Evolution of base composition and codon usage bias in the genus Flavivirus

The extent to which base composition and codon usage vary among RNA viruses, and the possible causes of this bias, is undetermined in most cases. A maximum-likelihood statistical method was used to test whether base composition and codon usage bias covary with arthropod association in the genus Flav...

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Bibliographic Details
Published in:Journal of molecular evolution 2001-04, Vol.52 (4), p.383-390
Main Authors: Jenkins, G M, Pagel, M, Gould, E A, de A Zanotto, P M, Holmes, E C
Format: Article
Language:English
Subjects:
Amino acids
Amino Acids - genetics
Animal diseases
Animals
Aquatic insects
Base Composition
Base Sequence
Codon
Disease transmission
Ecology
Evolution, Molecular
Evolutionary biology
Flavivirus
Flavivirus - classification
Flavivirus - genetics
Host-Parasite Interactions - genetics
Molecular biology
Mosquitoes
Phylogeny
Population genetics
Ribonucleic acid
RNA
Sequence Alignment
Species Specificity
Statistical methods
Virology
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Summary:The extent to which base composition and codon usage vary among RNA viruses, and the possible causes of this bias, is undetermined in most cases. A maximum-likelihood statistical method was used to test whether base composition and codon usage bias covary with arthropod association in the genus Flavivirus, a major source of disease in humans and animals. Flaviviruses are transmitted by mosquitoes, by ticks, or directly between vertebrate hosts. Those viruses associated with ticks were found to have a significantly lower G+C content than non-vector-borne flaviviruses and this difference was present throughout the genome at all amino acids and codon positions. In contrast, mosquito-borne viruses had an intermediate G+C content which was not significantly different from those of the other two groups. In addition, biases in dinucleotide and codon usage that were independent of base composition were detected in all flaviviruses, but these did not covary with arthropod association. However, the overall effect of these biases was slight, suggesting only weak selection at synonymous sites. A preliminary analysis of base composition, codon usage, and vector specificity in other RNA virus families also revealed a possible association between base composition and vector specificity, although with biases different from those seen in the Flavivirus genus.
ISSN:0022-2844
1432-1432
DOI:10.1007/s002390010168