Mobile elements drive recombination hotspots in the core genome of Staphylococcus aureus.
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.
1] Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DU, UK [2].
Richard G
RG
Everitt
1] Department of Statistics, University of Oxford, 1 South Parks Road, Oxford OX1 3TG, UK [2].
Xavier
X
Didelot
1] Department of Statistics, University of Oxford, 1 South Parks Road, Oxford OX1 3TG, UK [2] Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford OX3 7BN, UK.
Elizabeth M
EM
Batty
Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DU, UK.
Ruth R
RR
Miller
Department of Primary Care Health Sciences, University of Oxford, 23-38 Hythe Bridge Street, Oxford OX1 2ET, UK.
Kyle
K
Knox
Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DU, UK.
Bernadette C
BC
Young
1] Department of Statistics, University of Oxford, 1 South Parks Road, Oxford OX1 3TG, UK [2] Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford OX3 7BN, UK.
Rory
R
Bowden
Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford OX3 7BN, UK.
Adam
A
Auton
1] Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DU, UK [2] Department of Statistics, University of Oxford, 1 South Parks Road, Oxford OX1 3TG, UK.
Antonina
A
Votintseva
1] Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DU, UK [2] Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford OX3 7BN, UK.
Hanna
H
Larner-Svensson
Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DU, UK.
Jane
J
Charlesworth
1] Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DU, UK [2] Department of Statistics, University of Oxford, 1 South Parks Road, Oxford OX1 3TG, UK.
Tanya
T
Golubchik
1] Department of Statistics, University of Oxford, 1 South Parks Road, Oxford OX1 3TG, UK [2] Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford OX3 7BN, UK.
Camilla L C
CL
Ip
Oxford University Hospitals National Health Service Trust, John Radcliffe Hospital, Oxford OX3 9DU, UK.
Heather
H
Godwin
Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DU, UK.
Rowena
R
Fung
Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DU, UK.
Tim E A
TE
Peto
Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DU, UK.
A Sarah
AS
Walker
Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DU, UK.
Derrick W
DW
Crook
1] Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DU, UK [2] Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford OX3 7BN, UK.
Daniel J
DJ
Wilson
D002876:Chromosomes, Bacterial / Q000235:genetics; D004251:DNA Transposable Elements / Q000235:genetics*; D022761:Gene Transfer, Horizontal / Q000235:genetics; D014644:Genetic Variation; D016680:Genome, Bacterial / Q000235:genetics*; D016013:Likelihood Functions; D015810:Linkage Disequilibrium / Q000235:genetics; D010802:Phylogeny; D011995:Recombination, Genetic; D013045:Species Specificity; D013211:Staphylococcus aureus / Q000235:genetics* / Q000302:isolation & purification
D004251:DNA Transposable Elements