Analysis of synonymous codon usage in H5N1 virus and other influenza A viruses

Tong Zhou, Wanjun Gu, Jianmin Ma, Xiao Sun, Zuhong Lu

Research output: Contribution to journalArticle

102 Citations (Scopus)

Abstract

In this study, we calculated the codon usage bias in H5N1 virus and performed a comparative analysis of synonymous codon usage patterns in H5N1 virus, five other evolutionary related influenza A viruses and a influenza B virus. Codon usage bias in H5N1 genome is a little slight, which is mainly determined by the base compositions on the third codon position. By comparing synonymous codon usage patterns in different viruses, we observed that the codon usage pattern of H5N1 virus is similar with other influenza A viruses, but not influenza B virus, and the synonymous codon usage in influenza A virus genes is phylogenetically conservative, but not strain-specific. Synonymous codon usage in genes encoded by different influenza A viruses is genus conservative. Compositional constraints could explain most of the variation of synonymous codon usage among these virus genes, while gene function is also correlated to synonymous codon usages to a certain extent. However, translational selection and gene length have no effect on the variations of synonymous codon usage in these virus genes.

Original languageEnglish (US)
Pages (from-to)77-86
Number of pages10
JournalBioSystems
Volume81
Issue number1
DOIs
StatePublished - Jul 2005
Externally publishedYes

Fingerprint

H5N1 Subtype Influenza A Virus
influenza
Influenza
Influenza A virus
Viruses
codons
Codon
Virus
virus
Genes
Gene
gene
Influenza B virus
genes
viruses
analysis
Base Composition
Comparative Analysis
Genus

Keywords

  • GC content
  • H5N1
  • Influenza A virus
  • Mutational bias
  • Selection pressure
  • Synonymous codon usage

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Biotechnology
  • Drug Discovery

Cite this

Analysis of synonymous codon usage in H5N1 virus and other influenza A viruses. / Zhou, Tong; Gu, Wanjun; Ma, Jianmin; Sun, Xiao; Lu, Zuhong.

In: BioSystems, Vol. 81, No. 1, 07.2005, p. 77-86.

Research output: Contribution to journalArticle

Zhou, Tong ; Gu, Wanjun ; Ma, Jianmin ; Sun, Xiao ; Lu, Zuhong. / Analysis of synonymous codon usage in H5N1 virus and other influenza A viruses. In: BioSystems. 2005 ; Vol. 81, No. 1. pp. 77-86.
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