm:affiliation>Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei</wicri:regionArea><placeName><settlement type="city">Hefei</settlement><region type="province">Anhui</region></placeName></affiliation></author><author><name sortKey="Dong, Qing" sort="Dong, Qing" uniqKey="Dong Q" first="Qing" last="Dong">Qing Dong</name><affiliation wicri:level="1"><nlm:affiliation>Key Laboratory of Biomass Improvement and Conversion of Anhui Province, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Key Laboratory of Biomass Improvement and Conversion of Anhui Province</wicri:regionArea></affiliation></author><author><name sortKey="Jiang, Haiyang" sort="Jiang, Haiyang" uniqKey="Jiang H" first="Haiyang" last="Jiang">Haiyang Jiang</name><affiliation wicri:level="1"><nlm:affiliation>Key Laboratory of Biomass Improvement and Conversion of Anhui Province, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Key Laboratory of Biomass Improvement and Conversion of Anhui Province</wicri:regionArea></affiliation></author><author><name sortKey="Cai, Ronghao" sort="Cai, Ronghao" uniqKey="Cai R" first="Ronghao" last="Cai">Ronghao Cai</name><affiliation wicri:level="1"><nlm:affiliation>Key Laboratory of Biomass Improvement and Conversion of Anhui Province, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Key Laboratory of Biomass Improvement and Conversion of Anhui Province</wicri:regionArea></affiliation></author><author><name sortKey="Xiang, Yan" sort="Xiang, Yan" uniqKey="Xiang Y" first="Yan" last="Xiang">Yan Xiang</name><affiliation wicri:level="1"><nlm:affiliation>Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, China; Key Laboratory of Biomass Improvement and Conversion of Anhui Province, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, China; Key Laboratory of Biomass Improvement and Conversion of Anhui Province</wicri:regionArea><wicri:noRegion>China; Key Laboratory of Biomass Improvement and Conversion of Anhui Province</wicri:noRegion></affiliation></author></analytic><series><title level="j">Gene</title><idno type="eISSN">1879-0038</idno><imprint><date when="2016" type="published">2016</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Chromosomes, Plant (genetics)</term><term>Chromosomes, Plant (metabolism)</term><term>Gene Expression Regulation, Plant (physiology)</term><term>Genome-Wide Association Study (MeSH)</term><term>Plant Proteins (biosynthesis)</term><term>Plant Proteins (classification)</term><term>Plant Proteins (genetics)</term><term>Polycomb-Group Proteins (biosynthesis)</term><term>Polycomb-Group Proteins (classification)</term><term>Polycomb-Group Proteins (genetics)</term><term>Populus (genetics)</term><term>Populus (metabolism)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Chromosomes de plante (génétique)</term><term>Chromosomes de plante (métabolisme)</term><term>Populus (génétique)</term><term>Populus (métabolisme)</term><term>Protéines du groupe Polycomb (biosynthèse)</term><term>Protéines du groupe Polycomb (classification)</term><term>Protéines du groupe Polycomb (génétique)</term><term>Protéines végétales (biosynthèse)</term><term>Protéines végétales (classification)</term><term>Protéines végétales (génétique)</term><term>Régulation de l'expression des gènes végétaux (physiologie)</term><term>Étude d'association pangénomique (MeSH)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="biosynthesis" xml:lang="en"><term>Plant Proteins</term><term>Polycomb-Group Proteins</term></keywords><keywords scheme="MESH" type="chemical" qualifier="classification" xml:lang="en"><term>Plant Proteins</term><term>Polycomb-Group Proteins</term></keywords><keywords scheme="MESH" qualifier="biosynthèse" xml:lang="fr"><term>Protéines du groupe Polycomb</term><term>Protéines végétales</term></keywords><keywords scheme="MESH" qualifier="classification" xml:lang="fr"><term>Protéines du groupe Polycomb</term><term>Protéines végétales</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Chromosomes, Plant</term><term>Plant Proteins</term><term>Polycomb-Group Proteins</term><term>Populus</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Chromosomes de plante</term><term>Populus</term><term>Protéines du groupe Polycomb</term><term>Protéines végétales</term></keywords><keywords scheme="MESH" qualifier="metabolism" xml:lang="en"><term>Chromosomes, Plant</term><term>Populus</term></keywords><keywords scheme="MESH" qualifier="métabolisme" xml:lang="fr"><term>Chromosomes de plante</term><term>Populus</term></keywords><keywords scheme="MESH" qualifier="physiologie" xml:lang="fr"><term>Régulation de l'expression des gènes végétaux</term></keywords><keywords scheme="MESH" qualifier="physiology" xml:lang="en"><term>Gene Expression Regulation, Plant</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Genome-Wide Association Study</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Étude d'association pangénomique</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">The plant homeobox domain (PHD) proteins are widespread in eukaryotes, and play important roles in regulating chromatin and transcription. Comprehensive analyses of PHD-finger proteins have been performed in animals, but few plant PHD-finger proteins involved in growth and development have been characterized functionally. In this study, we conducted a genome-wide survey of PHD-finger proteins in Populus trichocarpa by describing the phylogenetic relationship, gene structure, and chromosomal location and microarray analyses of each predicted PHD-finger family member. We identified 73 PHD-finger genes (PtPHD1-73) and classified them into eleven subfamilies (A-K) by phylogenetic analysis. Seventy-two of the 73 genes were unevenly distributed on all 19 chromosomes, with seven segmental duplication events. Analysis of the Ka (non-synonymous substitution rate)/Ks (synonymous substitution rate) ratios suggested that the duplicated genes of the PHD-finger family mainly underwent purifying selection with restrictive functional divergence after the duplication events. Expression profiles analysis indicated that 67 PHD-finger genes were differentially expressed in various tissues. Quantitative real-time RT-PCR (qRT-PCR) analyses of nine selected PtPHD genes under high salinity, drought and cold stresses were also performed to explore their stress-related expression patterns. The results of this study provide a thorough overview of poplar PHD-finger proteins and will be valuable for further functional research of poplar PHD-finger genes to unravel their biological roles. </div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">26314912</PMID><DateCompleted><Year>2016</Year><Month>02</Month><Day>25</Day></DateCompleted><DateRevised><Year>2015</Year><Month>11</Month><Day>20</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1879-0038</ISSN><JournalIssue CitedMedium="Internet"><Volume>575</Volume><Issue>1</Issue><PubDate><Year>2016</Year><Month>Jan</Month><Day>01</Day></PubDate></JournalIssue><Title>Gene</Title><ISOAbbreviation>Gene</ISOAbbreviation></Journal><ArticleTitle>Genome-wide identification, classification and expression analysis of the PHD-finger protein family in Populus trichocarpa.</ArticleTitle><Pagination><MedlinePgn>75-89</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1016/j.gene.2015.08.042</ELocationID><ELocationID EIdType="pii" ValidYN="Y">S0378-1119(15)01012-4</ELocationID><Abstract><AbstractText>The plant homeobox domain (PHD) proteins are widespread in eukaryotes, and play important roles in regulating chromatin and transcription. Comprehensive analyses of PHD-finger proteins have been performed in animals, but few plant PHD-finger proteins involved in growth and development have been characterized functionally. In this study, we conducted a genome-wide survey of PHD-finger proteins in Populus trichocarpa by describing the phylogenetic relationship, gene structure, and chromosomal location and microarray analyses of each predicted PHD-finger family member. We identified 73 PHD-finger genes (PtPHD1-73) and classified them into eleven subfamilies (A-K) by phylogenetic analysis. Seventy-two of the 73 genes were unevenly distributed on all 19 chromosomes, with seven segmental duplication events. Analysis of the Ka (non-synonymous substitution rate)/Ks (synonymous substitution rate) ratios suggested that the duplicated genes of the PHD-finger family mainly underwent purifying selection with restrictive functional divergence after the duplication events. Expression profiles analysis indicated that 67 PHD-finger genes were differentially expressed in various tissues. Quantitative real-time RT-PCR (qRT-PCR) analyses of nine selected PtPHD genes under high salinity, drought and cold stresses were also performed to explore their stress-related expression patterns. The results of this study provide a thorough overview of poplar PHD-finger proteins and will be valuable for further functional research of poplar PHD-finger genes to unravel their biological roles. </AbstractText><CopyrightInformation>Copyright © 2015 Elsevier B.V. All rights reserved.</CopyrightInformation></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Wu</LastName><ForeName>Shengnan</ForeName><Initials>S</Initials><AffiliationInfo><Affiliation>Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, China; Key Laboratory of Biomass Improvement and Conversion of Anhui Province, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Wu</LastName><ForeName>Min</ForeName><Initials>M</Initials><AffiliationInfo><Affiliation>Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Dong</LastName><ForeName>Qing</ForeName><Initials>Q</Initials><AffiliationInfo><Affiliation>Key Laboratory of Biomass Improvement and Conversion of Anhui Province, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Jiang</LastName><ForeName>Haiyang</ForeName><Initials>H</Initials><AffiliationInfo><Affiliation>Key Laboratory of Biomass Improvement and Conversion of Anhui Province, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Cai</LastName><ForeName>Ronghao</ForeName><Initials>R</Initials><AffiliationInfo><Affiliation>Key Laboratory of Biomass Improvement and Conversion of Anhui Province, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Xiang</LastName><ForeName>Yan</ForeName><Initials>Y</Initials><AffiliationInfo><Affiliation>Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, China; Key Laboratory of Biomass Improvement and Conversion of Anhui Province, China.</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>2015</Year><Month>08</Month><Day>24</Day></ArticleDate></Article><MedlineJournalInfo><Country>Netherlands</Country><MedlineTA>Gene</MedlineTA><NlmUniqueID>7706761</NlmUniqueID><ISSNLinking>0378-1119</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D010940">Plant Proteins</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D063146">Polycomb-Group Proteins</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D032461" MajorTopicYN="N">Chromosomes, Plant</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName><QualifierName UI="Q000378" MajorTopicYN="N">metabolism</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D018506" MajorTopicYN="N">Gene Expression Regulation, Plant</DescriptorName><QualifierName UI="Q000502" MajorTopicYN="Y">physiology</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D055106" MajorTopicYN="N">Genome-Wide Association Study</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D010940" MajorTopicYN="Y">Plant Proteins</DescriptorName><QualifierName UI="Q000096" MajorTopicYN="N">biosynthesis</QualifierName><QualifierName UI="Q000145" MajorTopicYN="N">classification</QualifierName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D063146" MajorTopicYN="Y">Polycomb-Group Proteins</DescriptorName><QualifierName UI="Q000096" MajorTopicYN="N">biosynthesis</QualifierName><QualifierName UI="Q000145" MajorTopicYN="N">classification</QualifierName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D032107" MajorTopicYN="Y">Populus</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName><QualifierName UI="Q000378" MajorTopicYN="N">metabolism</QualifierName></MeshHeading></MeshHeadingList><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">Expression pattern</Keyword><Keyword MajorTopicYN="N">Phylogenetic analysis</Keyword><Keyword MajorTopicYN="N">Plant homeobox domain (PHD) proteins</Keyword><Keyword MajorTopicYN="N">Poplar</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2015</Year><Month>04</Month><Day>21</Day></PubMedPubDate><PubMedPubDate PubStatus="revised"><Year>2015</Year><Month>08</Month><Day>04</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2015</Year><Month>08</Month><Day>20</Day></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2015</Year><Month>8</Month><Day>29</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2015</Year><Month>9</Month><Day>1</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2016</Year><Month>2</Month><Day>26</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">26314912</ArticleId><ArticleId IdType="pii">S0378-1119(15)01012-4</ArticleId><ArticleId IdType="doi">10.1016/j.gene.2015.08.042</ArticleId></ArticleIdList></PubmedData></pubmed><affiliations><list><country><li>République populaire de Chine</li></country><region><li>Anhui</li></region><settlement><li>Hefei</li></settlement></list><tree><country name="République populaire de Chine"><noRegion><name sortKey="Wu, Shengnan" sort="Wu, Shengnan" uniqKey="Wu S" first="Shengnan" last="Wu">Shengnan Wu</name></noRegion><name sortKey="Cai, Ronghao" sort="Cai, Ronghao" uniqKey="Cai R" first="Ronghao" last="Cai">Ronghao Cai</name><name sortKey="Dong, Qing" sort="Dong, Qing" uniqKey="Dong Q" first="Qing" last="Dong">Qing Dong</name><name sortKey="Jiang, Haiyang" sort="Jiang, Haiyang" uniqKey="Jiang H" first="Haiyang" last="Jiang">Haiyang Jiang</name><name sortKey="Wu, Min" sort="Wu, Min" uniqKey="Wu M" first="Min" last="Wu">Min Wu</name><name sortKey="Xiang, Yan" sort="Xiang, Yan" uniqKey="Xiang Y" first="Yan" last="Xiang">Yan Xiang</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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