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Open Access Highly Accessed Research article

Impact of homologous and non-homologous recombination in the genomic evolution of Escherichia coli

Xavier Didelot1*, Guillaume Méric2, Daniel Falush3 and Aaron E Darling4

Author Affiliations

1 Department of Infectious Disease Epidemiology, Imperial College, Norfolk Place, London W2 1PG, UK

2 College of Medicine, Swansea University, Swansea, SA2 8PP, UK

3 Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, Leipzig 04103, Germany

4 Genome Center, University of California, Davis, CA 95616, USA

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BMC Genomics 2012, 13:256  doi:10.1186/1471-2164-13-256

Published: 19 June 2012

Abstract

Background

Escherichia coli is an important species of bacteria that can live as a harmless inhabitant of the guts of many animals, as a pathogen causing life-threatening conditions or freely in the non-host environment. This diversity of lifestyles has made it a particular focus of interest for studies of genetic variation, mainly with the aim to understand how a commensal can become a deadly pathogen. Many whole genomes of E. coli have been fully sequenced in the past few years, which offer helpful data to help understand how this important species evolved.

Results

We compared 27 whole genomes encompassing four phylogroups of Escherichia coli (A, B1, B2 and E). From the core-genome we established the clonal relationships between the isolates as well as the role played by homologous recombination during their evolution from a common ancestor. We found strong evidence for sexual isolation between three lineages (A+B1, B2, E), which could be explained by the ecological structuring of E. coli and may represent on-going speciation. We identified three hotspots of homologous recombination, one of which had not been previously described and contains the aroC gene, involved in the essential shikimate metabolic pathway. We also described the role played by non-homologous recombination in the pan-genome, and showed that this process was highly heterogeneous. Our analyses revealed in particular that the genomes of three enterohaemorrhagic (EHEC) strains within phylogroup B1 have converged from originally separate backgrounds as a result of both homologous and non-homologous recombination.

Conclusions

Recombination is an important force shaping the genomic evolution and diversification of E. coli, both by replacing fragments of genes with an homologous sequence and also by introducing new genes. In this study, several non-random patterns of these events were identified which correlated with important changes in the lifestyle of the bacteria, and therefore provide additional evidence to explain the relationship between genomic variation and ecological adaptation.