Dec 4, 2004

Identification of genes with fast-evolving regions in microbial genomes

Nucleic Acids Research
Yu ZhengSimon Kasif


Complete sequences of multiple strains of the same microbial species provide an invaluable source for studying the evolutionary dynamics between orthologous genes over a relatively short time scale. Usually the intensity of the selection pressure is inferred from a comparison between the nonsynonymous substitution rate and the synonymous substitution rate. In this paper, we propose an alternative method for detecting genes with one or more fast-evolving regions from pairwise comparisons of orthologous genes. Our method looks for regions with overrepresented nonsynonymous mutations along the alignment, and requires a higher nonsynonymous evolution rate in those regions than the neutral evolution rate. It identifies gene targets under intensive selection pressure that are not detected from the conventional rate comparison analysis. For those identified genes with known annotations, most of them have a clear role in processes such as bacterial defense and host-pathogen interactions. Gene sets reported from our method provide a measure of the phenotypic divergence between two closely related genomes.

Mentioned in this Paper

Peptide Hydrolases
Host-Pathogen Interactions
Genes, Bacterial
DNA Restriction Enzymes
Evolution, Neutral
Genome, Bacterial
Genome, Microbial

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