水稻中富含亮氨酸的重复序列和核苷酸结合位点(LRR-NBS)基因家族的生物信息学分析  

Bioinformatic Analysis of the LRR-NBS Gene Family in Rice

作　　者：孙学辉[1] 路铁刚[1] 贾士荣[1] 黄大昉[1] 

机构地区：[1]中国农业科学院生物技术研究所,北京100081

出　　处：《中国农业科学》2004年第1期1-7,共7页Scientia Agricultura Sinica

基　　金：国家自然基金资助项目 ( 3 0 3 40 0 49);"863"资助项目 (JY0 3 0 6)

摘　　要：采用HMM(HiddenMarkovModel) ,对源于日本晴的粳稻 (国际水稻测序计划 ,IRGSP)基因组和 9311的籼稻基因组 (北京华大 ,BGI)的蛋白质数据库进行了搜索 ,分别获得了 32 5和 344个富含亮氨酸的重复序列和核苷酸结合位点 (leucinerichrepeat-nucleotidebindingsite ,LRR -NBS)类的抗病基因的蛋白序列 ,并得到了与这些蛋白相应的cDNA序列。对粳稻蛋白功能结构域的分析表明 ,多个蛋白具有与植物防卫反应相关的结构域 ,还发现多个蛋白中存在着与转座 /反转座酶或蛋白所具有的结构域。对 2套数据同源性分析表明 ,粳稻中 4 8个基因在籼稻中可以确定存在orthologs基因 ,且几乎所有的粳稻基因在籼稻中都存在高度同源的对应基因。对这些蛋白的表达情况进行了EST库搜索 ,确定粳稻和籼稻中分别有 95和 79个蛋白表达。对粳稻和籼稻的所有LRR NBS类蛋白的NBS结构域氨基酸序列进行了多序列比对和系统进化分析 ,在粳稻中可以确定为 2 6 3个簇 ,这些簇大多只含 1个基因 ,是一个冗余度不高的基因家族。且除了个别族外 。Using two-step HMM (Hidden Markov Model) scan strategy, the protein and cDNA sequence of the LRR-NBS-like (leucine rich repeat-nucleotide binding site-like) resistance genes family with 325 and 344 numbers were obtained respectively from a Japonica cultivar Nippon bare genome (International Rice Genome Sequencing project, IRGSP) and an Indica cultivar 9311 genome (Beijing Genomic Center, BGI). By the domain analysis, many proteins of this family showed eyisting domains related to plant defense reaction and many proteins had several domains with relation to transposition/retrotransposition. 48 genes in IRGSP had orthologs in BGI through the homologous analysis, and almost all genes in IRGSP had high homologous genes in BGI. We confined that 95 and 79 genes expressing in Nippon bare and 9311 cell by EST search. Alignment and phylogenic analysis was performed to the LRR-NBS family, it showed 263 clusters in IRGSP, with only one gene in most cluster, excepting several individual genes, all genes showed homologous relations.

关 键 词：水稻 亮氨酸 重复序列 核苷酸 结合位点 LRR—NBS 基因家族 生物信息学分析 

分 类 号：S511[农业科学—作物学]