title: Analysis of synonymous codon usage in porcine reproductive and respiratory syndrome virus.
abstract: In this study, we calculated the relative synonymous codon usage (RSCU) values and codon usage bias (CUB) values to implement a comparative analysis of codon usage pattern of open reading frames (ORFs) which belong to the two main genotypes of porcine reproductive and respiratory syndrome virus (PRRSV). By analysis of synonymous codon usage values in each ORF of PRRSV, the optimal codons for most amino acids were all C or G-ended codons except GAU for Asp, CAU for His, UUU for Phe and CCU for Pro. The synonymous codon usage patterns in different ORFs of PRRSV were different and genetically conserved. Among them, ORF1a, ORF4, ORF5 and ORF7 could cluster these strains into the two main serotypes (EU and US). Due to mutational pressure, compositional constraint played an important role in shaping the synonymous codon usage pattern in different ORFs, and the synonymous codon usage diversity in ORFs was correlated with gene function. The degree of CUB for some particular amino acids under strong selection pressure probably served as a potential genetic marker for each ORF in PRRSV. However, gene length and translational selection in nature had no effect on the synonymous codon usage pattern in PRRSV. These conclusions could not only offer an insight into the synonymous codon usage pattern and differentiation of gene function, but also assist in understanding the discrepancy of evolution among ORFs in PRRSV.
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, 730046 Gansu, PR China.
authors.forename: Yong-sheng
authors.initials: YS
authors.lastname: Liu
authors.forename: Jian-hua
authors.initials: JH
authors.lastname: Zhou
authors.forename: Hao-tai
authors.initials: HT
authors.lastname: Chen
authors.forename: Li-na
authors.initials: LN
authors.lastname: Ma
authors.forename: Yao-zhong
authors.initials: YZ
authors.lastname: Ding
authors.forename: Meng
authors.initials: M
authors.lastname: Wang
authors.forename: Jie
authors.initials: J
authors.lastname: Zhang
mesh_terms: D000818:Animals; D003062:Codon / Q000032:analysis / Q000235:genetics; D004252:DNA Mutational Analysis; D019143:Evolution, Molecular; D016679:Genome, Viral; D016366:Open Reading Frames; D010802:Phylogeny; D017354:Point Mutation; D019318:Porcine Reproductive and Respiratory Syndrome / Q000821:virology; D019316:Porcine respiratory and reproductive syndrome virus / Q000145:classification / Q000235:genetics*; D012703:Serotyping; D013552:Swine / Q000821:virology*
chemical_list: D003062:Codon