Abstract
Advances in high-throughput DNA sequencing technologies have determined an explosion in the number of sequenced bacterial genomes. Comparative sequence analysis frequently reveals evidences of homologous recombination occurring with different mechanisms and rates in different species, but the large-scale use of computational methods to identify recombination events is hampered by their high computational costs. Here, we propose a new method to identify recombination events in large datasets of whole genome sequences. Using a filtering procedure of the gene conservation profiles of a test genome against a panel of strains, this algorithm identifies sets of contiguous genes acquired by homologous recombination. The locations of the recombination breakpoints are determined using a statistical test that is able to account for the differences in the natural rate of evolution between different genes. The algorithm was tested on a dataset of 75 genomes of Staphylococcus aureus and 50 genomes comprising different streptococcal species, and was able to detect intra-species recombination events in S. aureus and in Streptococcus pneumoniae. Furthermore, we found evidences of an inter-species exchange of genetic material between S. pneumoniae and Streptococcus mitis, a closely related commensal species that colonizes the same ecological niche. The method has been implemented in an R package, Reco, which is freely available from supplementary material, and provides a rapid screening tool to investigate recombination on a genome-wide scale from sequence data.
Highlights
Recombination, the integration of foreign DNA in the chromosome of an acceptor cell, is one of the major evolutionary forces in bacterial species
Since the efficiency of RecA-mediated recombination decreases with increasing sequence divergence [4], recombination events are far more likely to occur between closely related DNA sequences, homologous recombination is possible when the sequence identity between the recipient and donor strains is as small as 70% [5]
The extent to which recombination occurs in natural populations is either unknown or controversial but it is widely accepted that recombination plays a crucial role in the evolution of many bacterial species
Summary
Recombination, the integration of foreign DNA in the chromosome of an acceptor cell, is one of the major evolutionary forces in bacterial species. Homologous recombination occurs through the replacement of genomic segments with the homologous DNA from a donor of the same species, or from another, often closely related, species. Evidence of recombination involving the exchange of large chromosomal elements has been found in Staphylococcus aureus, involving the acquisition of sequences up to 557 kb [12]. These processes represent a major source of genomic diversity and are important in driving the emergence of clonal complexes and hypervirulent strains [10,11,12]
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