Inferring genomic flux in bacteria

Didelot, Xavier, Darling, Aaron and Falush, Daniel (2009) Inferring genomic flux in bacteria. Genome Research, 19 2: 306-317. doi:10.1101/gr.082263.108

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Author Didelot, Xavier
Darling, Aaron
Falush, Daniel
Title Inferring genomic flux in bacteria
Journal name Genome Research   Check publisher's open access policy
ISSN 1088-9051
Publication date 2009-02
Sub-type Article (original research)
DOI 10.1101/gr.082263.108
Open Access Status File (Publisher version)
Volume 19
Issue 2
Start page 306
End page 317
Total pages 12
Place of publication Cold Spring Harbor, NY, United States
Publisher Cold Spring Harbor Laboratory Press
Language eng
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.
Keyword Group-a streptococcus
Q-Index Code C1
Q-Index Status Provisional Code
Institutional Status UQ

Document type: Journal Article
Sub-type: Article (original research)
Collection: Institute for Molecular Bioscience - Publications
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Citation counts: TR Web of Science Citation Count  Cited 19 times in Thomson Reuters Web of Science Article | Citations
Scopus Citation Count Cited 24 times in Scopus Article | Citations
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Created: Thu, 03 Sep 2009, 08:51:35 EST by Mr Andrew Martlew on behalf of Institute for Molecular Bioscience