Phylogenetic, expression, and bioinformatic analysis of the ABC1 gene family in Populus trichocarpa.
Identifieur interne : 002550 ( Main/Exploration ); précédent : 002549; suivant : 002551Phylogenetic, expression, and bioinformatic analysis of the ABC1 gene family in Populus trichocarpa.
Auteurs : Zhanchao Wang [République populaire de Chine] ; Haizhen Zhang ; Jingli Yang ; Yunlin Chen ; Xuemei Xu ; Xuliang Mao ; Chenghao LiSource :
- TheScientificWorldJournal [ 1537-744X ] ; 2013.
Descripteurs français
- KwdFr :
- MESH :
- classification : Protéines végétales.
- composition chimique : Populus.
- génétique : Protéines végétales.
- méthodes : Biologie informatique.
- Phylogenèse, Régulation de l'expression des gènes végétaux.
English descriptors
- KwdEn :
- MESH :
- chemical , classification : Plant Proteins.
- chemical , genetics : Plant Proteins.
- chemistry : Populus.
- methods : Computational Biology.
- Gene Expression Regulation, Plant, Phylogeny.
Abstract
We studied 17 ABC1 genes in Populus trichocarpa, all of which contained an ABC1 domain consisting of about 120 amino acid residues. Most of the ABC1 gene products were located in the mitochondria or chloroplasts. All had a conserved VAVK-like motif and a DFG motif. Phylogenetic analysis grouped the genes into three subgroups. In addition, the chromosomal locations of the genes on the 19 Populus chromosomes were determined. Gene structure was studied through exon/intron organization and the MEME motif finder, while heatmap was used to study the expression diversity using EST libraries. According to the heatmap, PtrABC1P14 was highlighted because of the high expression in tension wood which related to secondary cell wall formation and cellulose synthesis, thus making a contribution to follow-up experiment in wood formation. Promoter cis-element analysis indicated that almost all of the ABC1 genes contained one or two cis-elements related to ABA signal transduction pathway and drought stress. Quantitative real-time PCR was carried out to evaluate the expression of all of the genes under abiotic stress conditions (ABA, CdCl2, high temperature, high salinity, and drought); the results showed that some of the genes were affected by these stresses and confirmed the results of promoter cis-element analysis.
DOI: 10.1155/2013/785070
PubMed: 24163630
PubMed Central: PMC3791817
Affiliations:
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first="Jingli" last="Yang">Jingli Yang</name></author><author><name sortKey="Chen, Yunlin" sort="Chen, Yunlin" uniqKey="Chen Y" first="Yunlin" last="Chen">Yunlin Chen</name></author><author><name sortKey="Xu, Xuemei" sort="Xu, Xuemei" uniqKey="Xu X" first="Xuemei" last="Xu">Xuemei Xu</name></author><author><name sortKey="Mao, Xuliang" sort="Mao, Xuliang" uniqKey="Mao X" first="Xuliang" last="Mao">Xuliang Mao</name></author><author><name sortKey="Li, Chenghao" sort="Li, Chenghao" uniqKey="Li C" first="Chenghao" last="Li">Chenghao Li</name></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2013">2013</date><idno type="RBID">pubmed:24163630</idno><idno type="pmid">24163630</idno><idno type="doi">10.1155/2013/785070</idno><idno type="pmc">PMC3791817</idno><idno type="wicri:Area/Main/Corpus">002427</idno><idno type="wicri:explorRef" wicri:stream="Main" wicri:step="Corpus" wicri:corpus="PubMed">002427</idno><idno 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Haizhen" sort="Zhang, Haizhen" uniqKey="Zhang H" first="Haizhen" last="Zhang">Haizhen Zhang</name></author><author><name sortKey="Yang, Jingli" sort="Yang, Jingli" uniqKey="Yang J" first="Jingli" last="Yang">Jingli Yang</name></author><author><name sortKey="Chen, Yunlin" sort="Chen, Yunlin" uniqKey="Chen Y" first="Yunlin" last="Chen">Yunlin Chen</name></author><author><name sortKey="Xu, Xuemei" sort="Xu, Xuemei" uniqKey="Xu X" first="Xuemei" last="Xu">Xuemei Xu</name></author><author><name sortKey="Mao, Xuliang" sort="Mao, Xuliang" uniqKey="Mao X" first="Xuliang" last="Mao">Xuliang Mao</name></author><author><name sortKey="Li, Chenghao" sort="Li, Chenghao" uniqKey="Li C" first="Chenghao" last="Li">Chenghao Li</name></author></analytic><series><title level="j">TheScientificWorldJournal</title><idno type="eISSN">1537-744X</idno><imprint><date when="2013" type="published">2013</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Computational Biology (methods)</term><term>Gene Expression Regulation, Plant (MeSH)</term><term>Phylogeny (MeSH)</term><term>Plant Proteins (classification)</term><term>Plant Proteins (genetics)</term><term>Populus (chemistry)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Biologie informatique (méthodes)</term><term>Phylogenèse (MeSH)</term><term>Populus (composition chimique)</term><term>Protéines végétales (classification)</term><term>Protéines végétales (génétique)</term><term>Régulation de l'expression des gènes végétaux (MeSH)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="classification" xml:lang="en"><term>Plant Proteins</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>Plant Proteins</term></keywords><keywords scheme="MESH" qualifier="chemistry" xml:lang="en"><term>Populus</term></keywords><keywords scheme="MESH" qualifier="classification" xml:lang="fr"><term>Protéines végétales</term></keywords><keywords scheme="MESH" qualifier="composition chimique" xml:lang="fr"><term>Populus</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Protéines végétales</term></keywords><keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Computational Biology</term></keywords><keywords scheme="MESH" qualifier="méthodes" xml:lang="fr"><term>Biologie informatique</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Gene Expression Regulation, Plant</term><term>Phylogeny</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Phylogenèse</term><term>Régulation de l'expression des gènes végétaux</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">We studied 17 ABC1 genes in Populus trichocarpa, all of which contained an ABC1 domain consisting of about 120 amino acid residues. Most of the ABC1 gene products were located in the mitochondria or chloroplasts. All had a conserved VAVK-like motif and a DFG motif. Phylogenetic analysis grouped the genes into three subgroups. In addition, the chromosomal locations of the genes on the 19 Populus chromosomes were determined. Gene structure was studied through exon/intron organization and the MEME motif finder, while heatmap was used to study the expression diversity using EST libraries. According to the heatmap, PtrABC1P14 was highlighted because of the high expression in tension wood which related to secondary cell wall formation and cellulose synthesis, thus making a contribution to follow-up experiment in wood formation. Promoter cis-element analysis indicated that almost all of the ABC1 genes contained one or two cis-elements related to ABA signal transduction pathway and drought stress. Quantitative real-time PCR was carried out to evaluate the expression of all of the genes under abiotic stress conditions (ABA, CdCl2, high temperature, high salinity, and drought); the results showed that some of the genes were affected by these stresses and confirmed the results of promoter cis-element analysis. </div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">24163630</PMID><DateCompleted><Year>2014</Year><Month>05</Month><Day>02</Day></DateCompleted><DateRevised><Year>2018</Year><Month>11</Month><Day>13</Day></DateRevised><Article PubModel="Electronic-eCollection"><Journal><ISSN IssnType="Electronic">1537-744X</ISSN><JournalIssue CitedMedium="Internet"><Volume>2013</Volume><PubDate><Year>2013</Year></PubDate></JournalIssue><Title>TheScientificWorldJournal</Title><ISOAbbreviation>ScientificWorldJournal</ISOAbbreviation></Journal><ArticleTitle>Phylogenetic, expression, and bioinformatic analysis of the ABC1 gene family in Populus trichocarpa.</ArticleTitle><Pagination><MedlinePgn>785070</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1155/2013/785070</ELocationID><Abstract><AbstractText>We studied 17 ABC1 genes in Populus trichocarpa, all of which contained an ABC1 domain consisting of about 120 amino acid residues. Most of the ABC1 gene products were located in the mitochondria or chloroplasts. All had a conserved VAVK-like motif and a DFG motif. Phylogenetic analysis grouped the genes into three subgroups. In addition, the chromosomal locations of the genes on the 19 Populus chromosomes were determined. Gene structure was studied through exon/intron organization and the MEME motif finder, while heatmap was used to study the expression diversity using EST libraries. According to the heatmap, PtrABC1P14 was highlighted because of the high expression in tension wood which related to secondary cell wall formation and cellulose synthesis, thus making a contribution to follow-up experiment in wood formation. Promoter cis-element analysis indicated that almost all of the ABC1 genes contained one or two cis-elements related to ABA signal transduction pathway and drought stress. Quantitative real-time PCR was carried out to evaluate the expression of all of the genes under abiotic stress conditions (ABA, CdCl2, high temperature, high salinity, and drought); the results showed that some of the genes were affected by these stresses and confirmed the results of promoter cis-element analysis. </AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Wang</LastName><ForeName>Zhanchao</ForeName><Initials>Z</Initials><AffiliationInfo><Affiliation>State Key Laboratory of Forest Genetics and Tree Breeding, Northeast Forestry University, 26 Hexing Road, Harbin 150040, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Zhang</LastName><ForeName>Haizhen</ForeName><Initials>H</Initials></Author><Author ValidYN="Y"><LastName>Yang</LastName><ForeName>Jingli</ForeName><Initials>J</Initials></Author><Author ValidYN="Y"><LastName>Chen</LastName><ForeName>Yunlin</ForeName><Initials>Y</Initials></Author><Author ValidYN="Y"><LastName>Xu</LastName><ForeName>Xuemei</ForeName><Initials>X</Initials></Author><Author ValidYN="Y"><LastName>Mao</LastName><ForeName>Xuliang</ForeName><Initials>X</Initials></Author><Author ValidYN="Y"><LastName>Li</LastName><ForeName>Chenghao</ForeName><Initials>C</Initials></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>2013</Year><Month>09</Month><Day>15</Day></ArticleDate></Article><MedlineJournalInfo><Country>United States</Country><MedlineTA>ScientificWorldJournal</MedlineTA><NlmUniqueID>101131163</NlmUniqueID><ISSNLinking>1537-744X</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D010940">Plant 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Mao</name><name sortKey="Xu, Xuemei" sort="Xu, Xuemei" uniqKey="Xu X" first="Xuemei" last="Xu">Xuemei Xu</name><name sortKey="Yang, Jingli" sort="Yang, Jingli" uniqKey="Yang J" first="Jingli" last="Yang">Jingli Yang</name><name sortKey="Zhang, Haizhen" sort="Zhang, Haizhen" uniqKey="Zhang H" first="Haizhen" last="Zhang">Haizhen Zhang</name></noCountry><country name="République populaire de Chine"><noRegion><name sortKey="Wang, Zhanchao" sort="Wang, Zhanchao" uniqKey="Wang Z" first="Zhanchao" last="Wang">Zhanchao Wang</name></noRegion></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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