title: Comparative [corrected] codon usage between the three main viruses in pestivirus genus and their natural susceptible livestock.
abstract: Classical swine fever virus, bovine viral diarrhea virus (BVDV), and border disease virus can cause serious livestock diseases. The relative synonymous codon usage value, the "effective number of codons" (ENC), the ratio of K(s) value to K(a) value and the principle component analysis were employed to analyze the genetic characteristics of open reading frame (ORF) and the four genes (the N(pro), Erns, E1, E2 genes) of the three viruses and the relationship of codon usage pattern between each virus and its most common host. The amount of under-represented codons is larger than the amount of over-represented ones in ORFs or the four genes of the three viruses. The ENC value and the ratio of K(s)/K(a) for each gene show that mutation pressure plays a role in their evolutional processes. In addition, the evidence that selection from the natural host might influences the codon usage patterns of virus is found in the differences of codon usage patterns of ORF and Erns gene of BVDV strain ZM-95 isolated from domestic pig and those of the rest of BVDV strains isolated from cattle. These results indicate that although a strong mutation pressure from the three pestiviruses takes part in their evolutional processes by the alternation of synonymous codons, translation selection from the susceptible livestock on some genes should not be ignored. The codon usage pattern of the three pestiviruses is a result caused by the equilibrium of mutation pressure from virus and translation selection from its host.
authors.affiliation: State Key Laboratory of Veterinary Etiological Biology, National Foot-and-Mouth Disease Reference Laboratory, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, 730046, Gansu, People's Republic of China. zhoujianhuazjh@163.com
authors.forename: Jian-hua
authors.initials: JH
authors.lastname: Zhou
authors.forename: Zong-liang
authors.initials: ZL
authors.lastname: Gao
authors.forename: Jie
authors.initials: J
authors.lastname: Zhang
authors.forename: Hao-tai
authors.initials: HT
authors.lastname: Chen
authors.forename: Zygmunt
authors.initials: Z
authors.lastname: Pejsak
authors.forename: Li-na
authors.initials: LN
authors.lastname: Ma
authors.forename: Yao-zhong
authors.initials: YZ
authors.lastname: Ding
authors.forename: Yong-sheng
authors.initials: YS
authors.lastname: Liu
mesh_terms: D000818:Animals; D018083:Border disease virus / Q000235:genetics* / Q000302:isolation & purification; D002417:Cattle; D006692:Classical Swine Fever Virus / Q000235:genetics* / Q000302:isolation & purification; D003062:Codon; D019295:Computational Biology; D030241:Diarrhea Virus 1, Bovine Viral / Q000235:genetics* / Q000302:isolation & purification; D058751:Livestock; D016366:Open Reading Frames; D012367:RNA, Viral / Q000235:genetics*; D017422:Sequence Analysis, DNA; D034421:Sus scrofa; D014764:Viral Proteins / Q000235:genetics*
chemical_list: D003062:Codon; D012367:RNA, Viral; D014764:Viral Proteins