Analysis of codon usage bias of envelope glycoprotein genes in nuclear polyhedrosis virus (NPV) and its relation to evolution.
Analysis of codon usage bias of envelope glycoprotein genes in nuclear polyhedrosis virus (NPV) and its relation to evolution.
复制标题
核型多角体病毒（NPV）包膜糖蛋白基因密码子使用偏倚分析及其与进化的关系
DOI：
10.1186/s12864-016-3021-7
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发表时间：
2016-08-24
期刊：
影响因子：
4.4
通讯作者：
Sun J
中科院分区：
文献类型：
--
作者：
Zhao Y;Zheng H;Xu A;Yan D;Jiang Z;Qi Q;Sun J
背景密码子使用偏性分析是一种非常通用的方法，用于进一步了解物种的遗传和进化路径。核型多角体病毒（NPV）囊膜糖蛋白基因密码子使用偏好性的研究目前还很不清楚。因此，密码子的使用偏好的NPV包膜糖蛋白进行了分析，在这里揭示不同的病毒物种之间的遗传和进化关系，在baculovirus genes.ResultsA共9236个密码子从18个不同种类的NPV的杆状病毒属进行此分析。核型多角体病毒糖蛋白密码子使用偏好性较弱。中性图分析和有效密码子数（ENC）值的相关性分析表明，自然选择是影响密码子使用偏性的主要因素，突变压力的影响相对较小。结论影响密码子偏好性的因素很多，如氨基酸组成、突变压力、自然选择、基因表达水平等，同时，由于基因突变的影响，密码子偏好性的大小与基因突变的程度有关。聚类分析还表明，病毒囊膜糖蛋白的密码子使用偏好可以作为杆状病毒属进化分类的有效手段。
BackgroundAnalysis 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.ResultsA 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.ConclusionsThere 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.