ArticleGenome biology2006
Genome-wide detection and analysis of homologous recombination among sequenced strains of Escherichia coli.
Article in Genome biology, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 37 papers.
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Who cites it
37 citing papers in PubMed.
- Article
- Co-evolution and Gene Transfers Drive Speciation Patterns in Host-Associated Bacteria.Molecular biology and evolution · 2024Article
- Discovery of novel treponemes associated with pododermatitis in elk (Applied and environmental microbiology · 2024Article
- RecBCD enzyme: mechanistic insights from mutants of a complex helicase-nuclease.Microbiology and molecular biology reviews : MMBR · 2023Review
- The microbial ecology of Escherichia coli in the vertebrate gut.FEMS microbiology reviews · 2022Review
- The population genetics of pathogenic Escherichia coli.Nature reviews. Microbiology · 2021Review
- Impact of homologous recombination on core genome phylogenies.BMC genomics · 2020Article
- Should Networks Supplant Tree Building?Microorganisms · 2020Review
- Stratified reconstruction of ancestral Escherichia coli diversification.BMC genomics · 2019Article
- Article
- Impermanence of bacterial clones.Proceedings of the National Academy of Sciences of the United States of America · 2015Article
- Recombinant transfer in the basic genome of Escherichia coli.Proceedings of the National Academy of Sciences of the United States of America · 2015Article
- Comparative genome analysis of Pseudogymnoascus spp. reveals primarily clonal evolution with small genome fragments exchanged between lineages.BMC genomics · 2015Article
- Inferring horizontal gene transfer.PLoS computational biology · 2015Article
- Large-scale intersubspecific recombination in the plant-pathogenic bacterium Xylella fastidiosa is associated with the host shift to mulberry.Applied and environmental microbiology · 2014Article
- Recombination blurs phylogenetic groups routine assignment in Escherichia coli: setting the record straight.PloS one · 2014Article
- Article
- Detecting genetic introgression: high levels of intersubspecific recombination found in Xylella fastidiosa in Brazil.Applied and environmental microbiology · 2012Article
- Population genomics of early events in the ecological differentiation of bacteria.Science (New York, N.Y.) · 2012Article
- Genome-wide survey of mutual homologous recombination in a highly sexual bacterial species.Genome biology and evolution · 2012Article
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
backgroundComparisons of complete bacterial genomes reveal evidence of lateral transfer of DNA across otherwise clonally diverging lineages. Some lateral transfer events result in acquisition of novel genomic segments and are easily detected through genome comparison. Other more subtle lateral transfers involve homologous recombination events that result in substitution of alleles within conserved genomic regions. This type of event is observed infrequently among distantly related organisms. It is reported to be more common within species, but the frequency has been difficult to quantify since the sequences under comparison tend to have relatively few polymorphic sites.
resultsHere we report a genome-wide assessment of homologous recombination among a collection of six complete Escherichia coli and Shigella flexneri genome sequences. We construct a whole-genome multiple alignment and identify clusters of polymorphic sites that exhibit atypical patterns of nucleotide substitution using a random walk-based method. The analysis reveals one large segment (approximately 100 kb) and 186 smaller clusters of single base pair differences that suggest lateral exchange between lineages. These clusters include portions of 10% of the 3,100 genes conserved in six genomes. Statistical analysis of the functional roles of these genes reveals that several classes of genes are over-represented, including those involved in recombination, transport and motility.
conclusionWe demonstrate that intraspecific recombination in E. coli is much more common than previously appreciated and may show a bias for certain types of genes. The described method provides high-specificity, conservative inference of past recombination events.
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