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Open Access Highly Accessed Research article

Short and long-term genome stability analysis of prokaryotic genomes

Matteo Brilli124*, Pietro Liò3, Vincent Lacroix2 and Marie-France Sagot12

Author affiliations

1 INRIA, Grenoble Rhône-Alpes, Lyon, France

2 Laboratoire de Biométrie et Biologie Évolutive, Universitè Lyon 1 UMR CNRS 5558, Lyon, France

3 Computer Laboratory, University of Cambridge, 15 JJ Thompson Avenue, Cambridge, CB3 0FD, UK

4 Present address: Fondazione Edmund Mach/CRI - Functional genomics - Via Mach 1, 38010 San Michele all’Adige, Trento, Italy

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Citation and License

BMC Genomics 2013, 14:309  doi:10.1186/1471-2164-14-309

Published: 8 May 2013

Abstract

Background

Gene organization dynamics is actively studied because it provides useful evolutionary information, makes functional annotation easier and often enables to characterize pathogens. There is therefore a strong interest in understanding the variability of this trait and the possible correlations with life-style. Two kinds of events affect genome organization: on one hand translocations and recombinations change the relative position of genes shared by two genomes (i.e. the backbone gene order); on the other, insertions and deletions leave the backbone gene order unchanged but they alter the gene neighborhoods by breaking the syntenic regions. A complete picture about genome organization evolution therefore requires to account for both kinds of events.

Results

We developed an approach where we model chromosomes as graphs on which we compute different stability estimators; we consider genome rearrangements as well as the effect of gene insertions and deletions. In a first part of the paper, we fit a measure of backbone gene order conservation (hereinafter called backbone stability) against phylogenetic distance for over 3000 genome comparisons, improving existing models for the divergence in time of backbone stability. Intra- and inter-specific comparisons were treated separately to focus on different time-scales. The use of multiple genomes of a same species allowed to identify genomes with diverging gene order with respect to their conspecific. The inter-species analysis indicates that pathogens are more often unstable with respect to non-pathogens. In a second part of the text, we show that in pathogens, gene content dynamics (insertions and deletions) have a much more dramatic effect on genome organization stability than backbone rearrangements.

Conclusion

In this work, we studied genome organization divergence taking into account the contribution of both genome order rearrangements and genome content dynamics. By studying species with multiple sequenced genomes available, we were able to explore genome organization stability at different time-scales and to find significant differences for pathogen and non-pathogen species. The output of our framework also allows to identify the conserved gene clusters and/or partial occurrences thereof, making possible to explore how gene clusters assembled during evolution.