Gene Flow, recombination, and positive selection in Stenotrophomonas maltophilia genomes: mechanisms underlying the diversity of the widespread opportunistic pathogen

S.maltophilia is a global multidrug-resistant human opportunistic pathogen in clinical environments. S. maltophiliais also ubiquitous in aqueous environments, soil and plants. Various molecular typing methods have revealed that S.maltophilia exhibits high levels of phenotypic and genotypic diversity. However, information regarding the genomic diversity within S. maltophiliaand the corresponding genetic mechanisms resulting in said diversity remain scarce. The genome sequences of 17 S.maltophilia strains were selected to investigate the mechanisms contributing to genetic diversity at the genome level. The core and large pan genomes of the species were first estimated, resulting in a large, open pan genome. A species phylogeny was also reconstructed based on 344 orthologous genes with one copy per genome, and the contribution of four evolutionary mechanisms to the species genome diversity was quantified: 15%-35% of the genes showed evidence for recombination, 0-25% of the genes in one genome were likely gained, 0-44% of the genes in some genomeswere likely lost, and less than 0.3% of the genes in a genome were under positive selection pressures. We observed that, among the four main mechanisms, homologous recombination plays a key role in maintaining diversity in S.maltophilia. In this study, we provide an overview of evolution in S.maltophilia to provide abetter understanding of its evolutionary dynamics and its relationship with genome diversity.The accepted manuscript in pdf format is listed with the files at the bottom of this page. The presentation of the authors' names and (or) special characters in the title of the manuscript may differ slightly between what is listed on this page and what is listed in the pdf file of the accepted manuscript; that in the pdf file of the accepted manuscript is what was submitted by the author