Genome-wide identification and characterization of R2R3MYB family in Cucumis sativus.
Genome-wide identification and characterization of R2R3MYB family in Cucumis sativus.
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DOI：
10.1371/journal.pone.0047576
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发表时间：
2012
期刊：
影响因子：
3.7
通讯作者：
Ren Z
中科院分区：
文献类型：
--
作者：
Li Q;Zhang C;Li J;Wang L;Ren Z
R2R3MYB蛋白是植物中最大的转录因子家族之一。虽然在一些物种中已经对该家族进行了全基因组分析，但对黄瓜(Cucumis sativus L.)中的R2R3MYB基因知之甚少。这项研究在最新的黄瓜基因组中鉴定了55个R2R3MYB基因，与其他物种相比，CsR2R3MYB家族包含的已鉴定基因数量最少，因为最近没有基因重复事件。这些结果也得到了基因组分布和基因复制分析的支持。系统发育分析表明，它们可分为11个亚组。还分析了与拟南芥、葡萄和甘氨酸R2R3MYB蛋白相似的进化关系和内含子-外显子组织，表明在植物物种的进化过程中，基因具有很强的保守性，但也存在特定功能基因的扩展。此外，我们还发现55个黄瓜R2R3MYB基因中有8个(∼14.54%)经历了选择性剪接事件，从一个基因产生了不同的转录本，这说明了转录组调控的极高复杂性。组织特异性表达谱显示，50个黄瓜R2R3MYB基因在至少一个组织中表达，其余5个基因在所有组织中的表达水平都很低，这表明黄瓜R2R3MYB基因参与了许多细胞过程。在非生物条件下(氯化钠、脱落酸和低温处理)的转录丰度水平分析确定了一组对一个或多个处理有反应的R2R3MYB基因。本研究对黄瓜R2R3MYB基因家族进行了比较基因组学分析，并为筛选CsR2R3MYB基因进行克隆和功能解剖提供了初步的步骤，可用于进一步研究它们在黄瓜生长发育中的作用。
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 R2R3MYB genes in the latest cucumber genome and the CsR2R3MYB 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 Arabidopsis, Vitis and Glycine 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 R2R3MYB 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 R2R3MYB 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 R2R3MYB 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 R2R3MYB genes that responded to one or more treatments. This study has produced a comparative genomics analysis of the cucumber R2R3MYB gene family and has provided the first steps towards the selection of CsR2R3MYB 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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