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PMID: 16557338 Published · ppublish English Journal Article Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't

Evolutionary basis of codon usage and nucleotide composition bias in vertebrate DNA viruses.

Journal of molecular evolution ·Vol. 62 ·No. 5 ·2006-05-00 ·Pages 551-63

Shackelton LA, Parrish CR, Holmes EC

Abstract

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.

MeSH Terms
Animals Base Composition/genetics Codon/genetics DNA Viruses/genetics Evolution, Molecular Genome, Viral/genetics Mutation/genetics Nucleotides/chemistry Selection, Genetic Vertebrates/virology
Chemicals
Codon Nucleotides
Authors & Affiliations
3 authors, click to expand affiliations / ORCID
Shackelton Laura A
Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK.
Parrish Colin R
Holmes Edward C
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Article Info
Journal
Journal of molecular evolution
Abbr.
J Mol Evol
ISSN
0022-2844
DOI
10.1007/s00239-005-0221-1
Published
2006-05-00
Epub
2006-00-22
Pages
551-63
Language
English
Region
Germany
NLM ID
0360051
Subset
IM
Grants
NIAID NIH HHS · R01AI028385 · United States
External Links
PubMed source DOI: 10.1007/s00239-005-0221-1 View journal details
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