ArticleMolecular biology and evolution2014
Efficient inference of recombination hot regions in bacterial genomes.
Article in Molecular biology and evolution, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 42 papers.
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42 citing papers in PubMed, 75 citations in OpenAlex.
- Epistasis and co-adaptation in bacterial genome evolution.Nature reviews. Genetics · 2026Review
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- Emergence and global spread of a dominant multidrug-resistant clade within Acinetobacter baumannii.Nature communications · 2025Article
- Homologous recombination shapes the architecture and evolution of bacterial genomes.Nucleic acids research · 2025Article
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- Homologous Recombination Shapes the Architecture and Evolution of Bacterial Genomes.bioRxiv : the preprint server for biology · 2024Article
- RecGraph: recombination-aware alignment of sequences to variation graphs.Bioinformatics (Oxford, England) · 2024Article
- Dynamics of bacterial recombination in the human gut microbiome.PLoS biology · 2024Article
- The Helicobacter pylori Genome Project: insights into H. pylori population structure from analysis of a worldwide collection of complete genomes.Nature communications · 2023Article
- Systems-Based Approach for Optimization of Assembly-Free Bacterial MLST Mapping.Life (Basel, Switzerland) · 2022Article
- Horizontal gene transfer and adaptive evolution in bacteria.Nature reviews. Microbiology · 2022Review
- Zoonotic Transmission ofFrontiers in microbiology · 2022Article
- Quantifying bacterial evolution in the wild: A birthday problem for Campylobacter lineages.PLoS genetics · 2021Article
- Of Traits and Trees: Probabilistic Distances under Continuous Trait Models for Dissecting the Interplay among Phylogeny, Model, and Data.Systematic biology · 2021Article
- Natural Horizontal Gene Transfer of Antimicrobial Resistance Genes inFrontiers in microbiology · 2021Article
- Gene pool transmission of multidrug resistance among Campylobacter from livestock, sewage and human disease.Environmental microbiology · 2019Article
- The recombination-cold region as an epidemiological marker of recombinogenic opportunistic pathogen Mycobacterium avium.BMC genomics · 2019Article
- Patterns of inter- and intrasubspecific homologous recombination inform eco-evolutionary dynamics of Xylella fastidiosa.The ISME journal · 2019Article
- Article
- Analysis of genetic recombination and the pan-genome of a highly recombinogenic bacteriophage species.Microbial genomics · 2019Article
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Authors and funding
5 authors at 4 institutions in 3 countries.
Funding
Abstract
In eukaryotes, detailed surveys of recombination rates have shown variation at multiple genomic scales and the presence of "hotspots" of highly elevated recombination. In bacteria, studies of recombination rate variation are less developed, in part because there are few analysis methods that take into account the clonal context within which bacterial evolution occurs. Here, we focus in particular on identifying "hot regions" of the genome where DNA is transferred frequently between isolates. We present a computationally efficient algorithm based on the recently developed "chromosome painting" algorithm, which characterizes patterns of haplotype sharing across a genome. We compare the average genome wide painting, which principally reflects clonal descent, with the painting for each site which additionally reflects the specific deviations at the site due to recombination. Using simulated data, we show that hot regions have consistently higher deviations from the genome wide average than normal regions. We applied our approach to previously analyzed Escherichia coli genomes and revealed that the new method is highly correlated with the number of recombination events affecting each site inferred by ClonalOrigin, a method that is only applicable to small numbers of genomes. Furthermore, we analyzed recombination hot regions in Campylobacter jejuni by using 200 genomes. We identified three recombination hot regions, which are enriched for genes related to membrane proteins. Our approach and its implementation, which is downloadable from https://github.com/bioprojects/orderedPainting, will help to develop a new phase of population genomic studies of recombination in prokaryotes.
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