title: Genome-wide survey of codons under  diversifying selection in a highly recombining  bacterial species, Helicobacter pylori.
abstract: Selection has been a central issue in biology in eukaryotes as well as prokaryotes. Inference of selection in recombining bacterial species, compared with clonal ones, has been a challenge. It is not known how codons under diversifying selection are distributed along the chromosome or among functional categories or how frequently such codons are subject to mutual homologous recombination. Here, we explored these questions by analysing genes present in >90% among 29 genomes of Helicobacter pylori, one of the bacterial species with the highest mutation and recombination rates. By a method for recombining sequences, we identified codons under diversifying selection (dN/dS> 1), which were widely distributed and accounted for ∼0.2% of all the codons of the genome. The codons were enriched in genes of host interaction/cell surface and genome maintenance (DNA replication,recombination, repair, and restriction modification system). The encoded amino acid residues were sometimes found adjacent to critical catalytic/binding residues in protein structures.Furthermore, by estimating the intensity of homologous recombination at a single nucleotide level, we found that these codons appear to be more frequently subject to recombination.We expect that the present study provides a new approach to population genomics of selection in recombining prokaryotes.
authors.forename: Koji
authors.initials: K
authors.lastname: Yahara
authors.forename: Yoshikazu
authors.initials: Y
authors.lastname: Furuta
authors.forename: Shinpei
authors.initials: S
authors.lastname: Morimoto
authors.forename: Chie
authors.initials: C
authors.lastname: Kikutake
authors.forename: Sho
authors.initials: S
authors.lastname: Komukai
authors.forename: Dorota
authors.initials: D
authors.lastname: Matelska
authors.forename: Stanisław
authors.initials: S
authors.lastname: Dunin-Horkawicz
authors.forename: Janusz M
authors.initials: JM
authors.lastname: Bujnicki
authors.forename: Ikuo
authors.initials: I
authors.lastname: Uchiyama
authors.forename: Ichizo
authors.initials: I
authors.lastname: Kobayashi
mesh_terms: D003062:Codon; D019143:Evolution, Molecular; D014644:Genetic Variation; D016680:Genome, Bacterial; D016480:Helicobacter pylori / Q000235:genetics*; D011995:Recombination, Genetic; D012641:Selection, Genetic
chemical_list: D003062:Codon