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

被引：176

作者：

Gu, WJ ^{[1
]}

Zhou, T ^{[1
]}

Ma, JM ^{[1
]}

Sun, X ^{[1
]}

Lu, ZH ^{[1
]}

机构：

[1] SE Univ, Minist Educ, Key Lab Mol & Biomol Elect, Nanjing 210096, Jiangsu, Peoples R China

来源：

VIRUS RESEARCH | 2004年 / 101卷 / 02期

基金：

中国国家自然科学基金;

关键词：

synonymous codon usage; mutational bias; selection pressure; base composition; SARS; Coronavirus;

D O I：

10.1016/j.virusres.2004.01.006

中图分类号：

Q93 [微生物学];

学科分类号：

071005 ; 100705 ;

摘要：

In this study, we calculated the codon usage bias in severe acute respiratory syndrome Coronavirus (SARSCoV) and per-formed 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. (C) 2004 Elsevier B.V. All rights reserved.

引用

页码：155 / 161

页数：7