ArticleGenetics2010
Inference of homologous recombination in bacteria using whole-genome sequences.
Article in Genetics, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 106 papers.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
106 citing papers in PubMed.
- Exploring genetic variations and plasmid diversity in Escherichia coli strains isolated from Hospital Wastewater.BMC genomics · 2026Article
- Fast hospital discharge rates blur within-hospital 'transmission footprint' in bacterial genomes, as showcased with Staphylococcus aureus.PLoS computational biology · 2026Article
- Quantifying plasmid movement in drug-resistant Shigella species using phylodynamic inference.PLoS pathogens · 2025Article
- A Pandemic-Scale Ancestral Recombination Graph for SARS-CoV-2.bioRxiv : the preprint server for biology · 2025Article
- Article
- Article
- Investigating Additive and Replacing Horizontal Gene Transfers Using Phylogenies and Whole Genomes.Genome biology and evolution · 2024Article
- RecGraph: recombination-aware alignment of sequences to variation graphs.Bioinformatics (Oxford, England) · 2024Article
- Evolution of homologous recombination rates across bacteria.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- A general and efficient representation of ancestral recombination graphs.bioRxiv : the preprint server for biology · 2024Article
- Review
- Geographic population structure and distinct intra-population dynamics of globally abundant freshwater bacteria.The ISME journal · 2024Article
- Recombination-aware phylogenetic analysis sheds light on the evolutionary origin of SARS-CoV-2.Scientific reports · 2024Article
- The era of the ARG: An introduction to ancestral recombination graphs and their significance in empirical evolutionary genomics.PLoS genetics · 2024Review
- Population genetic analysis of clinicalFrontiers in cellular and infection microbiology · 2024Article
- Recombination-mediated dissemination of Methicillin-resistant S. aureus clonal complex 1 in the Egyptian health care settings.Annals of clinical microbiology and antimicrobials · 2023Article
- Article
- Phylogenetic Analysis of Bacterial Pathogen Genomes.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Distinguishing imported cases from locally acquired cases within a geographically limited genomic sample of an infectious disease.Bioinformatics (Oxford, England) · 2023Article
- A scalable analytical approach from bacterial genomes to epidemiology.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2022Article
46 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
Bacteria and archaea reproduce clonally, but sporadically import DNA into their chromosomes from other organisms. In many of these events, the imported DNA replaces an homologous segment in the recipient genome. Here we present a new method to reconstruct the history of recombination events that affected a given sample of bacterial genomes. We introduce a mathematical model that represents both the donor and the recipient of each DNA import as an ancestor of the genomes in the sample. The model represents a simplification of the previously described coalescent with gene conversion. We implement a Monte Carlo Markov chain algorithm to perform inference under this model from sequence data alignments and show that inference is feasible for whole-genome alignments through parallelization. Using simulated data, we demonstrate accurate and reliable identification of individual recombination events and global recombination rate parameters. We applied our approach to an alignment of 13 whole genomes from the Bacillus cereus group. We find, as expected from laboratory experiments, that the recombination rate is higher between closely related organisms and also that the genome contains several broad regions of elevated levels of recombination. Application of the method to the genomic data sets that are becoming available should reveal the evolutionary history and private lives of populations of bacteria and archaea. The methods described in this article have been implemented in a computer software package, ClonalOrigin, which is freely available from http://code.google.com/p/clonalorigin/.
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Registered trials
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.