Analysis of synonymous codon usage in SARS Coronavirus and other viruses in the Nidovirales

Abstract

In this study, we calculated the codon usage bias in severe acute respiratory syndrome Coronavirus (SARSCoV) and performed a comparative analysis of synonymous codon usage patterns in SARSCoV and 10 other evolutionary related viruses in the Nidovirales. Although there is a significant variation in codon usage bias among different SARSCoV genes, codon usage bias in SARSCoV 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 synonymous codon usage pattern in these virus genes was virus specific and phylogenetically conserved, but it was not host specific. Phylogenetic analysis based on codon usage pattern suggested that SARSCoV was diverged far from all three known groups of Coronavirus. 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.

Fig. 1

A plot of the values of the first axis and the second axis of each gene in CA (abbreviations of the viruses: AIBV, avian infectious bronchitis virus; BCoV, bovine Coronavirus; EAV, equine arteritis virus; HCoV 229E, human Coronavirus 229E; LDEV, lactate dehydrogenase elevating virus; MHV, murine hepatitis virus; PEDV, porcine epidemic diarrhea virus; PRRSV, porcine reproductive and respiratory syndrome virus; SARSCoV, SARS Coronavirus; SHFV, simian hemorrhagic fever virus; TGV, transmissible gastroenteritis virus. f₁′ and f₂′, respectively, represent the values of the first and the second axis of each gene in CA).

Fig. 2

A dot plot of the first axis value in correspondence analysis and GC_3S of each gene (f₁′ denotes the first axis value in correspondence analysis of each gene, and GC_3S denotes the G+C content on the third synonymous codon position of each gene).

Fig. 3

ENC vs. GC_3S plot of all virus genes (ENC denotes the effective number of codon of each gene, and GC_3S denotes the G+C content on the third synonymous codon position of each gene. The solid line represents the relationship between GG3S and ENC under random codon usage assumption).