Inferring genomic flux in bacteria
- 1 Department of Statistics, University of Warwick, Coventry CV4 7AL, United Kingdom;
- 2 Institute for Molecular Bioscience, University of Queensland, St. Lucia QLD 4072, Australia;
- 3 Environmental Research Institute, Department of Microbiology, University College Cork, Cork, Ireland
Abstract
Acquisition and loss of genetic material are essential forces in bacterial microevolution. They have been repeatedly linked with adaptation of lineages to new lifestyles, and in particular, pathogenicity. Comparative genomics has the potential to elucidate this genetic flux, but there are many methodological challenges involved in inferring evolutionary events from collections of genome sequences. Here we describe a model-based method for using whole-genome sequences to infer the patterns of genome content evolution. A fundamental property of our model is that it allows the rates at which genetic elements are gained or lost to vary in time and from one lineage to another. Our approach is purely sequence based, and does not rely on gene identification. We show how inference can be performed under our model and illustrate its use on three datasets from Francisella tularensis, Streptococcus pyogenes, and Escherichia coli. In all three examples, we found interesting variations in the rates of genetic material gain and loss, which strongly correlate with their lifestyle. The algorithms we describe are implemented in a computer software named GenoPlast.
Footnotes
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↵4 Present address: Genome Center, University of California, Davis, CA 95616, USA.
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↵5 Corresponding author.
↵E-mail X.Didelot{at}warwick.ac.uk; fax 44-02476-524532.
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[Supplemental material is available online at www.genome.org. The GenoPlast software is freely available from http://go.warwick.ac.uk/genoplast/.]
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Article published online before print. Article and publication date are at http://www.genome.org/cgi/doi/10.1101/gr.082263.108.
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- Received June 18, 2008.
- Accepted October 29, 2008.
- Copyright © 2009 by Cold Spring Harbor Laboratory Press
