生物
密码子使用偏好性
系统发育树
基因组
遗传学
适应性
GC含量
寄主(生物学)
宿主适应
自然选择
系统发育学
适应(眼睛)
基因
进化生物学
选择(遗传算法)
生态学
人工智能
计算机科学
神经科学
作者
Wenlong Wang,Lei Zhou,Xinna Ge,Jun Han,Xin Guo,Yongning Zhang,Hanchun Yang
出处
期刊:Virology
[Elsevier]
日期:2023-10-01
卷期号:587: 109879-109879
标识
DOI:10.1016/j.virol.2023.109879
摘要
Porcine enteric alphacoronavirus (PEAV) is a newly emerging swine enteropathogen that poses a threat to the swine industry. To understand the PEAV genome evolution, we performed a comprehensive analysis of the codon usage patterns in fifty-nine PEAV strains currently available. Phylogenetic analysis showed that PEAV can be divided into six lineages. Effective number of codons analysis demonstrated that the PEAV genome exhibits a low codon usage bias (CUB). Nucleotide composition analysis indicated that the PEAV genome has the most abundant nucleotide U content, with GC content (39.37% ± 0.08%) much lower than AU content (60.63% ± 0.08%). Neutrality and effective number of codons plot analyses suggested that natural selection rather than mutation pressure dominates the CUB of PEAV. Host adaptation analysis revealed that PEAV fits the codon usage pattern of non-human primates, humans and mice better than that of pigs. Our data enriches information on PEAV evolution, host adaptability, and cross-species transmission.
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