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Background  Drug treatments and vaccine designs against the opportunistic human pathogen  Pseudomonas aeruginosa  have multiple issues, all associated with the diverse genetic traits present in this pathogen, ranging from multi-drug resistant genes to the molecular machinery for the biosynthesis of biofilms. Several candidate vaccines against  P. aeruginosa  have been developed, which target the outer membrane proteins; however, major issues arise when attempting to establish complete protection against this pathogen due to its presumably genotypic variation at the strain level. To shed light on this concern, we proposed this study to assess the  P. aeruginosa  pangenome and its molecular evolution across multiple strains.    Results  The  P. aeruginosa  pangenome was estimated to contain more than 16,000 non-redundant genes, and approximately 15 % of these constituted the core genome. Functional analyses of the accessory genome indicated a wide presence of genetic elements directly associated with pathogenicity. An in-depth molecular evolution analysis revealed the full landscape of selection forces acting on the  P. aeruginosa  pangenome, in which purifying selection drives evolution in the genome of this human pathogen. We also detected distinctive positive selection in a wide variety of outer membrane proteins, with the data supporting the concept of substantial genetic variation in proteins probably recognized as antigens. Approaching the evolutionary information of genes under extremely positive selection, we designed a new Multi-Locus Sequencing Typing assay for an informative, rapid, and cost-effective genotyping of  P. aeruginosa  clinical isolates.    Conclusions  We report the unprecedented pangenome characterization of  P. aeruginosa  on a large scale, which included almost 200 bacterial genomes from one single species and a molecular evolutionary analysis at the pangenome scale. Evolutionary information presented here provides a clear explanation of the issues associated with the use of protein conjugates from pili, flagella, or secretion systems as antigens for vaccine design, which exhibit high genetic variation in terms of non-synonymous substitutions in  P. aeruginosa  strains.    Electronic supplementary material  The online version of this article (doi:10.1186/s12864-016-2364-4) contains supplementary material, which is available to authorized users.

Pangenome-wide and molecular evolution analyses of the Pseudomonas aeruginosa species