ArticleMolecular biology and evolution2013
Chromosome painting in silico in a bacterial species reveals fine population structure.
Article in Molecular biology and evolution, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 61 papers.
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61 citing papers in PubMed.
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- Fine-scale population structure of JapaneseMicrobial genomics · 2025Article
- Beyond Low Prevalence: Exploring Antibiotic Resistance and Virulence Profiles in Sri Lankan Helicobacter pylori with Comparative Genomics.Microorganisms · 2025Article
- Graphite: painting genomes using a colored de Bruijn graph.NAR genomics and bioinformatics · 2024Article
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- The Helicobacter pylori Genome Project: insights into H. pylori population structure from analysis of a worldwide collection of complete genomes.Nature communications · 2023Article
- Genetic determinants of Biofilm formation of Helicobacter pylori using whole-genome sequencing.BMC microbiology · 2023Article
- Comparative genomics of two Vietnamese Helicobacter pylori strains, CHC155 from a non-cardia gastric cancer patient and VN1291 from a duodenal ulcer patient.Scientific reports · 2023Article
- Mutations Related to Antibiotics Resistance inAntibiotics (Basel, Switzerland) · 2023Article
- Phylogenetic Analysis of Bacterial Pathogen Genomes.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Recombination events drives the emergence of ColombianVirulence · 2022Article
- Repeated out-of-Africa expansions of Helicobacter pylori driven by replacement of deleterious mutations.Nature communications · 2022Article
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- Population genomics of the food-borne pathogenMicrobial genomics · 2022Article
- Genomic differentiation within East AsianMicrobial genomics · 2022Article
- Genome-wide association study of gastric cancer- and duodenal ulcer-derivedMicrobial genomics · 2021Article
1 more citing papers are in PubMed but not listed here.
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8 authors.
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Abstract
Identifying population structure forms an important basis for genetic and evolutionary studies. Most current methods to identify population structure have limitations in analyzing haplotypes and recombination across the genome. Recently, a method of chromosome painting in silico has been developed to overcome these shortcomings and has been applied to multiple human genome sequences. This method detects the genome-wide transfer of DNA sequence chunks through homologous recombination. Here, we apply it to the frequently recombining bacterial species Helicobacter pylori that has infected Homo sapiens since their birth in Africa and shows wide phylogeographic divergence. Multiple complete genome sequences were analyzed including sequences from Okinawa, Japan, that we recently sequenced. The newer method revealed a finer population structure than revealed by a previous method that examines only MLST housekeeping genes or a phylogenetic network analysis of the core genome. Novel subgroups were found in Europe, Amerind, and East Asia groups. Examination of genetic flux showed some singleton strains to be hybrids of subgroups and revealed evident signs of population admixture in Africa, Europe, and parts of Asia. We expect this approach to further our understanding of intraspecific bacterial evolution by revealing population structure at a finer scale.
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