Genome-wide identification and expression analysis of the IQD gene family in Populus trichocarpa.
Identifieur interne : 001F01 ( Main/Corpus ); précédent : 001F00; suivant : 001F02Genome-wide identification and expression analysis of the IQD gene family in Populus trichocarpa.
Auteurs : Hui Ma ; Lin Feng ; Zhu Chen ; Xue Chen ; Hualin Zhao ; Yan XiangSource :
- Plant science : an international journal of experimental plant biology [ 1873-2259 ] ; 2014.
English descriptors
- KwdEn :
- Acetates (pharmacology), Amino Acid Motifs (MeSH), Amino Acid Sequence (MeSH), Arabidopsis (genetics), Binding Sites (MeSH), Brachypodium (drug effects), Brachypodium (genetics), Calmodulin (metabolism), Chromosomes, Plant (genetics), Conserved Sequence (genetics), Cyclopentanes (pharmacology), Expressed Sequence Tags (MeSH), Gene Duplication (MeSH), Gene Expression Profiling (MeSH), Gene Expression Regulation, Plant (drug effects), Genes, Plant (MeSH), Genome-Wide Association Study (MeSH), Molecular Sequence Data (MeSH), Multigene Family (MeSH), Oryza (drug effects), Oryza (genetics), Oxylipins (pharmacology), Phylogeny (MeSH), Plant Proteins (chemistry), Plant Proteins (genetics), Plant Proteins (metabolism), Polyethylene Glycols (pharmacology), Populus (drug effects), Populus (genetics), Time Factors (MeSH).
- MESH :
- chemical , chemistry : Plant Proteins.
- chemical , genetics : Plant Proteins.
- chemical , metabolism : Calmodulin, Plant Proteins.
- chemical , pharmacology : Acetates, Cyclopentanes, Oxylipins, Polyethylene Glycols.
- drug effects : Brachypodium, Gene Expression Regulation, Plant, Oryza, Populus.
- genetics : Arabidopsis, Brachypodium, Chromosomes, Plant, Conserved Sequence, Oryza, Populus.
- Amino Acid Motifs, Amino Acid Sequence, Binding Sites, Expressed Sequence Tags, Gene Duplication, Gene Expression Profiling, Genes, Plant, Genome-Wide Association Study, Molecular Sequence Data, Multigene Family, Phylogeny, Time Factors.
Abstract
IQD proteins are downstream targets of calcium sensors, which play important roles in development and responses to environmental cues in plants. Comprehensive analyses of IQD genes have been conducted in Arabidopsis, rice, tomato, and Brachypodium distachyon, but have not been reported from poplar. The availability of the Populus trichocarpa genome sequence allowed us to conduct phylogenetic, gene structure, chromosomal location, and microarray analyses of the predicted IQD genes in P. trichocarpa. We identified 40 IQD genes (PtIQD1-40) classified in four subfamilies (I-IV). Gene structure and protein motif analyses showed that these genes are relatively conserved within each subfamily. The 40 PtIQD genes are distributed on 18 of the 19 chromosomes, with 16 gene pairs involved in segmental duplication events. The Ka/Ks ratios of the 16 segmentally-duplicated gene pairs show that the duplicated pairs underwent purifying selection with restrictive functional divergence after the duplication events. Analyses of microarray data for 38 PtIQD genes showed tissue/organ-specific expression patterns. We also performed quantitative real-time RT-PCR (qRT-PCR) analyses of twelve selected PtIQD genes in plants treated with MeJA and PEG in order to explore their stress-related expression patterns. Our results will be valuable for further analysis of poplar IQD genes to characterize their important biological functions.
DOI: 10.1016/j.plantsci.2014.08.017
PubMed: 25443837
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pubmed:25443837Le document en format XML
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Electronic address: Xiangyanahau@sina.com.</nlm:affiliation></affiliation></author></analytic><series><title level="j">Plant science : an international journal of experimental plant biology</title><idno type="eISSN">1873-2259</idno><imprint><date when="2014" type="published">2014</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Acetates (pharmacology)</term><term>Amino Acid Motifs (MeSH)</term><term>Amino Acid Sequence (MeSH)</term><term>Arabidopsis (genetics)</term><term>Binding Sites (MeSH)</term><term>Brachypodium (drug effects)</term><term>Brachypodium (genetics)</term><term>Calmodulin (metabolism)</term><term>Chromosomes, Plant (genetics)</term><term>Conserved Sequence (genetics)</term><term>Cyclopentanes (pharmacology)</term><term>Expressed Sequence Tags (MeSH)</term><term>Gene Duplication (MeSH)</term><term>Gene Expression Profiling (MeSH)</term><term>Gene Expression Regulation, Plant (drug effects)</term><term>Genes, Plant (MeSH)</term><term>Genome-Wide Association Study (MeSH)</term><term>Molecular Sequence Data (MeSH)</term><term>Multigene Family (MeSH)</term><term>Oryza (drug effects)</term><term>Oryza (genetics)</term><term>Oxylipins (pharmacology)</term><term>Phylogeny (MeSH)</term><term>Plant Proteins (chemistry)</term><term>Plant Proteins (genetics)</term><term>Plant Proteins (metabolism)</term><term>Polyethylene Glycols (pharmacology)</term><term>Populus (drug effects)</term><term>Populus (genetics)</term><term>Time Factors (MeSH)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="chemistry" 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" type="chemical" qualifier="metabolism" xml:lang="en"><term>Calmodulin</term><term>Plant Proteins</term></keywords><keywords scheme="MESH" type="chemical" qualifier="pharmacology" xml:lang="en"><term>Acetates</term><term>Cyclopentanes</term><term>Oxylipins</term><term>Polyethylene Glycols</term></keywords><keywords scheme="MESH" qualifier="drug effects" xml:lang="en"><term>Brachypodium</term><term>Gene Expression Regulation, Plant</term><term>Oryza</term><term>Populus</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Arabidopsis</term><term>Brachypodium</term><term>Chromosomes, Plant</term><term>Conserved Sequence</term><term>Oryza</term><term>Populus</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Amino Acid Motifs</term><term>Amino Acid Sequence</term><term>Binding Sites</term><term>Expressed Sequence Tags</term><term>Gene Duplication</term><term>Gene Expression Profiling</term><term>Genes, Plant</term><term>Genome-Wide Association Study</term><term>Molecular Sequence Data</term><term>Multigene Family</term><term>Phylogeny</term><term>Time Factors</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">IQD proteins are downstream targets of calcium sensors, which play important roles in development and responses to environmental cues in plants. Comprehensive analyses of IQD genes have been conducted in Arabidopsis, rice, tomato, and Brachypodium distachyon, but have not been reported from poplar. The availability of the Populus trichocarpa genome sequence allowed us to conduct phylogenetic, gene structure, chromosomal location, and microarray analyses of the predicted IQD genes in P. trichocarpa. We identified 40 IQD genes (PtIQD1-40) classified in four subfamilies (I-IV). Gene structure and protein motif analyses showed that these genes are relatively conserved within each subfamily. The 40 PtIQD genes are distributed on 18 of the 19 chromosomes, with 16 gene pairs involved in segmental duplication events. The Ka/Ks ratios of the 16 segmentally-duplicated gene pairs show that the duplicated pairs underwent purifying selection with restrictive functional divergence after the duplication events. Analyses of microarray data for 38 PtIQD genes showed tissue/organ-specific expression patterns. We also performed quantitative real-time RT-PCR (qRT-PCR) analyses of twelve selected PtIQD genes in plants treated with MeJA and PEG in order to explore their stress-related expression patterns. Our results will be valuable for further analysis of poplar IQD genes to characterize their important biological functions. </div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">25443837</PMID><DateCompleted><Year>2015</Year><Month>07</Month><Day>21</Day></DateCompleted><DateRevised><Year>2020</Year><Month>09</Month><Day>30</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1873-2259</ISSN><JournalIssue CitedMedium="Internet"><Volume>229</Volume><PubDate><Year>2014</Year><Month>Dec</Month></PubDate></JournalIssue><Title>Plant science : an international journal of experimental plant biology</Title><ISOAbbreviation>Plant Sci</ISOAbbreviation></Journal><ArticleTitle>Genome-wide identification and expression analysis of the IQD gene family in Populus trichocarpa.</ArticleTitle><Pagination><MedlinePgn>96-110</MedlinePgn></Pagination><ELocationID EIdType="pii" ValidYN="Y">S0168-9452(14)00202-7</ELocationID><ELocationID EIdType="doi" ValidYN="Y">10.1016/j.plantsci.2014.08.017</ELocationID><Abstract><AbstractText>IQD proteins are downstream targets of calcium sensors, which play important roles in development and responses to environmental cues in plants. Comprehensive analyses of IQD genes have been conducted in Arabidopsis, rice, tomato, and Brachypodium distachyon, but have not been reported from poplar. The availability of the Populus trichocarpa genome sequence allowed us to conduct phylogenetic, gene structure, chromosomal location, and microarray analyses of the predicted IQD genes in P. trichocarpa. We identified 40 IQD genes (PtIQD1-40) classified in four subfamilies (I-IV). Gene structure and protein motif analyses showed that these genes are relatively conserved within each subfamily. The 40 PtIQD genes are distributed on 18 of the 19 chromosomes, with 16 gene pairs involved in segmental duplication events. The Ka/Ks ratios of the 16 segmentally-duplicated gene pairs show that the duplicated pairs underwent purifying selection with restrictive functional divergence after the duplication events. Analyses of microarray data for 38 PtIQD genes showed tissue/organ-specific expression patterns. We also performed quantitative real-time RT-PCR (qRT-PCR) analyses of twelve selected PtIQD genes in plants treated with MeJA and PEG in order to explore their stress-related expression patterns. Our results will be valuable for further analysis of poplar IQD genes to characterize their important biological functions. </AbstractText><CopyrightInformation>Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.</CopyrightInformation></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Ma</LastName><ForeName>Hui</ForeName><Initials>H</Initials><AffiliationInfo><Affiliation>Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei 230036, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Feng</LastName><ForeName>Lin</ForeName><Initials>L</Initials><AffiliationInfo><Affiliation>Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei 230036, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Chen</LastName><ForeName>Zhu</ForeName><Initials>Z</Initials><AffiliationInfo><Affiliation>Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei 230036, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Chen</LastName><ForeName>Xue</ForeName><Initials>X</Initials><AffiliationInfo><Affiliation>Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei 230036, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Zhao</LastName><ForeName>Hualin</ForeName><Initials>H</Initials><AffiliationInfo><Affiliation>Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei 230036, 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 230036, China; Key Laboratory of Crop Biology of 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><PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2014</Year><Month>09</Month><Day>06</Day></ArticleDate></Article><MedlineJournalInfo><Country>Ireland</Country><MedlineTA>Plant Sci</MedlineTA><NlmUniqueID>9882015</NlmUniqueID><ISSNLinking>0168-9452</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D000085">Acetates</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D002147">Calmodulin</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D003517">Cyclopentanes</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance 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