Genome-wide analysis of the R2R3-MYB transcription factor gene family in sweet orange (Citrus sinensis).
Identifieur interne : 000A60 ( Main/Exploration ); précédent : 000A59; suivant : 000A61Genome-wide analysis of the R2R3-MYB transcription factor gene family in sweet orange (Citrus sinensis).
Auteurs : Chaoyang Liu [République populaire de Chine] ; Xia Wang ; Yuantao Xu ; Xiuxin Deng ; Qiang XuSource :
- Molecular biology reports [ 1573-4978 ] ; 2014.
English descriptors
- KwdEn :
- Chromosome Mapping, Citrus sinensis (classification), Citrus sinensis (genetics), Cluster Analysis, Computational Biology (methods), Gene Duplication, Gene Expression Profiling, Genes, Plant, Genome-Wide Association Study, Genomics (methods), Molecular Sequence Annotation, Multigene Family, Phylogeny, Position-Specific Scoring Matrices, Protein Interaction Domains and Motifs, Transcription Factors (chemistry), Transcription Factors (genetics).
- MESH :
- chemical , chemistry : Transcription Factors.
- classification : Citrus sinensis.
- genetics : Citrus sinensis, Transcription Factors.
- methods : Computational Biology, Genomics.
- Chromosome Mapping, Cluster Analysis, Gene Duplication, Gene Expression Profiling, Genes, Plant, Genome-Wide Association Study, Molecular Sequence Annotation, Multigene Family, Phylogeny, Position-Specific Scoring Matrices, Protein Interaction Domains and Motifs.
Abstract
MYB transcription factor represents one of the largest gene families in plant genomes. Sweet orange (Citrus sinensis) is one of the most important fruit crops worldwide, and recently the genome has been sequenced. This provides an opportunity to investigate the organization and evolutionary characteristics of sweet orange MYB genes from whole genome view. In the present study, we identified 100 R2R3-MYB genes in the sweet orange genome. A comprehensive analysis of this gene family was performed, including the phylogeny, gene structure, chromosomal localization and expression pattern analyses. The 100 genes were divided into 29 subfamilies based on the sequence similarity and phylogeny, and the classification was also well supported by the highly conserved exon/intron structures and motif composition. The phylogenomic comparison of MYB gene family among sweet orange and related plant species, Arabidopsis, cacao and papaya suggested the existence of functional divergence during evolution. Expression profiling indicated that sweet orange R2R3-MYB genes exhibited distinct temporal and spatial expression patterns. Our analysis suggested that the sweet orange MYB genes may play important roles in different plant biological processes, some of which may be potentially involved in citrus fruit quality. These results will be useful for future functional analysis of the MYB gene family in sweet orange.
DOI: 10.1007/s11033-014-3563-1
PubMed: 25008995
Affiliations:
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first="Yuantao" last="Xu">Yuantao Xu</name></author><author><name sortKey="Deng, Xiuxin" sort="Deng, Xiuxin" uniqKey="Deng X" first="Xiuxin" last="Deng">Xiuxin Deng</name></author><author><name sortKey="Xu, Qiang" sort="Xu, Qiang" uniqKey="Xu Q" first="Qiang" last="Xu">Qiang Xu</name></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2014">2014</date><idno type="RBID">pubmed:25008995</idno><idno type="pmid">25008995</idno><idno type="doi">10.1007/s11033-014-3563-1</idno><idno type="wicri:Area/PubMed/Corpus">000294</idno><idno type="wicri:Area/PubMed/Curation">000294</idno><idno type="wicri:Area/PubMed/Checkpoint">000294</idno><idno type="wicri:Area/Ncbi/Merge">001752</idno><idno type="wicri:Area/Ncbi/Curation">001752</idno><idno type="wicri:Area/Ncbi/Checkpoint">001752</idno><idno type="wicri:Area/Main/Merge">000A61</idno><idno type="wicri:Area/Main/Curation">000A60</idno><idno 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sortKey="Xu, Yuantao" sort="Xu, Yuantao" uniqKey="Xu Y" first="Yuantao" last="Xu">Yuantao Xu</name></author><author><name sortKey="Deng, Xiuxin" sort="Deng, Xiuxin" uniqKey="Deng X" first="Xiuxin" last="Deng">Xiuxin Deng</name></author><author><name sortKey="Xu, Qiang" sort="Xu, Qiang" uniqKey="Xu Q" first="Qiang" last="Xu">Qiang Xu</name></author></analytic><series><title level="j">Molecular biology reports</title><idno type="eISSN">1573-4978</idno><imprint><date when="2014" type="published">2014</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Chromosome Mapping</term><term>Citrus sinensis (classification)</term><term>Citrus sinensis (genetics)</term><term>Cluster Analysis</term><term>Computational Biology (methods)</term><term>Gene Duplication</term><term>Gene Expression Profiling</term><term>Genes, Plant</term><term>Genome-Wide Association Study</term><term>Genomics (methods)</term><term>Molecular Sequence Annotation</term><term>Multigene Family</term><term>Phylogeny</term><term>Position-Specific Scoring Matrices</term><term>Protein Interaction Domains and Motifs</term><term>Transcription Factors (chemistry)</term><term>Transcription Factors (genetics)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="chemistry" xml:lang="en"><term>Transcription Factors</term></keywords><keywords scheme="MESH" qualifier="classification" xml:lang="en"><term>Citrus sinensis</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Citrus sinensis</term><term>Transcription Factors</term></keywords><keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Computational Biology</term><term>Genomics</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Chromosome Mapping</term><term>Cluster Analysis</term><term>Gene Duplication</term><term>Gene Expression Profiling</term><term>Genes, Plant</term><term>Genome-Wide Association Study</term><term>Molecular Sequence Annotation</term><term>Multigene Family</term><term>Phylogeny</term><term>Position-Specific Scoring Matrices</term><term>Protein Interaction Domains and Motifs</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">MYB transcription factor represents one of the largest gene families in plant genomes. Sweet orange (Citrus sinensis) is one of the most important fruit crops worldwide, and recently the genome has been sequenced. This provides an opportunity to investigate the organization and evolutionary characteristics of sweet orange MYB genes from whole genome view. In the present study, we identified 100 R2R3-MYB genes in the sweet orange genome. A comprehensive analysis of this gene family was performed, including the phylogeny, gene structure, chromosomal localization and expression pattern analyses. The 100 genes were divided into 29 subfamilies based on the sequence similarity and phylogeny, and the classification was also well supported by the highly conserved exon/intron structures and motif composition. The phylogenomic comparison of MYB gene family among sweet orange and related plant species, Arabidopsis, cacao and papaya suggested the existence of functional divergence during evolution. Expression profiling indicated that sweet orange R2R3-MYB genes exhibited distinct temporal and spatial expression patterns. Our analysis suggested that the sweet orange MYB genes may play important roles in different plant biological processes, some of which may be potentially involved in citrus fruit quality. These results will be useful for future functional analysis of the MYB gene family in sweet orange.</div></front></TEI><affiliations><list><country><li>République populaire de Chine</li></country></list><tree><noCountry><name sortKey="Deng, Xiuxin" sort="Deng, Xiuxin" uniqKey="Deng X" first="Xiuxin" last="Deng">Xiuxin Deng</name><name sortKey="Wang, Xia" sort="Wang, Xia" uniqKey="Wang X" first="Xia" last="Wang">Xia Wang</name><name sortKey="Xu, Qiang" sort="Xu, Qiang" uniqKey="Xu Q" first="Qiang" last="Xu">Qiang Xu</name><name sortKey="Xu, Yuantao" sort="Xu, Yuantao" uniqKey="Xu Y" first="Yuantao" last="Xu">Yuantao Xu</name></noCountry><country name="République populaire de Chine"><noRegion><name sortKey="Liu, Chaoyang" sort="Liu, Chaoyang" uniqKey="Liu C" first="Chaoyang" last="Liu">Chaoyang Liu</name></noRegion></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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