Mobile elements drive recombination hotspots in the core genome of Staphylococcus aureus

Everitt, R. G., Didelot, X., Batty, E. M., Miller, R. R., Knox, K., Young, B. C., Bowden, R., Auton, A., Votintseva, A., Larner-Svensson, H., Charlesworth, J., Golubchik, T., Ip, C. L.C., Godwin, H., Fung, R., Peto, T. E.A., Walker, A. S., Crook, D. W. and Wilson, D. J. (2014) Mobile elements drive recombination hotspots in the core genome of Staphylococcus aureus. Nature Communications, 5. 3956. ISSN 2041-1723 doi: 10.1038/ncomms4956

Abstract/Summary

Horizontal gene transfer is an important driver of bacterial evolution, but genetic exchange in the core genome of clonal species, including the major pathogen Staphylococcus aureus, is incompletely understood. Here we reveal widespread homologous recombination in S. aureus at the species level, in contrast to its near-complete absence between closely related strains. We discover a patchwork of hotspots and coldspots at fine scales falling against a backdrop of broad-scale trends in rate variation. Over megabases, homoplasy rates fluctuate 1.9-fold, peaking towards the origin-of-replication. Over kilobases, we find core recombination hotspots of up to 2.5-fold enrichment situated near fault lines in the genome associated with mobile elements. The strongest hotspots include regions flanking conjugative transposon ICE6013, the staphylococcal cassette chromosome (SCC) and genomic island νSaα. Mobile element-driven core genome transfer represents an opportunity for adaptation and challenges our understanding of the recombination landscape in predominantly clonal pathogens, with important implications for genotype–phenotype mapping.

Item Type	Article
URI	https://reading-clone.eprints-hosting.org/id/eprint/37676
Identification Number/DOI	10.1038/ncomms4956
Refereed	Yes
Divisions	Science > School of Mathematical, Physical and Computational Sciences > Department of Mathematics and Statistics Science > School of Mathematical, Physical and Computational Sciences > Department of Mathematics and Statistics > Applied Statistics
Uncontrolled Keywords	Biological sciences Evolution Genetics Microbiology
Publisher	Nature Publishing Group
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