title: Genome-wide survey of mutual homologous recombination in a highly sexual bacterial species.
abstract: The nature of a species remains a fundamental and controversial question. The era of genome/metagenome sequencing has intensified the debate in prokaryotes because of extensive horizontal gene transfer. In this study, we conducted a genome-wide survey of outcrossing homologous recombination in the highly sexual bacterial species Helicobacter pylori. We conducted multiple genome alignment and analyzed the entire data set of one-to-one orthologous genes for its global strains. We detected mosaic structures due to repeated recombination events and discordant phylogenies throughout the genomes of this species. Most of these genes including the "core" set of genes and horizontally transferred genes showed at least one recombination event. Taking into account the relationship between the nucleotide diversity and the minimum number of recombination events per nucleotide, we evaluated the recombination rate in every gene. The rate appears constant across the genome, but genes with a particularly high or low recombination rate were detected. Interestingly, genes with high recombination included those for DNA transformation and for basic cellular functions, such as biosynthesis and metabolism. Several highly divergent genes with a high recombination rate included those for host interaction, such as outer membrane proteins and lipopolysaccharide synthesis. These results provide a global picture of genome-wide distribution of outcrossing homologous recombination in a bacterial species for the first time, to our knowledge, and illustrate how a species can be shaped by mutual homologous recombination.
authors.affiliation: Division of Biostatistics, Graduate School of Medicine, Kurume University, Fukuoka, Japan.
authors.forename: Koji
authors.initials: K
authors.lastname: Yahara
authors.forename: Mikihiko
authors.initials: M
authors.lastname: Kawai
authors.forename: Yoshikazu
authors.initials: Y
authors.lastname: Furuta
authors.forename: Noriko
authors.initials: N
authors.lastname: Takahashi
authors.forename: Naofumi
authors.initials: N
authors.lastname: Handa
authors.forename: Takeshi
authors.initials: T
authors.lastname: Tsuru
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: D019295:Computational Biology / Q000379:methods; D019143:Evolution, Molecular; D022761:Gene Transfer, Horizontal / Q000235:genetics*; D005798:Genes, Bacterial; D014644:Genetic Variation; D016680:Genome, Bacterial; D016480:Helicobacter pylori / Q000235:genetics*; D059765:Homologous Recombination / Q000235:genetics*; D010802:Phylogeny; D016415:Sequence Alignment