Article

Virus Genes

, Volume 38, Issue 1, pp 104-112

Analysis of synonymous codon usage in classical swine fever virus

  • Pan TaoAffiliated withState Key Laboratory of Virology, College of Life Sciences, Wuhan University
  • , Li DaiAffiliated withKey Laboratory of MOE for Development Biology, College of Life Sciences, Wuhan University
  • , Mengcheng LuoAffiliated withState Key Laboratory of Virology, College of Life Sciences, Wuhan University
  • , Fangqiang TangAffiliated withState Key Laboratory of Virology, College of Life Sciences, Wuhan University
  • , Po TienAffiliated withState Key Laboratory of Virology, College of Life Sciences, Wuhan University
  • , Zishu PanAffiliated withState Key Laboratory of Virology, College of Life Sciences, Wuhan University Email author 

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Abstract

Using the complete genome sequences of 35 classical swine fever viruses (CSFV) representing all three genotypes and all three kinds of virulence, we analyzed synonymous codon usage and the relative dinucleotide abundance in CSFV. The general correlation between base composition and codon usage bias suggests that mutational pressure rather than natural selection is the main factor that determines the codon usage bias in CSFV. Furthermore, we observed that the relative abundance of dinucleotides in CSFV is independent of the overall base composition but is still the result of differential mutational pressure, which also shapes codon usage. In addition, other factors, such as the subgenotypes and aromaticity, also influence the codon usage variation among the genomes of CSFV. This study represents the most comprehensive analysis to date of CSFV codon usage patterns and provides a basic understanding of the mechanisms for codon usage bias.

Keywords

Classical swine fever virus (CSFV) Synonymous codon usage Mutational bias Dinucleotide bias Subgenotype