甘蓝型油菜NBS-LRR基因家族的鉴定及密码子偏好性分析

Identification and codon bias of NBS-LRR gene family in Brassica napus

NBS-LRR(nucleotide binding site and leucine rich repeat)是庞大且复杂的基因家族,对植物的抗病性具有非常重要的作用。为深入了解甘蓝型油菜NBS-LRR基因家族,合理开发利用基因资源,对甘蓝型油菜(Brassica napus L.)及相关物种的NBS-LRR基因进行了生物信息学分析,包括基因家族鉴定、系统进化分析、保守基序、基因结构、染色体定位以及密码子偏好性分析等。以拟南芥为参考,在甘蓝型油菜中鉴定到463个NBS-LRR基因家族成员,根据结构域将其分成TIR-NBS-LRR和CC-NBS-LRR两类,再分别细分为4和8个亚组。19条染色体均有NBS-LRR基因,其中ChrC09上分布最多,达到53个;NBS-LRR基因以基因簇形式存在居多,可推测抗病基因NBSLRR发生了大规模片段复制。分析5个物种(甘蓝、白菜、甘蓝型油菜、水稻和拟南芥)的NBS-LRR家族基因密码子偏好性,结果发现,甘蓝型油菜抗病基因有效密码子数范围与甘蓝(B. oleracea L.)更加相近。然后进一步对甘蓝型油菜和白菜(B. rapa L.)与甘蓝的共线直系同源关系进行偏好性分析,并获得相同发现,推测甘蓝型油菜可能和甘蓝在抗病基因密码子的使用偏好上更为相似。

NBS-LRR(nucleotide binding site and leucine rich repeat) is a large complex gene family playing important role in plant disease resistance. For better understanding of NBS-LRR gene family in Brassica napus(L.),bioinformatics analyses were conducted in B. napus and other 4 species(B. oleracea, B. rapa and Arabidopsis thaliana and Oryza sativa). As a whole, family identification, phylogenetic analysis, conserved motif, gene structure,chromosome localization and codon bias were analyzed. Results showed that 463 NBS-LRR members were identified in B. napus. Referenced by A. thaliana, the members were divided into 2 groups, TIR-NBS-LRR and CCNBS-LRR, which were further divided into 4 and 8 subgroups respectively. All 19 chromosomes contained NBSLRR genes. Among them, 53 genes distributed on ChrC09. The NBS-LRR genes were mostly presented in clusters.Large-scale fragment replication of the genes was speculated. Results of codon bias analysis of the family in the 5 species showed that ENC(effective number of codon) of B. napus genes was 37.76 to 61.00, which was similar to B.oleracea in their preference. Codon bias features by preference of collinear homologous relationship showed more similarity between B. napus and B. oleracea.