ArticleBMC bioinformatics2023
Detecting patterns of accessory genome coevolution in Staphylococcus aureus using data from thousands of genomes.
Article in BMC bioinformatics, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
What it found
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Who cites it
8 citing papers in PubMed, 12 citations in OpenAlex.
- Genome-wide co-occurrence patterns link mobile genetic elements, antimicrobial resistance and defense systems in Pseudomonas aeruginosa.BMC genomics · 2026Article
- Unraveling the tempo and mode of horizontal gene transfer in bacteria.Trends in microbiology · 2025Review
- Whole-genome recombination and dynamic accessory genomes drive the phenotypic diversity of Mycobacterium abscessus subspecies.Annals of clinical microbiology and antimicrobials · 2025Article
- Evolutionary dynamics of the accessory genomes ofmSphere · 2024Article
- Global genetic diversity and Asian clades evolution: a phylogeographic study ofAntimicrobial agents and chemotherapy · 2024Article
- Dynamics of bacterial recombination in the human gut microbiome.PLoS biology · 2024Article
- Contingency, repeatability, and predictability in the evolution of a prokaryotic pangenome.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Genetics of antibiotic resistance in methicillin-resistantBiotechnologia · 2024Review
Corrections and comments
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
Abstract
Bacterial genomes exhibit widespread horizontal gene transfer, resulting in highly variable genome content that complicates the inference of genetic interactions. In this study, we develop a method for detecting coevolving genes from large datasets of bacterial genomes based on pairwise comparisons of closely related individuals, analogous to a pedigree study in eukaryotic populations. We apply our method to pairs of genes from the Staphylococcus aureus accessory genome of over 75,000 annotated gene families using a database of over 40,000 whole genomes. We find many pairs of genes that appear to be gained or lost in a coordinated manner, as well as pairs where the gain of one gene is associated with the loss of the other. These pairs form networks of rapidly coevolving genes, primarily consisting of genes involved in virulence, mechanisms of horizontal gene transfer, and antibiotic resistance, particularly the SCCmec complex. While we focus on gene gain and loss, our method can also detect genes that tend to acquire substitutions in tandem, or genotype-phenotype or phenotype-phenotype coevolution. Finally, we present the R package DeCoTUR that allows for the computation of our method.
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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.