ArticleGenome research2009
Inferring genomic flux in bacteria.
Article in Genome research, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed.
- KPop: accurate and scalable comparative analysis of microbial genomes by sequence embeddings.Genome biology · 2025Article
- Persistent, Private, and Mobile Genes: A Model for Gene Dynamics in Evolving Pangenomes.Molecular biology and evolution · 2025Article
- Differences in genetic flux in invasiveHeliyon · 2022Article
- The Population Genomics of Increased Virulence and Antibiotic Resistance in Human Commensal Escherichia coli over 30 Years in France.Applied and environmental microbiology · 2022Article
- Phylogenetic Methods for Genome-Wide Association Studies in Bacteria.Methods in molecular biology (Clifton, N.J.) · 2021Article
- Fitness Tradeoffs of Antibiotic Resistance in Extraintestinal Pathogenic Escherichia coli.Genome biology and evolution · 2018Article
- Bayesian Inference of the Evolution of a Phenotype Distribution on a Phylogenetic Tree.Genetics · 2016Article
- Measurably evolving pathogens in the genomic era.Trends in ecology & evolution · 2015Review
- Genome-wide patterns of recombination in the opportunistic human pathogen Pseudomonas aeruginosa.Genome biology and evolution · 2014Article
- The Harvest suite for rapid core-genome alignment and visualization of thousands of intraspecific microbial genomes.Genome biology · 2014Article
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- Progressive genome-wide introgression in agricultural Campylobacter coli.Molecular ecology · 2013Article
- Reproductive clonality of pathogens: a perspective on pathogenic viruses, bacteria, fungi, and parasitic protozoa.Proceedings of the National Academy of Sciences of the United States of America · 2012Article
- Impact of homologous and non-homologous recombination in the genomic evolution of Escherichia coli.BMC genomics · 2012Article
- After the bottleneck: Genome-wide diversification of the Mycobacterium tuberculosis complex by mutation, recombination, and natural selection.Genome research · 2012Article
- Genomes-based phylogeny of the genus Xanthomonas.BMC microbiology · 2012Article
- Article
- Population genetics, taxonomy, phylogeny and evolution of Borrelia burgdorferi sensu lato.Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases · 2011Review
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Authors and funding
3 authors.
Funding
Abstract
Acquisition and loss of genetic material are essential forces in bacterial microevolution. They have been repeatedly linked with adaptation of lineages to new lifestyles, and in particular, pathogenicity. Comparative genomics has the potential to elucidate this genetic flux, but there are many methodological challenges involved in inferring evolutionary events from collections of genome sequences. Here we describe a model-based method for using whole-genome sequences to infer the patterns of genome content evolution. A fundamental property of our model is that it allows the rates at which genetic elements are gained or lost to vary in time and from one lineage to another. Our approach is purely sequence based, and does not rely on gene identification. We show how inference can be performed under our model and illustrate its use on three datasets from Francisella tularensis, Streptococcus pyogenes, and Escherichia coli. In all three examples, we found interesting variations in the rates of genetic material gain and loss, which strongly correlate with their lifestyle. The algorithms we describe are implemented in a computer software named GenoPlast.
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