ArticleJournal of bacteriology2013
Evolution of pan-genomes of Escherichia coli, Shigella spp., and Salmonella enterica.
Article in Journal of bacteriology, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 65 papers.
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Who cites it
65 citing papers in PubMed.
- Genomic Markers Distinguishing Shiga Toxin-ProducingPathogens (Basel, Switzerland) · 2025Article
- Emergence of potentially disinfection-resistant, naturalized Escherichia coli populations across food- and water-associated engineered environments.Scientific reports · 2024Article
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- Mutational Signatures in Wild Type Escherichia coli Strains Reveal Predominance of DNA Polymerase Errors.Genome biology and evolution · 2024Article
- Bacterial Flora and Treatment Strategies in Women With Escherichia coli Urinary Tract Infections.Cureus · 2024Article
- Whole genome sequencing and antimicrobial resistance among clinical isolates of Shigella sonnei in Addis Ababa, Ethiopia.PloS one · 2024Article
- Tracing the Evolutionary Pathways of Serogroup O78 Avian PathogenicAntibiotics (Basel, Switzerland) · 2023Article
- Genetic Determinants of Escherichia coli Survival in Beach Sand.Applied and environmental microbiology · 2023Article
- Effect of Mannan-rich fraction supplementation on commercial broiler intestinum tenue and cecum microbiota.Animal microbiome · 2022Article
- Distinct evolutionary trajectories in theMicrobial genomics · 2022Article
- To kill or to be killed: pangenome analysis of Escherichia coli strains reveals a tailocin specific for pandemic ST131.BMC biology · 2022Article
- Using unique ORFan genes as strain-specific identifiers for Escherichia coli.BMC microbiology · 2022Article
- Physicochemical classification of organisms.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- Pandora: nucleotide-resolution bacterial pan-genomics with reference graphs.Genome biology · 2021Article
- Different evolutionary trends form the twilight zone of the bacterial pan-genome.Microbial genomics · 2021Article
- A retrospective analysis of antimicrobial resistance in pathogenicInternational journal of veterinary science and medicine · 2021Article
- Niche and local geography shape the pangenome of wastewater- and livestock-associated Enterobacteriaceae.Science advances · 2021Article
- Epi-Gene: An R-Package for Easy Pan-Genome Analysis.BioMed research international · 2021Article
- Article
- Building genomes to understand biology.Nature communications · 2020Review
5 more citing papers are in PubMed but not listed here.
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Multiple sequencing of genomes belonging to a bacterial species allows one to analyze and compare statistics and dynamics of the gene complements of species, their pan-genomes. Here, we analyzed multiple genomes of Escherichia coli, Shigella spp., and Salmonella enterica. We demonstrate that the distribution of the number of genomes harboring a gene is well approximated by a sum of two power functions, describing frequent genes (present in many strains) and rare genes (present in few strains). The virtual absence of Shigella-specific genes not present in E. coli genomes confirms previous observations that Shigella is not an independent genus. While the pan-genome size is increasing with each new strain, the number of genes present in a fixed fraction of strains stabilizes quickly. For instance, slightly fewer than 4,000 genes are present in at least half of any group of E. coli genomes. Comparison of S. enterica and E. coli pan-genomes revealed the existence of a common periphery, that is, genes present in some but not all strains of both species. Analysis of phylogenetic trees demonstrates that rare genes from the periphery likely evolve under horizontal transfer, whereas frequent periphery genes may have been inherited from the periphery genome of the common ancestor.
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