Five annotated genomes of Mycoplasma hyorhinis were analyzed for clarifying evolutionary dynamics driving the overall codon usage pattern. Information entropy used for estimating nucleotide usage pattern at the gene level indicates that multiple evolutionary dynamics participate in forcing nucleotide usage bias at every codon position. Moreover, nucleotide usage bias directly contributes to synonymous codon usage biases with two different extremes. The overrepresented codons tended to have A/T in the third codon position, and the underrepresented codons strongly used G/C in the third position. Furthermore, correspondence analysis and neutrality plot reflect an obvious interplay between mutation pressure and natural selection mediating codon usage in M. hyorhinis genome. Due to significant bias in usages between A/T and G/C at the gene level, different selective forces have been proposed to contribute to codon usage preference in M. hyorhinis genome, including nucleotide composition constraint derived from mutation pressure, translational selection involved in natural selection, and strand-specific mutational bias represented by different nucleotide skew index. The systemic analyses of codon usage for M. hyorhinis can enable us to better understand the mechanisms of evolution in this species.

中文翻译：

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核苷酸使用显着影响猪鼻支原体中同义密码子的使用

分析了猪支原体的五个带注释的基因组，以阐明驱动整体密码子使用模式的进化动力学。用于在基因水平上估计核苷酸使用模式的信息熵表明，多个进化动力学参与迫使每个密码子位置的核苷酸使用偏差。此外，核苷酸使用偏向直接导致具有两个不同极端的同义密码子使用偏向。过多的密码子倾向于在第三个密码子位置使用 A/T，而较少使用的密码子在第三个位置强烈使用 G/C。此外，对应分析和中性图反映了突变压力和自然选择介导的 M. hyorhinis 基因组密码子使用之间的明显相互作用。由于 A/T 和 G/C 在基因水平上的使用存在显着偏差，已经提出了不同的选择力来促进 M. hyorhinis 基因组中的密码子使用偏好，包括源自突变压力的核苷酸组成约束、自然选择中涉及的翻译选择以及由不同核苷酸偏斜指数表示的链特异性突变偏向。M. hyorhinis 密码子使用的系统分析可以使我们更好地了解该物种的进化机制。