Genome-wide identification and analysis of the Populus trichocarpa TIFY gene family.
Identifieur interne : 001351 ( Main/Corpus ); précédent : 001350; suivant : 001352Genome-wide identification and analysis of the Populus trichocarpa TIFY gene family.
Auteurs : Yue Wang ; Feng Pan ; Danmei Chen ; Wenyuan Chu ; Huanlong Liu ; Yan XiangSource :
- Plant physiology and biochemistry : PPB [ 1873-2690 ] ; 2017.
English descriptors
- KwdEn :
- Chromosomes, Plant (genetics), Gene Expression Profiling (MeSH), Gene Expression Regulation, Plant (genetics), Gene Expression Regulation, Plant (physiology), Phylogeny (MeSH), Plant Proteins (genetics), Plant Proteins (metabolism), Populus (genetics), Populus (metabolism), Reverse Transcriptase Polymerase Chain Reaction (MeSH).
- MESH :
- chemical , genetics : Plant Proteins.
- genetics : Chromosomes, Plant, Gene Expression Regulation, Plant, Populus.
- chemical , metabolism : Plant Proteins, Populus.
- physiology : Gene Expression Regulation, Plant.
- Gene Expression Profiling, Phylogeny, Reverse Transcriptase Polymerase Chain Reaction.
Abstract
The plant-specific TIFY proteins are widely present in land plants and play the important roles in the regulation of plant stress-responses. In this study, we carried out a bioinformatics analysis of TIFY genes in Populus trichocarpa by determining the phylogenetic relationship, chromosomal location and gene structure and expression profiles analysis under stresses. The 24 TIFY genes were identified and classified into four subfamilies (ZML, JAZ, PPD and TIFY). The 24 TIFY genes were irregularly located on 13 of the 19 chromosomes; ten gene pairs were involved in large-scale interchromosomal segmental duplication events; we identified 17 collinear TIFY gene pairs in the Populus trichocarpa genome. Numerous abiotic stress cis-elements were widely found in the promoter regions. Analysis of the Ka/Ks ratios indicated that the paralogs of the PtTIFY family principally underwent purifying selection. Microarray data and qRT-PCR analysis revealed that 24 PtTIFY genes were differentially expressed in various tissues. Quantitative real-time RT-PCR analysis of TIFY genes expression in response to salt, JA hormones and low-temperature stress revealed their stress-responses profiles. The results of this study provided valuable information for further exploration of the TIFY gene family in Populus trichocarpa.
DOI: 10.1016/j.plaphy.2017.04.015
PubMed: 28431355
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Electronic address: 525503912@qq.com.</nlm:affiliation></affiliation></author><author><name sortKey="Chen, Danmei" sort="Chen, Danmei" uniqKey="Chen D" first="Danmei" last="Chen">Danmei Chen</name><affiliation><nlm:affiliation>Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, 230036, China. Electronic address: 872106864@qq.com.</nlm:affiliation></affiliation></author><author><name sortKey="Chu, Wenyuan" sort="Chu, Wenyuan" uniqKey="Chu W" first="Wenyuan" last="Chu">Wenyuan Chu</name><affiliation><nlm:affiliation>Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, 230036, China. Electronic address: 1182732812@qq.com.</nlm:affiliation></affiliation></author><author><name sortKey="Liu, Huanlong" sort="Liu, Huanlong" uniqKey="Liu H" first="Huanlong" last="Liu">Huanlong Liu</name><affiliation><nlm:affiliation>Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, 230036, China. Electronic address: 1641999267@qq.com.</nlm:affiliation></affiliation></author><author><name sortKey="Xiang, Yan" sort="Xiang, Yan" uniqKey="Xiang Y" first="Yan" last="Xiang">Yan Xiang</name><affiliation><nlm:affiliation>Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, 230036, China; Key Laboratory of Biomass Improvement and Conversion, Anhui Agriculture University, Hefei, 230036, China. 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Electronic address: xiangyanahau@sina.com.</nlm:affiliation></affiliation></author></analytic><series><title level="j">Plant physiology and biochemistry : PPB</title><idno type="eISSN">1873-2690</idno><imprint><date when="2017" type="published">2017</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Chromosomes, Plant (genetics)</term><term>Gene Expression Profiling (MeSH)</term><term>Gene Expression Regulation, Plant (genetics)</term><term>Gene Expression Regulation, Plant (physiology)</term><term>Phylogeny (MeSH)</term><term>Plant Proteins (genetics)</term><term>Plant Proteins (metabolism)</term><term>Populus (genetics)</term><term>Populus (metabolism)</term><term>Reverse Transcriptase Polymerase Chain Reaction (MeSH)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>Plant Proteins</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Chromosomes, Plant</term><term>Gene Expression Regulation, Plant</term><term>Populus</term></keywords><keywords scheme="MESH" type="chemical" qualifier="metabolism" xml:lang="en"><term>Plant Proteins</term><term>Populus</term></keywords><keywords scheme="MESH" qualifier="physiology" xml:lang="en"><term>Gene Expression Regulation, Plant</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Gene Expression Profiling</term><term>Phylogeny</term><term>Reverse Transcriptase Polymerase Chain Reaction</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">The plant-specific TIFY proteins are widely present in land plants and play the important roles in the regulation of plant stress-responses. In this study, we carried out a bioinformatics analysis of TIFY genes in Populus trichocarpa by determining the phylogenetic relationship, chromosomal location and gene structure and expression profiles analysis under stresses. The 24 TIFY genes were identified and classified into four subfamilies (ZML, JAZ, PPD and TIFY). The 24 TIFY genes were irregularly located on 13 of the 19 chromosomes; ten gene pairs were involved in large-scale interchromosomal segmental duplication events; we identified 17 collinear TIFY gene pairs in the Populus trichocarpa genome. Numerous abiotic stress cis-elements were widely found in the promoter regions. Analysis of the Ka/Ks ratios indicated that the paralogs of the PtTIFY family principally underwent purifying selection. Microarray data and qRT-PCR analysis revealed that 24 PtTIFY genes were differentially expressed in various tissues. Quantitative real-time RT-PCR analysis of TIFY genes expression in response to salt, JA hormones and low-temperature stress revealed their stress-responses profiles. The results of this study provided valuable information for further exploration of the TIFY gene family in Populus trichocarpa.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">28431355</PMID><DateCompleted><Year>2017</Year><Month>12</Month><Day>29</Day></DateCompleted><DateRevised><Year>2020</Year><Month>09</Month><Day>30</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1873-2690</ISSN><JournalIssue CitedMedium="Internet"><Volume>115</Volume><PubDate><Year>2017</Year><Month>Jun</Month></PubDate></JournalIssue><Title>Plant physiology and biochemistry : PPB</Title><ISOAbbreviation>Plant Physiol Biochem</ISOAbbreviation></Journal><ArticleTitle>Genome-wide identification and analysis of the Populus trichocarpa TIFY gene family.</ArticleTitle><Pagination><MedlinePgn>360-371</MedlinePgn></Pagination><ELocationID EIdType="pii" ValidYN="Y">S0981-9428(17)30135-3</ELocationID><ELocationID EIdType="doi" ValidYN="Y">10.1016/j.plaphy.2017.04.015</ELocationID><Abstract><AbstractText>The plant-specific TIFY proteins are widely present in land plants and play the important roles in the regulation of plant stress-responses. In this study, we carried out a bioinformatics analysis of TIFY genes in Populus trichocarpa by determining the phylogenetic relationship, chromosomal location and gene structure and expression profiles analysis under stresses. The 24 TIFY genes were identified and classified into four subfamilies (ZML, JAZ, PPD and TIFY). The 24 TIFY genes were irregularly located on 13 of the 19 chromosomes; ten gene pairs were involved in large-scale interchromosomal segmental duplication events; we identified 17 collinear TIFY gene pairs in the Populus trichocarpa genome. Numerous abiotic stress cis-elements were widely found in the promoter regions. Analysis of the Ka/Ks ratios indicated that the paralogs of the PtTIFY family principally underwent purifying selection. Microarray data and qRT-PCR analysis revealed that 24 PtTIFY genes were differentially expressed in various tissues. Quantitative real-time RT-PCR analysis of TIFY genes expression in response to salt, JA hormones and low-temperature stress revealed their stress-responses profiles. The results of this study provided valuable information for further exploration of the TIFY gene family in Populus trichocarpa.</AbstractText><CopyrightInformation>Copyright © 2017 Elsevier Masson SAS. All rights reserved.</CopyrightInformation></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Wang</LastName><ForeName>Yue</ForeName><Initials>Y</Initials><AffiliationInfo><Affiliation>Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, 230036, China. Electronic address: 2578152444@qq.com.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Pan</LastName><ForeName>Feng</ForeName><Initials>F</Initials><AffiliationInfo><Affiliation>Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, 230036, China. Electronic address: 525503912@qq.com.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Chen</LastName><ForeName>Danmei</ForeName><Initials>D</Initials><AffiliationInfo><Affiliation>Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, 230036, China. 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Electronic address: 1641999267@qq.com.</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, 230036, China; Key Laboratory of Biomass Improvement and Conversion, Anhui Agriculture University, Hefei, 230036, China. Electronic address: xiangyanahau@sina.com.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2017</Year><Month>04</Month><Day>13</Day></ArticleDate></Article><MedlineJournalInfo><Country>France</Country><MedlineTA>Plant Physiol Biochem</MedlineTA><NlmUniqueID>9882449</NlmUniqueID><ISSNLinking>0981-9428</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D010940">Plant Proteins</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D032461" MajorTopicYN="N">Chromosomes, Plant</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D020869" MajorTopicYN="N">Gene Expression Profiling</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D018506" MajorTopicYN="N">Gene Expression Regulation, Plant</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName><QualifierName UI="Q000502" MajorTopicYN="N">physiology</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D010802" MajorTopicYN="N">Phylogeny</DescriptorName></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="D032107" MajorTopicYN="N">Populus</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName><QualifierName UI="Q000378" MajorTopicYN="Y">metabolism</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D020133" MajorTopicYN="N">Reverse Transcriptase Polymerase Chain Reaction</DescriptorName></MeshHeading></MeshHeadingList><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">Phylogenetic analysis</Keyword><Keyword MajorTopicYN="N">Populus trichocarpa</Keyword><Keyword MajorTopicYN="N">Stress-responses profiles</Keyword><Keyword MajorTopicYN="N">TIFY genes</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2017</Year><Month>02</Month><Day>07</Day></PubMedPubDate><PubMedPubDate PubStatus="revised"><Year>2017</Year><Month>04</Month><Day>11</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2017</Year><Month>04</Month><Day>12</Day></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2017</Year><Month>4</Month><Day>22</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2017</Year><Month>12</Month><Day>30</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2017</Year><Month>4</Month><Day>22</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">28431355</ArticleId><ArticleId IdType="pii">S0981-9428(17)30135-3</ArticleId><ArticleId IdType="doi">10.1016/j.plaphy.2017.04.015</ArticleId></ArticleIdList></PubmedData></pubmed></record>Pour manipuler ce document sous Unix (Dilib)
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