School of Environmental Science and Engineering, Tianjin University, Tianjin, 300072, People's Republic of China,
World J Microbiol Biotechnol. 2013 Nov;29(11):2015-24. doi: 10.1007/s11274-013-1364-7. Epub 2013 May 8.
The codon usage patterns of rhizobia have received increasing attention. However, little information is available regarding the conserved features of the codon usage patterns in a typical rhizobial genus. The codon usage patterns of six completely sequenced strains belonging to the genus Rhizobium were analysed as model rhizobia in the present study. The relative neutrality plot showed that selection pressure played a role in codon usage in the genus Rhizobium. Spearman's rank correlation analysis combined with correspondence analysis (COA) showed that the codon adaptation index and the effective number of codons (ENC) had strong correlation with the first axis of the COA, which indicated the important role of gene expression level and the ENC in the codon usage patterns in this genus. The relative synonymous codon usage of Cys codons had the strongest correlation with the second axis of the COA. Accordingly, the usage of Cys codons was another important factor that shaped the codon usage patterns in Rhizobium genomes and was a conserved feature of the genus. Moreover, the comparison of codon usage between highly and lowly expressed genes showed that 20 unique preferred codons were shared among Rhizobium genomes, revealing another conserved feature of the genus. This is the first report of the codon usage patterns in the genus Rhizobium.
根瘤菌的密码子使用模式受到了越来越多的关注。然而，关于典型根瘤菌属中密码子使用模式的保守特征，信息却很少。本研究以 6 株完全测序的根瘤菌菌株为模式根瘤菌，分析了它们的密码子使用模式。相对中性绘图显示，选择压力在根瘤菌属的密码子使用中发挥了作用。Spearman 秩相关分析与对应分析（COA）相结合的结果表明，密码子适应指数和有效密码子数（ENC）与 COA 的第一轴具有很强的相关性，这表明基因表达水平和 ENC 在该属的密码子使用模式中起着重要作用。半胱氨酸密码子的相对同义密码子使用与 COA 的第二轴相关性最强。因此，半胱氨酸密码子的使用是塑造根瘤菌基因组密码子使用模式的另一个重要因素，也是该属的一个保守特征。此外，对高表达基因和低表达基因之间的密码子使用进行比较，发现根瘤菌基因组中有 20 个独特的偏好密码子，这揭示了该属的另一个保守特征。这是首次报道根瘤菌属的密码子使用模式。
