Abstract
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.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-3021-7) contains supplementary material, which is available to authorized users.
Highlights
Analysis of codon usage bias is an extremely versatile method using in furthering understanding of the genetic and evolutionary paths of species
It is observed that Choristoneura occidentalis nuclear polyhedrosis virus (NPV)(ChocNPV), Choristoneura fumiferana MNPV(CfMNPV), Choristoneura rosaceana NPV(CrNPV), Choristoneura murinana NPV(CmNPV), Orgyia pseudotsugata MNPV(OpMNPV), Hyphantria cunea NPV(HycuNPV), Antheraea pernyi NPV(AnpeNPV), Choristoneura fumiferana DEF MNPV(CfDEFMNPV), Anticarsia gemmatalis NPV(AgNPV), Condylorrhiza vestigialis MNPV(CvMNPV) and Epiphyas postvittana NPV(EppoNPV) belong to Group 1, indicating that their evolutionary relationship is similar
The variation range of their effective number of codons (ENC) value and GC content in the third position (GC3) content are relatively smaller (47.9 ≤ ENC ≤ 52.5 and 51.9 ≤ GC3 ≤ 66.7, respectively). It suggests that the closer the evolution of species classification, the more similar their codon usage bias
Summary
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. 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. During an organisms evolutionary history, preference for using a particular synonymous codon will be formed within a species or gene in the long-term. Codon usage bias itself refers to such cases in which codons are utilized in higher frequency than other synonymous codons during the process of translation, often as a result of adaptive evolution [1]. Analysis of codon usage bias is of vital significance in the quest to improve exogenous gene expression levels within host cells. Thoroughly understanding codon usage bias plays a central role in making accurate prediction of related gene functions
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