Genetic Engineering Department, CINVESTAV Irapuato, Guanajuato, Mexico.
Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico.
J Mol Evol. 2022 Dec;90(6):438-451. doi: 10.1007/s00239-022-10074-0. Epub 2022 Sep 26.
Codon usage is the outcome of different evolutionary processes and can inform us about the conditions in which organisms live and evolve. Here, we present R_ENC', which is an improvement to the original S index developed by dos Reis et al. (2004). Our index is less sensitive to G+C content, which greatly affects synonymous codon usage in prokaryotes, making it better suited to detect selection acting on codon usage. We used R_ENC' to estimate the extent of selected codon usage bias in 1800 genomes representing 26 prokaryotic phyla. We found that Gammaproteobacteria, Betaproteobacteria, Actinobacteria, and Firmicutes are the phyla/subphyla showing more genomes with selected codon usage bias. In particular, we found that several lineages within Gammaproteobacteria and Firmicutes show a similar set of functional terms enriched in genes under selected codon usage bias, indicating convergent evolution. We also show that selected codon usage bias tends to evolve in genes coding for the translation machinery before other functional GO terms. Finally, we discuss the possibility to use R_ENC' to predict whether lineages evolved in copiotrophic or oligotrophic environments.
密码子使用是不同进化过程的结果，可以为我们提供有关生物生存和进化条件的信息。在这里，我们提出了 R_ENC'，这是对 dos Reis 等人（2004 年）开发的原始 S 指数的改进。我们的指数对 G+C 含量的敏感性较低，G+C 含量对原核生物中同义密码子的使用有很大影响，因此更适合检测对密码子使用的选择作用。我们使用 R_ENC'来估计代表 26 个原核门的 1800 个基因组中选择的密码子使用偏倚的程度。我们发现，γ变形菌门、β变形菌门、放线菌门和厚壁菌门是显示更多具有选择的密码子使用偏倚的基因组的门/亚门。特别是，我们发现γ变形菌门和厚壁菌门中的几个谱系显示出在选择的密码子使用偏倚下富集的相似的功能术语，表明趋同进化。我们还表明，选择的密码子使用偏倚倾向于在编码翻译机制的基因中进化，然后是其他功能 GO 术语。最后，我们讨论了使用 R_ENC'来预测谱系是否在富营养或贫营养环境中进化的可能性。
