拟南芥和水稻SET结构域基因家族全基因组鉴定、分类和表达

Genome-wide identification,classification and expression analyses of SET domain gene family in Arabidopsis and rice

SET(Su(var),Enhancer of zeste(E(z)),and Trithorax)结构域基因家族是一组含有保守SET结构域的蛋白的统称,它们参与蛋白甲基化,影响染色体结构,并且调控基因表达,在植物发育中起着重要的作用。分析拟南芥和水稻中SET结构域基因家族进化关系,对研究这一基因家族中各成员的功能有着重要的意义。我们系统地鉴定了47个拟南芥(Arabidopsis thaliana)和43个水稻(Orysa sativa japonica cultivar Nipponbare)的SET结构域基因,染色体定位和基因复制分析表明SET结构域基因扩增是由片段复制和反转录引起的,根据这些结构域差异和系统发育分析把拟南芥和水稻的SET结构域基因划分成5个亚家族。通过分析SET结构域基因家族在拟南芥和水稻各个发育阶段的表达谱,发现SET结构域基因绝大部分至少在一个组织中表达;大部分在花和花粉中高表达;一些SET结构域基因在某些组织中有特异的表达模式,表明与组织发育有密切的关系。在拟南芥和水稻中分别找到了4个差异表达基因。拟南芥4个差异基因都在花粉管高表达,水稻4个差异基因有3个在雄性花蕊中高表达,另一个在幼穗中高表达。

SET（Su（var）, Enhancer of zeste （E（z））, and Trithorax） domain protein family members share the conserved SET domain. They participate in protein methylation, chromosome structure adjustment, and gene expression regulation, and play important roles in plant development. In this study, bioinformatics analysis identified 47 and 43 SET domain genes in Arabidopsis and rice, respectively. A comprehensive overview of this gene family was presented, including the gene structure, phylogeny, chromosome distribution, and conserved motifs. As a result, the SET domain genes were organized into 5 subfamilies on basis of phylogenetic relationship. Chromosome localization and gene duplication analysis showed that segmental and retrotransposition-like event may result in the SET domain gene expansion. By analyzing the developmental expression pattern of SET domain genes in Arabidopsis and rice, most of the SET domain genes were shown to be expressed in at least one tissue with the most expression in flower and pollen. Some genes showed specific expression patterns in certain tissues at certain stages, suggesting that they were closely related to tissue development. Differentially expressed genes were discovered in Arabidopsis and rice. All of the 4 differentially expressed genes in Arabidopsis were highly expressed in mature pollen. Three of the 4 differentially expressed genes in rice were highly expressed in stamen and the remaining one in young panicle.