Evolutionary Basis of Codon Usage and Nucleotide Composition Bias in Vertebrate DNA Viruses

被引:0
作者
Laura A. Shackelton
Colin R. Parrish
Edward C. Holmes
机构
[1] University of Oxford,Department of Zoology
[2] Cornell University,J.A. Baker Institute, Department of Microbiology and Immunology, College of Veterinary Medicine
[3] The Pennsylvania State University,Center for Infectious Disease Dynamics, Department of Biology, Mueller Laboratory
来源
Journal of Molecular Evolution | 2006年 / 62卷
关键词
DNA viruses; Codon bias; Base composition; Mutation pressure; Natural selection; Dinucleotide bias; CpG;
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摘要
Understanding the extent and causes of biases in codon usage and nucleotide composition is essential to the study of viral evolution, particularly the interplay between viruses and host cells or immune responses. To understand the common features and differences among viruses we analyzed the genomic characteristics of a representative collection of all sequenced vertebrate-infecting DNA viruses. This revealed that patterns of codon usage bias are strongly correlated with overall genomic GC content, suggesting that genome-wide mutational pressure, rather than natural selection for specific coding triplets, is the main determinant of codon usage. Further, we observed a striking difference in CpG content between DNA viruses with large and small genomes. While the majority of large genome viruses show the expected frequency of CpG, most small genome viruses had CpG contents far below expected values. The exceptions to this generalization, the large gammaherpesviruses and iridoviruses and the small dependoviruses, have sufficiently different life-cycle characteristics that they may help reveal some of the factors shaping the evolution of CpG usage in viruses.
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页码:551 / 563
页数:12
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