The Gene Flow between Plasmids and Chromosomes: Insights from Bioinformatics Analyses

Abstract

Despite the key-role of plasmids in the horizontal spreading of genetic information within the prokaryotic community, their evolutionary dynamics has been poorly explored. Recently, a computational pipeline (Blast2Network) based on similarity networks reconstruction has been developed. Adopting this strategy we analyzed the genome of Synechococcus sp. PCC 7002, a cyanobacterium that possesses six plasmids and one chromosome and that can be considered as a model microorganism to analyze the interrelationships existing between different plasmids and between plasmids and chromosome. The aims of our work were: i) the identification and the analysis of the possible evolutionary relationships existing within and among the six Synechococcus sp. PCC 7002 plasmids at both intra- and intermolecular level, ii) the analysis of the gene flow (if any) existing between chromosome and plasmids of different size inhabiting the same cytoplasm. A deep analysis of the obtained networks suggested that i) intra-molecular rearrangements did not occur very recently in evolution of plasmids; ii) evolutionary relationships exist between both plasmids and plasmids and chromosome; iii) these exchanges may involve a single gene, operons or gene clusters. Besides, the overall degree of sequence identity/similarity shared by interconnected proteins suggests that plasmids are more prone to recombine between them rather than with chromosome.