两种植物病原黄单胞菌基因组中同义密码子使用的分析

Analysis of synonymous codon usage in two phytopathogen genomes of Xanthomonas campestris pv. campestris and X. axonopodis pv. citri

根据已释放的基因组序列,对野油菜黄单胞菌野油菜致病变种(Xanthomonas campestris pv.campestris,Xcc)和地毯草黄单胞菌柑桔致病变种(X.axonopodis pv.citri,Xac)的密码子使用进行了分析。相对同义密码子使用值(relative sy-nonymous codon usage,RSCU)的计算表明,它们具有高度相似的密码子使用模式。2个基因组密码子第3位的GC含量(GC3s)平均达0.806±0.077(Xcc)和0.791±0.075(Xac),倾向于使用GC含量较高的密码子。对有效密码子数量和密码子适应指数的分析表明,Xcc与Xac基因组中,高表达基因具有较高的GC含量,倾向于使用少数种类的密码子,而低表达基因具有较高的AT含量,倾向于随机地使用密码子。对密码子使用绝对次数进行的对应分析也证明了上述结论。同时,计算也证明了基因在基因组中的位置不影响密码子使用的模式。因此,基因组的GC含量、基因的表达水平和基因的种类与起源是影响这2个基因组密码子使用的主要因素。

Statistics of codon usage in the genomes of bacterial phytopathogen Xanthomonas campestris pv. campestris and X. axonopodis pv. citri were calculated based on the published genomic data. Codon usages in these bacteria were dominated by codons containing high-GC content, with the average GC content at synonymously variable third position of codons (GC3s) being 0. 806 ± 0. 077 (Xcc)and 0. 791±0. 075(Xac), respectively. Calculation of effective number of codon usage (Nc) and codon adaptation index (CAI) revealed that highly expressed genes exhibited higher frequencies of GC content and tend to use biased number of codons, while for lowly expressed genes, the opposite tendencies was true. Correspondence analyses based on absolute numbers of codon usage (N) were according to the above results. Comparative analysis revealed little difference between genes from leading and lagging DNA strands, so that gene location was not a contributive factor. Our findings suggest that for Xanthomonas genomes, highly GC content, gene expression level, and gene family and origination are fundamental factors to shape the pattern of biased codon usage.