基因组水平上水稻受体激酶基因家族的生物信息学分析

 对已完成全序列分析的籼稻(北京基因组信息中心,BGI)和接近完成全序列分析的粳稻(国际水稻基因组测序计划,IRGSP)的蛋白质数据库进行两步HMM(hidden markov model)模式匹配搜寻,在基因组水平上分别获得籼稻和粳稻受体激酶5个基因家族的成员序列共643和701个,对粳稻受体激酶进行了详细的生物信息学分析。对粳稻和籼稻的同源比较分析表明,受体激酶基因存在非常强的保守性,但不同基因在基因组水平上可能存在不同水平的扩增。对Swissprot数据库的同源分析表明,这些基因是植物特有的受体激酶。搜

Genome-wide Bioinformatics Analysis of the Rice Receptor-like Kinase Family

The protein databases annotated from the finished sequencing project of an indica cultivar (Beijing GenomicCenter, BGI) and quite near finished sequencing project of a japonica cultivar (international rice genome sequencing project,IRGSP) were scanned by two-step HMM (hidden markov model) strategy, the families of 643 and 701 numbers of RLKs(receptor-like kinases) were detected respectively, then the RLKs family of IRGSP were analyzed in detail using bioinformaticstools. The homologous analysis between IRGSP and BGI showed that the genes of RLKs is highly conservative, but someindividual genes amplified at the genome level. Analysis showed that the RLKs genes are plant specific with the result of theblasting against the protein database Swissprot. No similar genes were found from yeast proteins based on the blastingsearch. The expressions of RLKs' were obtained by searching the EST database. The family of LRR-RLKs was clusteredbased on the alignment of the kinase's domain. There are 229 clusters in LRR-RLKs gene family, and the whole family havethe relatively high redundancy.