title: Chromosome painting in silico in a bacterial species reveals fine population structure.
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.
authors.affiliation: Department of Medical Genome Sciences, Graduate School of Frontier Sciences, University of Tokyo, Tokyo, Japan.
authors.forename: Koji
authors.initials: K
authors.lastname: Yahara
authors.forename: Yoshikazu
authors.initials: Y
authors.lastname: Furuta
authors.forename: Kenshiro
authors.initials: K
authors.lastname: Oshima
authors.forename: Masaru
authors.initials: M
authors.lastname: Yoshida
authors.forename: Takeshi
authors.initials: T
authors.lastname: Azuma
authors.forename: Masahira
authors.initials: M
authors.lastname: Hattori
authors.forename: Ikuo
authors.initials: I
authors.lastname: Uchiyama
authors.forename: Ichizo
authors.initials: I
authors.lastname: Kobayashi
mesh_terms: D020223:Chromosome Painting; D002876:Chromosomes, Bacterial; D016000:Cluster Analysis; D003198:Computer Simulation; D004269:DNA, Bacterial / Q000737:chemistry* / Q000235:genetics; D019143:Evolution, Molecular; D051456:Gene Flow; D005827:Genetics, Microbial / Q000379:methods; D016480:Helicobacter pylori / Q000235:genetics; D010802:Phylogeny; D011995:Recombination, Genetic / Q000235:genetics
chemical_list: D004269:DNA, Bacterial
keywords: Helicobacter pylori; fineSTRUCTURE; homologous recombination; human evolution; phylogenetic network