ArticleProceedings of the National Academy of Sciences of the United States of America2015
Recombinant transfer in the basic genome of Escherichia coli.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 52 papers, 1 of them a synthesis that pooled it.
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Who cites it
52 citing papers in PubMed, 1 synthesis or guideline pooled it, 93 citations in OpenAlex.
- Phylogenetic Group Distribution of UropathogenicFrontiers in cellular and infection microbiology · 2022Pooled it
- Recombination shapes the dynamics of selective constraint in global populations of human gut bacteria.PLoS biology · 2026Article
- Article
- Reconstructing the Network of Horizontal Gene Exchange in Bacteria to Differentiate Direct and Indirect Transfers.Genome biology and evolution · 2026Article
- Dynamics of dN/dS within recombining bacterial populations.bioRxiv : the preprint server for biology · 2025Article
- Article
- Strainify: Strain-Level Microbiome Profiling for Low-Coverage Short-Read Metagenomic Datasets.bioRxiv : the preprint server for biology · 2025Article
- High-throughput conjugation reveals strain specific recombination patterns enabling precise trait mapping in Escherichia coli.PLoS genetics · 2025Article
- Unraveling the tempo and mode of horizontal gene transfer in bacteria.Trends in microbiology · 2025Review
- Lineage-specific variation in frequency and hotspots of recombination in invasive Escherichia coli.BMC genomics · 2025Article
- Evolution of homologous recombination rates across bacteria.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Modeling the mosaic structure of bacterial genomes to infer their evolutionary history.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Impact of Homologous Recombination on Core Genome Evolution and Host Adaptation of Pectobacterium parmentieri.Genome biology and evolution · 2024Article
- Dynamics of bacterial recombination in the human gut microbiome.PLoS biology · 2024Article
- Genetic Characterization of Carbapenem-ResistantAntibiotics (Basel, Switzerland) · 2023Article
- Genomic Analysis of a Hybrid Enteroaggregative HemorrhagicAntibiotics (Basel, Switzerland) · 2022Article
- Lipopolysaccharide core type diversity in theMicrobial genomics · 2021Article
- Article
- Whole genome phylogenies reflect the distributions of recombination rates for many bacterial species.eLife · 2021Article
- The population genetics of pathogenic Escherichia coli.Nature reviews. Microbiology · 2021Review
Corrections and comments
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Authors and funding
4 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
An approximation to the ∼4-Mbp basic genome shared by 32 strains of Escherichia coli representing six evolutionary groups has been derived and analyzed computationally. A multiple alignment of the 32 complete genome sequences was filtered to remove mobile elements and identify the most reliable ∼90% of the aligned length of each of the resulting 496 basic-genome pairs. Patterns of single base-pair mutations (SNPs) in aligned pairs distinguish clonally inherited regions from regions where either genome has acquired DNA fragments from diverged genomes by homologous recombination since their last common ancestor. Such recombinant transfer is pervasive across the basic genome, mostly between genomes in the same evolutionary group, and generates many unique mosaic patterns. The six least-diverged genome pairs have one or two recombinant transfers of length ∼40-115 kbp (and few if any other transfers), each containing one or more gene clusters known to confer strong selective advantage in some environments. Moderately diverged genome pairs (0.4-1% SNPs) show mosaic patterns of interspersed clonal and recombinant regions of varying lengths throughout the basic genome, whereas more highly diverged pairs within an evolutionary group or pairs between evolutionary groups having >1.3% SNPs have few clonal matches longer than a few kilobase pairs. Many recombinant transfers appear to incorporate fragments of the entering DNA produced by restriction systems of the recipient cell. A simple computational model can closely fit the data. Most recombinant transfers seem likely to be due to generalized transduction by coevolving populations of phages, which could efficiently distribute variability throughout bacterial genomes.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.