Virus Genes

, Volume 38, Issue 1, pp 104–112

Analysis of synonymous codon usage in classical swine fever virus

  • Pan Tao
  • Li Dai
  • Mengcheng Luo
  • Fangqiang Tang
  • Po Tien
  • Zishu Pan
Article

DOI: 10.1007/s11262-008-0296-z

Cite this article as:
Tao, P., Dai, L., Luo, M. et al. Virus Genes (2009) 38: 104. doi:10.1007/s11262-008-0296-z

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 usageMutational biasDinucleotide biasSubgenotype

Supplementary material

Copyright information

© Springer Science+Business Media, LLC 2008

Authors and Affiliations

  • Pan Tao
    • 1
  • Li Dai
    • 2
  • Mengcheng Luo
    • 1
  • Fangqiang Tang
    • 1
  • Po Tien
    • 1
  • Zishu Pan
    • 1
  1. 1.State Key Laboratory of Virology, College of Life SciencesWuhan UniversityWuhanChina
  2. 2.Key Laboratory of MOE for Development Biology, College of Life SciencesWuhan UniversityWuhanChina