title: Analysis of synonymous codon usage in foot-and-mouth disease virus.
abstract: In this study, we calculate the relative synonymous codon usage (RSCU) values and codon usage bias (CUB) values to carry out a comparative analysis of codon usage pattern for open reading frames (ORFs) among 85 samples which belong to all seven serotypes of foot-and-mouth disease virus (FMDV). Although the degree of CUB for ORFs is a relatively slight, there is a significant variation for CUB among different serotypes, which is mainly determined by codon usage pattern depending on RSCU. By comparison with RSCU values for all samples, although RSCU values fail to show the relationship of specific-lineage serotype, there are two main genetic populations existing in FMDV, namely (i) serotypes Asia 1, A, C & O; (ii) serotypes SAT 1, 2 & 3. This interesting characteristic may be formed by the mechanism of RNA virus recombination. The analysis of quantitative & qualitative evaluation based on CUB indicates interesting characteristic of codon usage, which suggests that more FMDV genome diversity may exist in specific-lineage serotypes rather than exist randomly. Furthermore, the relationship between amino acids and codon usage pattern indicates that mutation pressure rather than translational selection in nature is the important determinant of the codon usage bias observed. Our work might give some sight into some characteristics of FMDV ORF and some evolutionary information of this virus.
authors.affiliation: Key Laboratory of Animal Virology of Ministry of Agriculture, State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China. zhoujianhuazjh@163.com
authors.forename: Jian-Hua
authors.initials: JH
authors.lastname: Zhou
authors.forename: Jie
authors.initials: J
authors.lastname: Zhang
authors.forename: Hao-Tai
authors.initials: HT
authors.lastname: Chen
authors.forename: Li-Na
authors.initials: LN
authors.lastname: Ma
authors.forename: Yong-Sheng
authors.initials: YS
authors.lastname: Liu
mesh_terms: D000596:Amino Acids / Q000235:genetics; D001483:Base Sequence; D003062:Codon / Q000235:genetics*; D019143:Evolution, Molecular; D029544:Foot-and-Mouth Disease Virus / Q000235:genetics*; D016679:Genome, Viral; D009154:Mutation; D016366:Open Reading Frames / Q000235:genetics; D010802:Phylogeny; D012641:Selection, Genetic; D012703:Serotyping / Q000379:methods
chemical_list: D000596:Amino Acids; D003062:Codon