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Mol Biol Evol. 2014 Jun;31(6):1593-605. doi: 10.1093/molbev/msu082. Epub 2014 Feb 27.

Efficient inference of recombination hot regions in bacterial genomes.

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Department of Medical Genome Sciences, Graduate School of Frontier Sciences, University of Tokyo, Tokyo, JapanInstitute of Medical Science, University of Tokyo, Tokyo, JapanInstitute of Life Science, College of Medicine, Swansea University, Swansea, United Kingdom.
Department of Infectious Disease Epidemiology, Imperial College London, London, United Kingdom.
Department of Statistics, University of Oxford, Oxford, United Kingdom.
Institute of Life Science, College of Medicine, Swansea University, Swansea, United Kingdom.
Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany


In eukaryotes, detailed surveys of recombination rates have shown variation at multiple genomic scales and the presence of "hotspots" of highly elevated recombination. In bacteria, studies of recombination rate variation are less developed, in part because there are few analysis methods that take into account the clonal context within which bacterial evolution occurs. Here, we focus in particular on identifying "hot regions" of the genome where DNA is transferred frequently between isolates. We present a computationally efficient algorithm based on the recently developed "chromosome painting" algorithm, which characterizes patterns of haplotype sharing across a genome. We compare the average genome wide painting, which principally reflects clonal descent, with the painting for each site which additionally reflects the specific deviations at the site due to recombination. Using simulated data, we show that hot regions have consistently higher deviations from the genome wide average than normal regions. We applied our approach to previously analyzed Escherichia coli genomes and revealed that the new method is highly correlated with the number of recombination events affecting each site inferred by ClonalOrigin, a method that is only applicable to small numbers of genomes. Furthermore, we analyzed recombination hot regions in Campylobacter jejuni by using 200 genomes. We identified three recombination hot regions, which are enriched for genes related to membrane proteins. Our approach and its implementation, which is downloadable from, will help to develop a new phase of population genomic studies of recombination in prokaryotes.


chromosome painting; homologous recombination; population genomics; recombination hot region; recombination hotspot; selection

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