title: The Landscape of Realized Homologous Recombination in Pathogenic Bacteria.
abstract: Recombination enhances the adaptive potential of organisms by allowing genetic variants to be tested on multiple genomic backgrounds. Its distribution in the genome can provide insight into the evolutionary forces that underlie traits, such as the emergence of pathogenicity. Here, we examined landscapes of realized homologous recombination of 500 genomes from ten bacterial species and found all species have "hot" regions with elevated rates relative to the genome average. We examined the size, gene content, and chromosomal features associated with these regions and the correlations between closely related species. The recombination landscape is variable and evolves rapidly. For example in Salmonella, only short regions of around 1 kb in length are hot whereas in the closely related species Escherichia coli, some hot regions exceed 100 kb, spanning many genes. Only Streptococcus pyogenes shows evidence for the positive correlation between GC content and recombination that has been reported for several eukaryotes. Genes with function related to the cell surface/membrane are often found in recombination hot regions but E. coli is the only species where genes annotated as "virulence associated" are consistently hotter. There is also evidence that some genes with "housekeeping" functions tend to be overrepresented in cold regions. For example, ribosomal proteins showed low recombination in all of the species. Among specific genes, transferrin-binding proteins are recombination hot in all three of the species in which they were found, and are subject to interspecies recombination.
authors.affiliation: Biostatistics Center, Kurume University, Kurume, Fukuoka, Japan College of Medicine, Institute of Life Science, Swansea University, Swansea, United Kingdom.
authors.forename: Koji
authors.initials: K
authors.lastname: Yahara
authors.affiliation: Department of Infectious Disease Epidemiology, Imperial College London, London, United Kingdom.
authors.forename: Xavier
authors.initials: X
authors.lastname: Didelot
authors.affiliation: Department of Zoology, University of Oxford, Oxford, United Kingdom.
authors.forename: Keith A
authors.initials: KA
authors.lastname: Jolley
authors.affiliation: Department of Medical Genome Sciences, Graduate School of Frontier Sciences, University of Tokyo, Tokyo, Japan.
authors.forename: Ichizo
authors.initials: I
authors.lastname: Kobayashi
authors.affiliation: Department of Zoology, University of Oxford, Oxford, United Kingdom.
authors.forename: Martin C J
authors.initials: MC
authors.lastname: Maiden
authors.affiliation: College of Medicine, Institute of Life Science, Swansea University, Swansea, United Kingdom Department of Zoology, University of Oxford, Oxford, United Kingdom.
authors.forename: Samuel K
authors.initials: SK
authors.lastname: Sheppard
authors.affiliation: College of Medicine, Institute of Life Science, Swansea University, Swansea, United Kingdom Department of Medical Genome Sciences, Graduate School of Frontier Sciences, University of Tokyo, Tokyo, Japan danielfalush@googlemail.com.
authors.forename: Daniel
authors.initials: D
authors.lastname: Falush
mesh_terms: D001419:Bacteria / Q000235:genetics* / Q000472:pathogenicity; D001482:Base Composition; D005075:Biological Evolution; D016000:Cluster Analysis; D005798:Genes, Bacterial; D016680:Genome, Bacterial; D023281:Genomics; D059765:Homologous Recombination; D012641:Selection, Genetic; D014774:Virulence / Q000235:genetics
keywords: pathogenicity; population genomics; recombination; selection