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

Richard G. Everitt, Xavier Didelot, Elizabeth M. Batty, Ruth R Miller, Kyle Knox, Bernadette C. Young, Rory Bowden, Adam Auton, Antonina Votintseva, Hanna Larner-Svensson, Jane Charlesworth, Tanya Golubchik, Camilla L. C. Ip, Heather Godwin, Rowena Fung, Tim E. A. Peto, A. Sarah Walker, Derrick W. Crook and Daniel J. Wilson ()
Additional contact information
Richard G. Everitt: University of Oxford, John Radcliffe Hospital
Xavier Didelot: University of Oxford
Elizabeth M. Batty: University of Oxford
Ruth R Miller: University of Oxford, John Radcliffe Hospital
Kyle Knox: University of Oxford
Bernadette C. Young: University of Oxford, John Radcliffe Hospital
Rory Bowden: University of Oxford
Adam Auton: Wellcome Trust Centre for Human Genetics, Roosevelt Drive
Antonina Votintseva: University of Oxford, John Radcliffe Hospital
Hanna Larner-Svensson: University of Oxford, John Radcliffe Hospital
Jane Charlesworth: University of Oxford, John Radcliffe Hospital
Tanya Golubchik: University of Oxford, John Radcliffe Hospital
Camilla L. C. Ip: University of Oxford
Heather Godwin: Oxford University Hospitals National Health Service Trust, John Radcliffe Hospital
Rowena Fung: University of Oxford, John Radcliffe Hospital
Tim E. A. Peto: University of Oxford, John Radcliffe Hospital
A. Sarah Walker: University of Oxford, John Radcliffe Hospital
Derrick W. Crook: University of Oxford, John Radcliffe Hospital
Daniel J. Wilson: University of Oxford, John Radcliffe Hospital

Nature Communications, 2014, vol. 5, issue 1, 1-9

Abstract: Abstract 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.

Date: 2014
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DOI: 10.1038/ncomms4956

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