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Genome-wide survey of codons under diversifying selection in a highly recombining bacterial species, Helicobacter pylori

Yahara, K; Furuta, Y; Morimoto, S; Kikutake, C; Komukai, S; Matelska, D; Dunin-Horkawicz, S; ... Kobayashi, I; + view all (2016) Genome-wide survey of codons under diversifying selection in a highly recombining bacterial species, Helicobacter pylori. DNA Research , 23 (2) pp. 135-143. 10.1093/dnares/dsw003. Green open access

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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.

Type: Article
Title: Genome-wide survey of codons under diversifying selection in a highly recombining bacterial species, Helicobacter pylori
Open access status: An open access version is available from UCL Discovery
DOI: 10.1093/dnares/dsw003
Publisher version: https://doi.org/10.1093/dnares/dsw003
Language: English
Additional information: This work is licensed under a Creative Commons Attribution 4.0 International License. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/
Keywords: Science & Technology, Life Sciences & Biomedicine, Genetics & Heredity, selection, dN/dS, recombination, population genomics, bacteria, RESTRICTION-MODIFICATION SYSTEMS, POSITIVE NATURAL-SELECTION, FOLD-RECOGNITION MODELS, POPULATION-STRUCTURE, CRYSTAL-STRUCTURE, ESCHERICHIA-COLI, DNA RESTRICTION, RECBCD ENZYME, EVOLUTION, PROTEIN
UCL classification: UCL
UCL > Provost and Vice Provost Offices
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences > Div of Biosciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences > Div of Biosciences > Structural and Molecular Biology
URI: https://discovery.ucl.ac.uk/id/eprint/10058979
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