Genome-wide analysis of the WD-repeat protein family in cucumber and Arabidopsis
Genome-wide analysis of the WD-repeat protein family in cucumber and Arabidopsis
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黄瓜和拟南芥中 WD 重复蛋白家族的全基因组分析
DOI：
10.1007/s00438-013-0789-x
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发表时间：
2014-02-01
影响因子：
3.1
通讯作者：
Ren, Zhonghai
中科院分区：
文献类型：
--
作者：
Li, Qiang;Zhao, Panpan;Ren, Zhonghai
WD-重复序列（WDR）蛋白包括一个极其多样化的调节蛋白超家族。迄今为止，该家族的全基因组特征仅在拟南芥中进行，对黄瓜（Cucumis sativus L.）中的WDR基因知之甚少。本研究在最新的黄瓜基因组中鉴定了191个黄瓜WDR基因，并且与拟南芥相比，CsWDR家族包含较少数量的鉴定基因。本研究结果也得到了基因组分布和基因重复分析的支持。系统进化分析表明，WDR蛋白可分为21个亚类。此外，还鉴定了另外12个AtWDR蛋白，并提供了该基因家族在拟南芥中的完整概述，包括重复发生，染色体定位和重复事件。此外，对黄瓜和拟南芥中的这些基因进行了比较分析，结果表明，黄瓜和拟南芥在进化过程中具有很强的基因保守性，并且有特定功能基因的扩增。在非生物胁迫（NaCl，阿坝和低温处理）的转录丰度水平分析确定了6 CsWDR基因，响应于一个或多个处理。还分析了这六个基因的组织特异性表达谱。这项研究产生了比较基因组学分析的WDR基因家族在黄瓜和拟南芥，并提供了第一步CsWDR基因的克隆和功能解剖，可用于进一步研究其在黄瓜抗逆性的作用。
The WD-repeat (WDR) proteins comprise an astonishingly diverse superfamily of regulatory proteins. To date, genome-wide characterization of this family has only been conducted in Arabidopsis and little is known about WDR genes in cucumber (Cucumis sativus L.). This study identified 191 cucumber WDR genes in the latest cucumber genome and the CsWDR family contained a smaller number of identified genes compared to Arabidopsis. The results of this study were also supported by genome distribution and gene duplication analysis. Phylogenetic analysis showed that the WDR proteins could be classified into 21 subgroups. Moreover, an additional 12 AtWDR proteins were also identified and a complete overview of this gene family in Arabidopsis is presented, including the phylogeny, chromosome locations and duplication events. In addition, a comparative analysis between these genes in cucumber and Arabidopsis was performed and it suggested that there was strong gene conservation and that there was an expansion of particular functional genes during the evolution of the two species. The transcript abundance level analysis during abiotic stress (NaCl, ABA and low temperature treatments) identified six CsWDR genes that responded to one or more treatments. Tissue-specific expression profiles of these six genes were also analyzed. This study has produced a comparative genomics analysis of the WDR gene family in cucumber and Arabidopsis and provides the first steps towards the selection of CsWDR genes for cloning and functional dissection that can be used in further studies into their roles in cucumber stress resistance.