title: Analysis of codon usage bias of envelope glycoprotein genes in nuclear polyhedrosis virus (NPV) and its relation to evolution.
abstract: 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.
  
  
  
  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.
  
  
  
  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.
authors: Subtropical Sericulture and Mulberry Resources Protection and Safety Engineering Research Center, Guangdong Provincial Key Laboratory of Agro-animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, 510642, People's Republic of China.
authors: Yongchao
authors: Y
authors: Zhao
authors: Subtropical Sericulture and Mulberry Resources Protection and Safety Engineering Research Center, Guangdong Provincial Key Laboratory of Agro-animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, 510642, People's Republic of China.
authors: Hao
authors: H
authors: Zheng
authors: Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang Jiangsu, 212018, People's Republic of China.
authors: Anying
authors: A
authors: Xu
authors: Subtropical Sericulture and Mulberry Resources Protection and Safety Engineering Research Center, Guangdong Provincial Key Laboratory of Agro-animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, 510642, People's Republic of China.
authors: Donghua
authors: D
authors: Yan
authors: Subtropical Sericulture and Mulberry Resources Protection and Safety Engineering Research Center, Guangdong Provincial Key Laboratory of Agro-animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, 510642, People's Republic of China.
authors: Zijian
authors: Z
authors: Jiang
authors: Subtropical Sericulture and Mulberry Resources Protection and Safety Engineering Research Center, Guangdong Provincial Key Laboratory of Agro-animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, 510642, People's Republic of China.
authors: Qi
authors: Q
authors: Qi
authors: Subtropical Sericulture and Mulberry Resources Protection and Safety Engineering Research Center, Guangdong Provincial Key Laboratory of Agro-animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, 510642, People's Republic of China. cyfz@scau.edu.cn.
authors: Jingchen
authors: J
authors: Sun
mesh_terms: D016000:Cluster Analysis; D003062:Codon; D019143:Evolution, Molecular; D006023:Glycoproteins / Q000235:genetics*; D017924:Nucleopolyhedroviruses / Q000145:classification* / Q000235:genetics / Q000378:metabolism; D010802:Phylogeny; D012641:Selection, Genetic; D013045:Species Specificity; D014759:Viral Envelope Proteins / Q000235:genetics*
chemical_list: D003062:Codon; D006023:Glycoproteins; D014759:Viral Envelope Proteins
keywords: Codon usage bias; Envelope glycoprotein; Evolution; Nuclear polyhedrosis virus