Analysis of synonymous codon usage in enterovirus 71
Analysis of synonymous codon usage in enterovirus 71
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DOI：
10.1007/s13337-014-0215-y
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发表时间：
2014-05
期刊：
影响因子：
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通讯作者：
Hua Zhang;H. Cao;Feng-qi Li;Zi-ye Pan;Zhi-jun Wu;Yanhong Wang;Yudong Cui
中科院分区：
文献类型：
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作者：
Hua Zhang;H. Cao;Feng-qi Li;Zi-ye Pan;Zhi-jun Wu;Yanhong Wang;Yudong Cui
肠道病毒71型(EV71)是儿童手足口病的主要原因。在我们的研究中，我们利用代表所有三种基因型的42例EV71的全基因组序列，分析了EV71基因组中同义密码子的使用和相对二核苷酸丰度。碱基组成与密码子使用偏向之间的普遍相关性表明，突变压力而不是自然选择是决定EV71基因组密码子使用偏向的主要因素。此外，我们观察到EV71中二核苷酸的相对丰度与总的碱基组成无关，但仍然是差异突变压力的结果，这也决定了密码子的使用。此外，其他因素，如疏水性和芳香性，也影响EV71基因组间密码子使用的差异。这项研究代表了对EV71密码子使用模式的最全面的分析，并提供了对密码子使用偏向的机制的基本理解。
Enterovirus 71 (EV71) is the major cause of hand-foot-and-mouth disease in children. In our study, using the complete genome sequences of 42 EV71 representing all three genotypes, we analyzed synonymous codon usage and the relative dinucleotide abundance in EV71 genome. The general correlation between base composition and codon usage bias suggests that mutational pressure rather than natural selection is the main factor that determines the codon usage bias in EV71 genome. Furthermore, we observed that the relative abundance of dinucleotides in EV71 is independent of the overall base composition but is still the result of differential mutational pressure, which also shapes codon usage. In addition, other factors, such as hydrophobicity and aromaticity, also influence the codon usage variation among the genomes of EV71. This study represents the most comprehensive analysis of EV71 codon usage patterns and provides a basic understanding of the mechanisms for codon usage bias.