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

Yahara K, Furuta Y, Oshima K, Yoshida M, Azuma T, Hattori M, Uchiyama I, Kobayashi I - Mol. Biol. Evol. (2013)

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: Department of Medical Genome Sciences, Graduate School of Frontier Sciences, University of Tokyo, Tokyo, Japan.

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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Phylogenetic network. The colors indicate subgroups identified by fineSTRUCTURE (as in fig. 2 and table 1). Scale bar indicates substitutions per nucleic site.
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mst055-F3: Phylogenetic network. The colors indicate subgroups identified by fineSTRUCTURE (as in fig. 2 and table 1). Scale bar indicates substitutions per nucleic site.

Mentions: From the same genomic data, we also constructed a phylogenetic network (fig. 3). Within each clade, the strains are colored according to the population assignment by fineSTRUCTURE. The result appeared globally consistent with the fineSTRUCTURE population assignments. The clades of East Asia, Amerind, Asia2, Europe, and Africa1 are seemingly polytomous, suggesting rampant recombination.Fig. 3.


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

Yahara K, Furuta Y, Oshima K, Yoshida M, Azuma T, Hattori M, Uchiyama I, Kobayashi I - Mol. Biol. Evol. (2013)

Phylogenetic network. The colors indicate subgroups identified by fineSTRUCTURE (as in fig. 2 and table 1). Scale bar indicates substitutions per nucleic site.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3649679&req=5

mst055-F3: Phylogenetic network. The colors indicate subgroups identified by fineSTRUCTURE (as in fig. 2 and table 1). Scale bar indicates substitutions per nucleic site.
Mentions: From the same genomic data, we also constructed a phylogenetic network (fig. 3). Within each clade, the strains are colored according to the population assignment by fineSTRUCTURE. The result appeared globally consistent with the fineSTRUCTURE population assignments. The clades of East Asia, Amerind, Asia2, Europe, and Africa1 are seemingly polytomous, suggesting rampant recombination.Fig. 3.

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: Department of Medical Genome Sciences, Graduate School of Frontier Sciences, University of Tokyo, Tokyo, Japan.

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.

Show MeSH