水稻扩展蛋白家族的生物信息学分析

doi:10.3724/SP.J.1005.2014.0809

遗传 ›› 2014, Vol. 36 ›› Issue (8): 809-820.doi: 10.3724/SP.J.1005.2014.0809

水稻扩展蛋白家族的生物信息学分析

施杨, 徐筱, 李昊阳, 徐倩, 徐吉臣

北京林业大学,林木育种国家工程实验室,北京100083

收稿日期:2014-01-14 出版日期:2014-08-20 发布日期:2013-07-19
通讯作者: 徐吉臣,教授,研究方向：植物抗逆分子生物学。E-mail:jcxu282@sina.com
作者简介:施杨,硕士研究生,专业方向：植物抗逆分子生物学。Tel: 010-62336628; E-mail: xiandao_shiyang@126.com
基金资助:
国家自然科学基金项目(编号：31128016)资助

Bioinformatics analysis of the expansin gene family in rice

Yang Shi, Xiao Xu, Haoyang Li, Qian Xu, Jichen Xu

National Engineering Laboratory for Tree Breeding, Beijing Forestry University, Beijing 100083, China

Received:2014-01-14 Online:2014-08-20 Published:2013-07-19

摘要/Abstract

摘要： 扩展蛋白是植物细胞壁的重要组成部分,具有松驰细胞壁和增加细胞壁柔韧性的作用,在植物的生长发育及抗性等方面起到重要的作用。水稻的全基因组序列统计分析显示,水稻扩展蛋白基因家族包含58个成员,分属于A(34)、B(19)、LA(4)和LB(1)4个亚家族,分布在水稻10条染色体上的58个位点,且同一亚家族成员有成簇存在的现象。扩展蛋白基因长度范围为687~1128 bp,编码蛋白质具有保守的结构域,以及保守的半胱氨酸和色氨酸残基。多数情况下,亚家族成员之间的氨基酸一致率小于35%,而同一亚家族成员之间的氨基酸一致率大于35%。在内含子、外显子组成模式上,水稻扩展蛋白呈现明显的亚家族特异性,除个别基因以外,A类基因含有1或2个内含子,B类含有3个内含子,LA和LB类含有4个内含子。密码子使用统计显示,与其他物种相比,水稻中的扩展蛋白具有更多的密码子使用偏好性,有26个高频密码子存在。研究结果展示了水稻扩展蛋白基因家族的基本信息,为深入研究扩展蛋白基因的功能、探讨物种间的进化关系奠定基础。

关键词: 水稻, 扩展蛋白, 细胞壁, 基因家族, 生物信息学

Abstract: Expansin refers to a family of nonenzymatic proteins found in the plant cell wall with important roles in plant cell growth, developmental processes, and resistance to stress. Whole rice genome sequencing revealed that it contains 58 expansin genes, which belong to 4 subfamilies (A (34), B (19), LA (4) and LB (1)). All the genes were located on 10 of 12 rice chromosomes where several subfamily members clustered. Each of expansin genes ranged from 687 bp to 1128 bp in size. Sequence alignment showed that all expansins had three structural domains with two conserved amino acids of cystine in N-terminus and tryptophan in C-terminus. The amino acid identity of members among different subfamilies was less than 35%, while that among the same subfamily was more than 35%. Most genes of A subfamily had 1 or 2 introns, while genes of B, LA and LB subfamily had 3, 4 and 4 introns, respectively. Statistics analysis of codon usage showed that expansins in rice have 26 high-frequency codons which are more biased than those in other species. These bioinformatics findings will be helpful for the further study of the function and evolution of expansin genes.

Key words: rice, expansin, cell wall, gene family, bioinformatics

施杨, 徐筱, 李昊阳, 徐倩, 徐吉臣. 水稻扩展蛋白家族的生物信息学分析[J]. 遗传, 2014, 36(8): 809-820.

Yang Shi, Xiao Xu, Haoyang Li, Qian Xu, Jichen Xu. Bioinformatics analysis of the expansin gene family in rice[J]. HEREDITAS(Beijing), 2014, 36(8): 809-820.

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水稻扩展蛋白家族的生物信息学分析

Bioinformatics analysis of the expansin gene family in rice

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