PoplarV1, Main, Exploration, bibRecord, 002205

Genome-wide identification and expression analysis of the IQD gene family in Populus trichocarpa.

Identifieur interne : 002205 ( Main/Exploration ); précédent : 002204; suivant : 002206

Genome-wide identification and expression analysis of the IQD gene family in Populus trichocarpa.

Auteurs : Hui Ma [République populaire de Chine] ; Lin Feng [République populaire de Chine] ; Zhu Chen [République populaire de Chine] ; Xue Chen [République populaire de Chine] ; Hualin Zhao [République populaire de Chine] ; Yan Xiang [République populaire de Chine]

Source :

Plant science : an international journal of experimental plant biology [ 1873-2259 ] ; 2014.

RBID : pubmed:25443837

Descripteurs français

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

Affiliations:

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<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>
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<term>Oryza (genetics)</term>
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<term>Gènes de plante (MeSH)</term>
<term>Motifs d'acides aminés (MeSH)</term>
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<term>Oryza (génétique)</term>
<term>Oxylipines (pharmacologie)</term>
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<term>Séquence d'acides aminés (MeSH)</term>
<term>Étiquettes de séquences exprimées (MeSH)</term>
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<term>Binding Sites</term>
<term>Expressed Sequence Tags</term>
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<term>Gene Expression Profiling</term>
<term>Genes, Plant</term>
<term>Genome-Wide Association Study</term>
<term>Molecular Sequence Data</term>
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<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>
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<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>
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<Day>28</Day>
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<ArticleId IdType="doi">10.1016/j.plantsci.2014.08.017</ArticleId>
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<affiliations><list><country><li>République populaire de Chine</li>
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<name sortKey="Chen, Xue" sort="Chen, Xue" uniqKey="Chen X" first="Xue" last="Chen">Xue Chen</name>
<name sortKey="Chen, Zhu" sort="Chen, Zhu" uniqKey="Chen Z" first="Zhu" last="Chen">Zhu Chen</name>
<name sortKey="Feng, Lin" sort="Feng, Lin" uniqKey="Feng L" first="Lin" last="Feng">Lin Feng</name>
<name sortKey="Xiang, Yan" sort="Xiang, Yan" uniqKey="Xiang Y" first="Yan" last="Xiang">Yan Xiang</name>
<name sortKey="Zhao, Hualin" sort="Zhao, Hualin" uniqKey="Zhao H" first="Hualin" last="Zhao">Hualin Zhao</name>
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Genome-wide identification and expression analysis of the IQD gene family in Populus trichocarpa.

Genome-wide identification and expression analysis of the IQD gene family in Populus trichocarpa.

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