Research

Genome-wide detection and analysis of homologous recombination among sequenced strains of Escherichia coli

Bob Mau^1,2,3 , Jeremy D Glasner³ , Aaron E Darling⁴ and Nicole T Perna^3,5

¹  Department of Mathematics, Lincoln Drive, University of Wisconsin, Madison WI 53706, USA

²  Department of Oncology, University Ave, University of Wisconsin, Madison WI 53706, USA

³  Genome Center of Wisconsin, Henry Mall, University of Wisconsin, Madison WI 53706, USA

⁴  Department of Computer Science, W. Dayton St, University of Wisconsin, Madison WI 53706, USA

⁵  Department of Animal Health and Biomedical Sciences, Linden Drive, University of Wisconsin, Madison WI 53706, USA

author email corresponding author email

Genome Biology 2006, 7:R44doi:10.1186/gb-2006-7-5-r44

Published:	31 May 2006

Subject areas: Evolution, Genome studies, Model organisms

Abstract

Background

Comparisons of complete bacterial genomes reveal evidence of lateral transfer of DNA across otherwise clonally diverging lineages. Some lateral transfer events result in acquisition of novel genomic segments and are easily detected through genome comparison. Other more subtle lateral transfers involve homologous recombination events that result in substitution of alleles within conserved genomic regions. This type of event is observed infrequently among distantly related organisms. It is reported to be more common within species, but the frequency has been difficult to quantify since the sequences under comparison tend to have relatively few polymorphic sites.

Results

Here we report a genome-wide assessment of homologous recombination among a collection of six complete Escherichia coli and Shigella flexneri genome sequences. We construct a whole-genome multiple alignment and identify clusters of polymorphic sites that exhibit atypical patterns of nucleotide substitution using a random walk-based method. The analysis reveals one large segment (approximately 100 kb) and 186 smaller clusters of single base pair differences that suggest lateral exchange between lineages. These clusters include portions of 10% of the 3,100 genes conserved in six genomes. Statistical analysis of the functional roles of these genes reveals that several classes of genes are over-represented, including those involved in recombination, transport and motility.

Conclusion

We demonstrate that intraspecific recombination in E. coli is much more common than previously appreciated and may show a bias for certain types of genes. The described method provides high-specificity, conservative inference of past recombination events.