Chromosome painting in silico in a bacterial species reveals fine population structure

Koji Yahara, Yoshikazu Furuta, Kenshiro Oshima, Masaru Yoshida, Takeshi Azuma, Masahira Hattori, Ikuo Uchiyama, Ichizo Kobayashi

Research output: Contribution to journalArticle

41 Citations (Scopus)

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.

Original languageEnglish
Pages (from-to)1454-1464
Number of pages11
JournalMolecular Biology and Evolution
Volume30
Issue number6
DOIs
Publication statusPublished - 2013 Jun
Externally publishedYes

Fingerprint

Chromosome Painting
Computer Simulation
population structure
chromosome
genome
Genome
Population
recombination
transfer DNA
methodology
Far East
Helicobacter pylori
American Indians
Homologous Recombination
homologous recombination
Ryukyu Archipelago
Essential Genes
network analysis
Human Genome
East Asia

Keywords

  • fineSTRUCTURE
  • Helicobacter pylori
  • homologous recombination
  • human evolution
  • phylogenetic network

ASJC Scopus subject areas

  • Genetics
  • Molecular Biology
  • Ecology, Evolution, Behavior and Systematics

Cite this

Chromosome painting in silico in a bacterial species reveals fine population structure. / Yahara, Koji; Furuta, Yoshikazu; Oshima, Kenshiro; Yoshida, Masaru; Azuma, Takeshi; Hattori, Masahira; Uchiyama, Ikuo; Kobayashi, Ichizo.

In: Molecular Biology and Evolution, Vol. 30, No. 6, 06.2013, p. 1454-1464.

Research output: Contribution to journalArticle

Yahara, K, Furuta, Y, Oshima, K, Yoshida, M, Azuma, T, Hattori, M, Uchiyama, I & Kobayashi, I 2013, 'Chromosome painting in silico in a bacterial species reveals fine population structure', Molecular Biology and Evolution, vol. 30, no. 6, pp. 1454-1464. https://doi.org/10.1093/molbev/mst055
Yahara, Koji ; Furuta, Yoshikazu ; Oshima, Kenshiro ; Yoshida, Masaru ; Azuma, Takeshi ; Hattori, Masahira ; Uchiyama, Ikuo ; Kobayashi, Ichizo. / Chromosome painting in silico in a bacterial species reveals fine population structure. In: Molecular Biology and Evolution. 2013 ; Vol. 30, No. 6. pp. 1454-1464.
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