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Analysis of codon usage bias of envelope glycoprotein genes in nuclear polyhedrosis virus (NPV) and its relation to evolution

文献类型： 外文期刊

作者： Zhao, Yongchao 1 ; Zheng, Hao 1 ; Xu, Anying; Yan, Donghua 1 ; Jiang, Zijian 1 ; Qi, Qi 1 ; Sun, Jingchen 2 ;

作者机构： 1.South China Agr Univ, Subtrop Sericulture & Mulberry Resources Protect, Guangdong Prov Key Lab Agroanim Genom & Mol Breed, Coll Anim Sci, Guangzhou 510642, Guangdong, Peoples R China

2.South China Agr Univ, Subtrop Sericulture & Mulberry Resources Protect, Guangdong Prov Key Lab Agroanim

关键词： Nuclear polyhedrosis virus;Codon usage bias;Envelope glycoprotein;Evolution

期刊名称：BMC GENOMICS （ 影响因子：3.969； 五年影响因子：4.478 ）

ISSN： 1471-2164

年卷期： 2016 年 17 卷

页码：

收录情况： SCI

摘要： Background: Analysis of codon usage bias is an extremely versatile method using in furthering understanding of the genetic and evolutionary paths of species. Codon usage bias of envelope glycoprotein genes in nuclear polyhedrosis virus (NPV) has remained largely unexplored at present. Hence, the codon usage bias of NPV envelope glycoprotein was analyzed here to reveal the genetic and evolutionary relationships between different viral species in baculovirus genus. Results: A total of 9236 codons from 18 different species of NPV of the baculovirus genera were used to perform this analysis. Glycoprotein of NPV exhibits weaker codon usage bias. Neutrality plot analysis and correlation analysis of effective number of codons (ENC) values indicate that natural selection is the main factor influencing codon usage bias, and that the impact of mutation pressure is relatively smaller. Another cluster analysis shows that the kinship or evolutionary relationships of these viral species can be divided into two broad categories despite all of these 18 species are from the same baculovirus genus. Conclusions: There are many elements that can affect codon bias, such as the composition of amino acids, mutation pressure, natural selection, gene expression level, and etc. In the meantime, cluster analysis also illustrates that codon usage bias of virus envelope glycoprotein can serve as an effective means of evolutionary classification in baculovirus genus.

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