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Bioinformatics Advance Access published online on November 22, 2005
Bioinformatics, doi:10.1093/bioinformatics/bti793
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© The Author (2005). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org
Received July 27, 2005
Revised October 18, 2005
Accepted November 15, 2005

Article

Describing ancient horizontal gene transfers at the nucleotide and gene levels by comparative pathogenicity island genometrics

F. Collyn 1, L. Guy 2, M. Marceau 3, M. Simonet 3, and C.-A. H. Roten 2 *

1 Inserm E0364 - Université de Lille II, Faculté de Médecine Henri Warembourg, Institut Pasteur de Lille, 1 rue du Pr Calmette, F-59021 Lille, France; Département de Microbiologie Fondamentale, Bâtiment de Biologie, Faculté de Biologie et de Médecine, Université de Lausanne, CH-1015 Dorigny, Switzerland
2 Département de Microbiologie Fondamentale, Bâtiment de Biologie, Faculté de Biologie et de Médecine, Université de Lausanne, CH-1015 Dorigny, Switzerland
3 Inserm E0364 - Université de Lille II, Faculté de Médecine Henri Warembourg, Institut Pasteur de Lille, 1 rue du Pr Calmette, F-59021 Lille, France

* To whom correspondence should be addressed.
C.-A. H. Roten, E-mail: claude-alain.roten{at}unil.ch


  Abstract

Motivation: lateral gene transfer is a major mechanism contributing to bacterial genome dynamics and pathovar emergence via pathogenicity island (PAI) spreading. However, since few of these genomic exchanges are experimentally reproducible, it is difficult to establish evolutionary scenarios for the successive PAI transmissions between bacterial genera. Methods initially developed at the gene and/or nucleotide level for genomics, i.e. comparisons of concatenated sequences, ortholog frequency, gene order or dinucleotide usage, were combined and applied here to homologous PAIs: we call this approach comparative PAI genometrics".

Results: YAPI, a Yersinia PAI, and related islands were compared to measure evolutionary relationships between related modules. Through use of our genometric approach designed for tracking codon usage adaptation and gene phylogeny, an ancient inter-genus PAI transfer was oriented for the first time by characterizing the genomic environment in which the ancestral island emerged and its subsequent transfers to other bacterial genera.

Supplementary information: http://www.unil.ch/comparativegenometrics/collyn_et_al_2005/collyn.htm.


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