Abstract
BackgroundPublic 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.ResultsHere, 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.ConclusionThe 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: .
Highlights
Public databases contain multitude of complete bacterial genomes, including several genomes of the same species
Validation of segmentation parameters The loop coordinates of the E. coli K-12 and O157:H7 Sakai genomes validated by Hayashi et al [16] were used as a basis to define an alignment strategy and to develop a treatment of alignment results adapted to bacterial backbone/loop segmentations
These strains are known to belong to distantly related E. coli lineages [17] and their genomes are more distantly related between each other compared with genomes within other species [18]
Summary
Public databases contain multitude of complete bacterial genomes, including several genomes of the same species. Recent analyses have shown, using pairwise whole genome alignments, that it is possible to segment bacterial genomes into a common conserved backbone and strainspecific sequences called loops. There are mainly two kinds of approaches used for whole genome comparisons: whole proteome comparison studies and whole genomic sequence alignment studies. Both approaches are powerful tools to study genome organization and evolution rules with different time scale considerations. These approaches have been employed with success in a recent study comparing the genome of yeast S. cerevisiae to three related yeast species genomes [1,2]. Other resources provide precomputed alignments for genome of related species, such as EnteriX or Colibase for enterobacteria [9,10]
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