title: Analysis of synonymous codon usage in  Shigella flexneri  2a strain 301 and other Shigella and Escherichia coli strains.
abstract: In this study, we analysed synonymous codon usage in Shigella flexneri 2a strain 301 (Sf301) and performed a comparative analysis of synonymous codon usage patterns in Sf301 and other strains of Shigella and Escherichia coli. Although there was a significant variety in codon usage bias among different Sf301 genes, there was a slight but observable codon usage bias that could primarily be attributable to mutational pressure and translational selection. In addition, the relative abundance of dinucleotides in Sf301 was observed to be independent of the overall base composition but was still caused by differential mutational pressure; this also shaped codon usage. By comparing the relative synonymous codon usage values across different Shigella and E. coli strains, we suggested that the synonymous codon usage pattern in the Shigella genomes was strain specific. This study represents a comprehensive analysis of Shigella codon usage patterns and provides a basic understanding of the mechanisms underlying codon usage bias.
authors: State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing 102206, People's Republic of China.
authors: Xue Lian
authors: XL
authors: Luo
authors: Jian Guo
authors: JG
authors: Xu
authors: Chang Yun
authors: CY
authors: Ye
mesh_terms: D000818:Animals; D001482:Base Composition; D016000:Cluster Analysis; D003062:Codon; D004926:Escherichia coli / Q000235:genetics*; D014644:Genetic Variation; D009154:Mutation; D012760:Shigella / Q000235:genetics*; D012763:Shigella flexneri / Q000235:genetics*; D013045:Species Specificity
chemical_list: D003062:Codon