Proteus spp. bacteria frequently serve as opportunistic pathogens that can infect many animals and show positive survival and existence in various natural environments. The evolutionary pattern of Proteus spp. is an unknown topic, which benefits understanding the different evolutionary dynamics for excellent bacterial adaptation to various environments. Here, the eight whole genomes of different Proteus species were analyzed for the interplay between nucleotide usage and synonymous codon usage. Although the orthologous average nucleotide identity and average nucleotide identity display the genetic diversity of these Proteus species at the genome level, the principal component analysis further shows that these species sustain the specific genetic niche at the aspect of synonymous codon usage patterns. Interestingly, although these Proteus species have A/T rich genes with underrepresented G (guanine) or C (cytosine) at the third codon positions and overrepresented A or T at these positions, some synonymous codons with A or T end are obviously suppressed in usage. The overall codon usage pattern reflected by the effective number of codons (ENC) has a significantly positive correlation with GC3 content (GC content at the third codon position), and ENC has a significantly negative correlation with the adaptation index for these species. These results suggest that the mutation pressure caused by nucleotide composition constraint serves as a dominant evolutionary dynamic driving evolutionary trend of Proteus spp., along with other selections related to natural selection, replication and fine‐tune translation, and so on. Taken together, the analyses help to understand the evolutionary interplay between nucleotide and codon usage at the gene level of Proteus.

中文翻译：

---

同义密码子使用在变形杆菌进化过程中的意义和作用

变形杆菌属 细菌经常作为机会病原体，可以感染许多动物，并在各种自然环境中表现出积极的生存和存在。变形杆菌的进化模式。是一个未知的话题，这有助于理解不同的进化动力学，以实现细菌对各种环境的出色适应。在这里，分析了不同变形杆菌属物种的八个全基因组的核苷酸使用和同义密码子使用之间的相互作用。虽然直系同源平均核苷酸同一性和平均核苷酸同一性在基因组水平上显示了这些变形杆菌物种的遗传多样性，但主成分分析进一步表明这些物种在同义密码子使用模式方面维持特定的遗传生态位。有趣的是，尽管这些变形杆菌物种具有富含 A/T 的基因，但在第三个密码子位置上 G（鸟嘌呤）或 C（胞嘧啶）数量不足，而在这些位置上 A 或 T 数量过多，但某些具有 A 或 T 末端的同义密码子的使用明显受到抑制。由有效密码子数（ENC）反映的整体密码子使用模式与GC3含量（第三密码子位置的GC含量）呈显着正相关，ENC与这些物种的适应指数呈显着负相关。这些结果表明，核苷酸组成约束引起的突变压力与自然选择、复制和微调翻译等相关选择是变形杆菌属的主要进化动力驱动进化趋势。综合起来，