Short and long-term genome stability analysis of prokaryotic genomes

BMC Genomics

Research Article

Pietro Liò¹  Marie-France Sagot²  Matteo Brilli³  Vincent Lacroix⁴ 

[1] Computer Laboratory, University of Cambridge, 15 JJ Thompson Avenue, CB3 0FD, Cambridge, UK;INRIA, Grenoble Rhône-Alpes, Lyon, France;Laboratoire de Biométrie et Biologie Évolutive, Universitè Lyon 1 UMR CNRS, 5558, Lyon, France;INRIA, Grenoble Rhône-Alpes, Lyon, France;Laboratoire de Biométrie et Biologie Évolutive, Universitè Lyon 1 UMR CNRS, 5558, Lyon, France;Fondazione Edmund Mach/CRI - Functional genomics - Via Mach 1, 38010, San Michele all’Adige, Trento, Italy;Laboratoire de Biométrie et Biologie Évolutive, Universitè Lyon 1 UMR CNRS, 5558, Lyon, France;

关键词: Gene Cluster;    Gene Order;    Core Gene;    Phylogenetic Distance;    Accessory Gene;   

DOI  :  10.1186/1471-2164-14-309

 received in 2012-08-13, accepted in 2013-04-11,  发布年份 2013

来源: Springer

【 摘 要 】

BackgroundGene 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.ResultsWe 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.ConclusionIn 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.

【 授权许可】

CC BY   
© Brilli et al.; licensee BioMed Central Ltd. 2013