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

Mau, B; Glasner, JD; Darling, AE; Perna, NT

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

Mau, B Glasner, JD Darling, AE

Perna, NT

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Publication Type:: Journal Article
Citation:: Genome Biology, 2006, 7 (5)
Issue Date:: 2006-05-31

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Field	Value	Language
dc.contributor.author	Mau, B	en_US
dc.contributor.author	Glasner, JD	en_US
dc.contributor.author	Darling, AE https://orcid.org/0000-0003-2397-7925	en_US
dc.contributor.author	Perna, NT	en_US
dc.date.issued	2006-05-31	en_US
dc.identifier.citation	Genome Biology, 2006, 7 (5)	en_US
dc.identifier.issn	1474-760X	en_US
dc.identifier.uri	http://hdl.handle.net/10453/23569
dc.description.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. © 2006 Mau et al.; licensee BioMed Central Ltd.	en_US
dc.relation.ispartof	Genome Biology	en_US
dc.relation.isbasedon	10.1186/gb-2006-7-5-r44	en_US
dc.subject.classification	Bioinformatics	en_US
dc.title	Genome-wide detection and analysis of homologous recombination among sequenced strains of Escherichia coli	en_US
dc.type	Journal Article
utslib.citation.volume	5	en_US
utslib.citation.volume	7	en_US
utslib.for	0605 Microbiology	en_US
utslib.for	05 Environmental Sciences	en_US
utslib.for	06 Biological Sciences	en_US
utslib.for	08 Information and Computing Sciences	en_US
pubs.embargo.period	Not known	en_US
pubs.organisational-group	/University of Technology Sydney
pubs.organisational-group	/University of Technology Sydney/Faculty of Science
pubs.organisational-group	/University of Technology Sydney/Strength - ithree - Institute of Infection, Immunity and Innovation
utslib.copyright.status	closed_access
pubs.issue	5	en_US
pubs.publication-status	Published	en_US
pubs.volume	7	en_US

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. © 2006 Mau et al.; licensee BioMed Central Ltd.

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http://hdl.handle.net/10453/23569