Abstract
BackgroundPhylogenetic methods are well-established bioinformatic tools for sequence analysis, allowing to describe the non-independencies of sequences because of their common ancestor. However, the evolutionary profiles of bacterial genes are often complicated by hidden paralogy and extensive and/or (multiple) horizontal gene transfer (HGT) events which make bifurcating trees often inappropriate. In this context, plasmid sequences are paradigms of network-like relationships characterizing the evolution of prokaryotes. Actually, they can be transferred among different organisms allowing the dissemination of novel functions, thus playing a pivotal role in prokaryotic evolution. However, the study of their evolutionary dynamics is complicated by the absence of universally shared genes, a prerequisite for phylogenetic analyses.ResultsTo overcome such limitations we developed a bioinformatic package, named Blast2Network (B2N), allowing the automatic phylogenetic profiling and the visualization of homology relationships in a large number of plasmid sequences. The software was applied to the study of 47 completely sequenced plasmids coming from Escherichia, Salmonella and Shigella spps.ConclusionThe tools implemented by B2N allow to describe and visualize in a new way some of the evolutionary features of plasmid molecules of Enterobacteriaceae; in particular it helped to shed some light on the complex history of Escherichia, Salmonella and Shigella plasmids and to focus on possible roles of unannotated proteins.The proposed methodology is general enough to be used for comparative genomic analyses of bacteria.
Highlights
Phylogenetic methods are well-established bioinformatic tools for sequence analysis, allowing to describe the non-independencies of sequences because of their common ancestor
Visual representation of sequence homology network B2N was used to study the relationships existing between homologous proteins from all the completely sequenced plasmids available from three γ-Proteobacterial genera: Escherichia, Shigella, Salmonella
We report that the tools implemented by B2N allow to describe and to visualize in a new way some of the evolutionary features of plasmid molecules of Enterobacteriaceae; the most important results obtained by B2N on the Enterobacteriaceae dataset are related to the possibility, by means of phylogenetic profiling and network relationships of proteins, to uncover some of the molecular history, which shaped the evolution of this group of plasmids
Summary
Phylogenetic methods are well-established bioinformatic tools for sequence analysis, allowing to describe the non-independencies of sequences because of their common ancestor. The evolutionary profiles of bacterial genes are often complicated by hidden paralogy and extensive and/or (multiple) horizontal gene transfer (HGT) events which make bifurcating trees often inappropriate. In this context, plasmid sequences are paradigms of networklike relationships characterizing the evolution of prokaryotes. The same plasmid can be hosted by different organisms inhabiting different environments (e.g.: pH, temperature and chemical composition) and cohabiting with different genetic backgrounds These factors may shape both the functional role(s) of the proteins, and the compositional features of plasmid DNA, such as GC or oligomers contents, some of the last being a very specific signature even at close phylogenetic distances [10]
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