ArticleMicrobial genomics2021
Different evolutionary trends form the twilight zone of the bacterial pan-genome.
Article in Microbial genomics, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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Who cites it
25 citing papers in PubMed.
- A generative model for bipartite gene-sharing networks.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Pan genome clustering identifies a novel mosaic prophage specific to Salmonella Enteritidis lineage associated with the invasive disease in India.PLoS neglected tropical diseases · 2026Article
- Epistasis and co-adaptation in bacterial genome evolution.Nature reviews. Genetics · 2026Review
- A decade of antimicrobial resistance inMicrobiology spectrum · 2026Article
- A metabolic atlas of the Klebsiella pneumoniae species complex reveals lineage-specific metabolism and capacity for intra-species co-operation.PLoS biology · 2025Article
- Integrative Multi-Omics Identify Key Secondary Metabolites Linked to Acid Tolerance inMicroorganisms · 2025Article
- The Kocurious case of Noodlococcus: genomic insights intoMicrobial genomics · 2025Article
- Lineage-specific variation in frequency and hotspots of recombination in invasive Escherichia coli.BMC genomics · 2025Article
- Competitive behaviors in Serratia marcescens are coordinately regulated by a lifestyle switch frequently inactivated in the clinical environment.Cell host & microbe · 2025Article
- Roles of mobile genetic elements and biosynthetic gene clusters in environmental adaptation of acidophilic archaeonFrontiers in microbiology · 2025Article
- MosAIC: An annotated collection of mosquito-associated bacteria with high-quality genome assemblies.PLoS biology · 2024Article
- Evolutionary dynamics of the accessory genomes ofmSphere · 2024Article
- Genomic revisitation and reclassification of the genusmSphere · 2024Article
- Average Nucleotide Identity basedbioRxiv : the preprint server for biology · 2024Article
- Antimicrobial resistance heterogeneity among multidrug-resistant Gram-negative pathogens: Phenotypic, genotypic, and proteomic analysis.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- The bacterial genetic determinants of Escherichia coli capacity to cause bloodstream infections in humans.PLoS genetics · 2023Article
- Tackling the Pangenome Dilemma Requires the Concerted Analysis of Multiple Population Genetic Processes.Genome biology and evolution · 2023Article
- Challenges in prokaryote pangenomics.Microbial genomics · 2023Review
- Genomic analysis unveils genome degradation events and gene flux in the emergence and persistence of S. Paratyphi A lineages.PLoS pathogens · 2023Article
- Pan-Genome Analysis of Staphylococcus aureus Reveals Key Factors Influencing Genomic Plasticity.Microbiology spectrum · 2022Article
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7 authors.
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Abstract
The pan-genome is defined as the combined set of all genes in the gene pool of a species. Pan-genome analyses have been very useful in helping to understand different evolutionary dynamics of bacterial species: an open pan-genome often indicates a free-living lifestyle with metabolic versatility, while closed pan-genomes are linked to host-restricted, ecologically specialized bacteria. A detailed understanding of the species pan-genome has also been instrumental in tracking the phylodynamics of emerging drug resistance mechanisms and drug-resistant pathogens. However, current approaches to analyse a species' pan-genome do not take the species population structure into account, nor do they account for the uneven sampling of different lineages, as is commonplace due to over-sampling of clinically relevant representatives. Here we present the application of a population structure-aware approach for classifying genes in a pan-genome based on within-species distribution. We demonstrate our approach on a collection of 7500
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