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

 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

Bioinformatic Analysis of the LRR-NBS Gene Family in Rice

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.