ArticleNucleic acids research2004
Identification of genes with fast-evolving regions in microbial genomes.
Article in Nucleic acids research, 2004. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed.
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- Temporal shifts in antibiotic resistance elements govern phage-pathogen conflicts.Science (New York, N.Y.) · 2021Article
- A Fifth of the Protein World: Rossmann-like Proteins as an Evolutionarily Successful Structural unit.Journal of molecular biology · 2021Article
- Distinct patterns of mutational sensitivity forMicrobial genomics · 2020Article
- Intelligent Design of 14-3-3 Docking Proteins Utilizing Synthetic Evolution Artificial Intelligence (SYN-AI).ACS omega · 2019Article
- A GWAS on Helicobacter pylori strains points to genetic variants associated with gastric cancer risk.BMC biology · 2018Article
- Evolutionary Ecology of Prokaryotic Immune Mechanisms.Microbiology and molecular biology reviews : MMBR · 2016Review
- Molecular Evolution of the Yersinia Major Outer Membrane Protein C (OmpC).Evolutionary bioinformatics online · 2016Article
- Comparative analysis of Wolbachia surface protein in D. melanoagster, A. tabida and B. malayi.Bioinformation · 2012Article
- Horizontal gene transfer and assortative recombination within the Acinetobacter baumannii clinical population provide genetic diversity at the single carO gene, encoding a major outer membrane protein channel.Journal of bacteriology · 2011Article
- The phylogeny of Sodalis-like symbionts as reconstructed using surface-encoding loci.FEMS microbiology letters · 2011Article
- The phage-host arms race: shaping the evolution of microbes.BioEssays : news and reviews in molecular, cellular and developmental biology · 2011Review
- Accelerated microevolution in an outer membrane protein (OMP) of the intracellular bacteria Wolbachia.BMC evolutionary biology · 2010Article
- Maximum-likelihood model averaging to profile clustering of site types across discrete linear sequences.PLoS computational biology · 2009Article
- Protein evolution in deep sea bacteria: an analysis of amino acids substitution rates.BMC evolutionary biology · 2008Article
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3 authors.
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No grant is acknowledged in the PubMed record.
Abstract
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.
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