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Genome-Wide Identification and Characterization of R2R3MYB Family in Cucumis sativus ( R2R3MYB Family in Cucumis sativus)

The R2R3MYB proteins comprise one of the largest families of transcription factors in plants. Although genome-wide analysis of this family has been carried out in some species, little is known about R2R3MYB genes in cucumber ( Cucumis sativus L.). ; This study has identified 55 genes in the latest c... Full description

Journal Title: 2012 Vol.7(10), p.e47576
Main Author: Li, Qiang
Other Authors: Zhang, Cunjia , Li, Jing , Wang, Lina , Ren, Zhonghai
Format: Electronic Article Electronic Article
Language: English
Subjects:
ID: E-ISSN: 1932-6203 ; DOI: 10.1371/journal.pone.0047576
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recordid: plos10.1371/journal.pone.0047576
title: Genome-Wide Identification and Characterization of R2R3MYB Family in Cucumis sativus ( R2R3MYB Family in Cucumis sativus)
format: Article
creator:
  • Li, Qiang
  • Zhang, Cunjia
  • Li, Jing
  • Wang, Lina
  • Ren, Zhonghai
subjects:
  • Research Article
  • Biology
  • Genetics And Genomics
  • Plant Biology
  • Biochemistry
ispartof: 2012, Vol.7(10), p.e47576
description: The R2R3MYB proteins comprise one of the largest families of transcription factors in plants. Although genome-wide analysis of this family has been carried out in some species, little is known about R2R3MYB genes in cucumber ( Cucumis sativus L.). ; This study has identified 55 genes in the latest cucumber genome and the family contained the smallest number of identified genes compared to other species that have been studied due to the absence of recent gene duplication events. These results were also supported by genome distribution and gene duplication analysis. Phylogenetic analysis showed that they could be classified into 11 subgroups. The evolutionary relationships and the intron - exon organizations that showed similarities with , and R2R3MYB proteins were also analyzed and suggested strong gene conservation but also the expansions of particular functional genes during the evolution of the plant species. In addition, we found that 8 out of 55 (∼14.54%) cucumber genes underwent alternative splicing events, producing a variety of transcripts from a single gene, which illustrated the extremely high complexity of transcriptome regulation. Tissue-specific expression profiles showed that 50 cucumber genes were expressed in at least one of the tissues and the other 5 genes showed very low expression in all tissues tested, which suggested that cucumber genes took part in many cellular processes. The transcript abundance level analysis during abiotic conditions (NaCl, ABA and low temperature treatments) identified a group of genes that responded to one or more treatments. ; This study has produced a comparative genomics analysis of the cucumber gene family and has provided the first steps towards the selection of genes for cloning and functional dissection that can be used in further studies to uncover their roles in cucumber growth and development.
language: eng
source:
identifier: E-ISSN: 1932-6203 ; DOI: 10.1371/journal.pone.0047576
fulltext: fulltext
issn:
  • 1932-6203
  • 19326203
url: Link


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titleGenome-Wide Identification and Characterization of R2R3MYB Family in Cucumis sativus ( R2R3MYB Family in Cucumis sativus)
creatorLi, Qiang ; Zhang, Cunjia ; Li, Jing ; Wang, Lina ; Ren, Zhonghai
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subjectResearch Article ; Biology ; Genetics And Genomics ; Plant Biology ; Biochemistry
descriptionThe R2R3MYB proteins comprise one of the largest families of transcription factors in plants. Although genome-wide analysis of this family has been carried out in some species, little is known about R2R3MYB genes in cucumber ( Cucumis sativus L.). ; This study has identified 55 genes in the latest cucumber genome and the family contained the smallest number of identified genes compared to other species that have been studied due to the absence of recent gene duplication events. These results were also supported by genome distribution and gene duplication analysis. Phylogenetic analysis showed that they could be classified into 11 subgroups. The evolutionary relationships and the intron - exon organizations that showed similarities with , and R2R3MYB proteins were also analyzed and suggested strong gene conservation but also the expansions of particular functional genes during the evolution of the plant species. In addition, we found that 8 out of 55 (∼14.54%) cucumber genes underwent alternative splicing events, producing a variety of transcripts from a single gene, which illustrated the extremely high complexity of transcriptome regulation. Tissue-specific expression profiles showed that 50 cucumber genes were expressed in at least one of the tissues and the other 5 genes showed very low expression in all tissues tested, which suggested that cucumber genes took part in many cellular processes. The transcript abundance level analysis during abiotic conditions (NaCl, ABA and low temperature treatments) identified a group of genes that responded to one or more treatments. ; This study has produced a comparative genomics analysis of the cucumber gene family and has provided the first steps towards the selection of genes for cloning and functional dissection that can be used in further studies to uncover their roles in cucumber growth and development.
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descriptionThe R2R3MYB proteins comprise one of the largest families of transcription factors in plants. Although genome-wide analysis of this family has been carried out in some species, little is known about R2R3MYB genes in cucumber ( Cucumis sativus L.). ; This study has identified 55 genes in the latest cucumber genome and the family contained the smallest number of identified genes compared to other species that have been studied due to the absence of recent gene duplication events. These results were also supported by genome distribution and gene duplication analysis. Phylogenetic analysis showed that they could be classified into 11 subgroups. The evolutionary relationships and the intron - exon organizations that showed similarities with , and R2R3MYB proteins were also analyzed and suggested strong gene conservation but also the expansions of particular functional genes during the evolution of the plant species. In addition, we found that 8 out of 55 (∼14.54%) cucumber genes underwent alternative splicing events, producing a variety of transcripts from a single gene, which illustrated the extremely high complexity of transcriptome regulation. Tissue-specific expression profiles showed that 50 cucumber genes were expressed in at least one of the tissues and the other 5 genes showed very low expression in all tissues tested, which suggested that cucumber genes took part in many cellular processes. The transcript abundance level analysis during abiotic conditions (NaCl, ABA and low temperature treatments) identified a group of genes that responded to one or more treatments. ; This study has produced a comparative genomics analysis of the cucumber gene family and has provided the first steps towards the selection of genes for cloning and functional dissection that can be used in further studies to uncover their roles in cucumber growth and development.
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abstractThe R2R3MYB proteins comprise one of the largest families of transcription factors in plants. Although genome-wide analysis of this family has been carried out in some species, little is known about R2R3MYB genes in cucumber ( Cucumis sativus L.). ; This study has identified 55 genes in the latest cucumber genome and the family contained the smallest number of identified genes compared to other species that have been studied due to the absence of recent gene duplication events. These results were also supported by genome distribution and gene duplication analysis. Phylogenetic analysis showed that they could be classified into 11 subgroups. The evolutionary relationships and the intron - exon organizations that showed similarities with , and R2R3MYB proteins were also analyzed and suggested strong gene conservation but also the expansions of particular functional genes during the evolution of the plant species. In addition, we found that 8 out of 55 (∼14.54%) cucumber genes underwent alternative splicing events, producing a variety of transcripts from a single gene, which illustrated the extremely high complexity of transcriptome regulation. Tissue-specific expression profiles showed that 50 cucumber genes were expressed in at least one of the tissues and the other 5 genes showed very low expression in all tissues tested, which suggested that cucumber genes took part in many cellular processes. The transcript abundance level analysis during abiotic conditions (NaCl, ABA and low temperature treatments) identified a group of genes that responded to one or more treatments. ; This study has produced a comparative genomics analysis of the cucumber gene family and has provided the first steps towards the selection of genes for cloning and functional dissection that can be used in further studies to uncover their roles in cucumber growth and development.
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doi10.1371/journal.pone.0047576
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date2012-10-23