Systematic determination of the mosaic structure of bacterial genomes: species backbone versus strain-specific loops

Abstract

Background: Public databases now contain multitude of complete bacterial genomes, including several genomes of the same species. The available data offers new opportunities to address questions about bacterial genome evolution, a task that requires reliable fine comparison data of closely related genomes. Recent analyses have shown, using pairwise whole genome alignments, that it is possible to segment bacterial genomes into a common conserved backbone and strain-specific sequences called loops.

Results: Here, we generalize this approach and propose a strategy that allows systematic and non-biased genome segmentation based on multiple genome alignments. Segmentation analyses, as applied to 13 different bacterial species, confirmed the feasibility of our approach to discern the 'mosaic' organization of bacterial genomes. Segmentation results are available through a Web interface permitting functional analysis, extraction and visualization of the backbone/loops structure of documented genomes. To illustrate the potential of this approach, we performed a precise analysis of the mosaic organization of three E. coli strains and functional characterization of the loops.

Conclusion: The segmentation results including the backbone/loops structure of 13 bacterial species genomes are new and available for use by the scientific community at the URL: http://genome.jouy.inra.fr/mosaic.

Figure 1

Flow diagram of bacterial genomes segmentation in MOSAIC. The bacterial genomes segmentation includes four main steps in MOSAIC: NCBI bacterial genomes selection using Mummer and MGA, processing of genome alignments using MGA, backbone/loops segmentation and database integration using Perl scripts.

Figure 2

Graphical visualization of the backbone/loop structure available through the Web interface of Mosaic. 'Physical map' mode of MOSAIC corresponding to the graphical visualization of a 15 kb portion of the E. coli K-12, O157:H7 Sakai and CFT073 segmented genomes (data correspond to the comparison of three E. coli strains described in results). Genbank annotations are indicated with coloured arrows. Supplementary annotations are indicated as red boxes. Backbone is indicated in grey whereas loops appear in green.

Figure 3

Distribution of the loop sizes of three E. coli genomes (K-12, SAKAI and CFT073). Loop sizes range from 20 bp to 40 120 to 151 690 bp. Log10 scale is used on the x-axis.