title: Gene flow, recombination, and positive selection in Stenotrophomonas maltophilia: mechanisms underlying the diversity of the widespread opportunistic pathogen.
abstract: Stenotrophomonas maltophilia is a global multidrug-resistant human opportunistic pathogen in clinical environments. Stenotrophomonas maltophilia is 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. maltophilia and 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 genomes were 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 a better understanding of its evolutionary dynamics and its relationship with genome diversity.
authors.affiliation: a Beijing Institute of Biotechnology, Beijing, China.|b Institute of Translational Medicine, The Second Military Medical University, Shanghai, China.
authors.forename: Dong
authors.initials: D
authors.lastname: Yu
authors.affiliation: a Beijing Institute of Biotechnology, Beijing, China.|c College of Life Science, Anhui University, Hefei, Anhui, China.
authors.forename: Zhiqiu
authors.initials: Z
authors.lastname: Yin
authors.affiliation: a Beijing Institute of Biotechnology, Beijing, China.
authors.forename: Beiping
authors.initials: B
authors.lastname: Li
authors.affiliation: a Beijing Institute of Biotechnology, Beijing, China.
authors.forename: Yuan
authors.initials: Y
authors.lastname: Jin
authors.affiliation: a Beijing Institute of Biotechnology, Beijing, China.
authors.forename: Hongguang
authors.initials: H
authors.lastname: Ren
authors.affiliation: a Beijing Institute of Biotechnology, Beijing, China.
authors.forename: Jing
authors.initials: J
authors.lastname: Zhou
authors.affiliation: a Beijing Institute of Biotechnology, Beijing, China.
authors.forename: Wei
authors.initials: W
authors.lastname: Zhou
authors.affiliation: a Beijing Institute of Biotechnology, Beijing, China.|c College of Life Science, Anhui University, Hefei, Anhui, China.
authors.forename: Long
authors.initials: L
authors.lastname: Liang
authors.affiliation: a Beijing Institute of Biotechnology, Beijing, China.
authors.forename: Junjie
authors.initials: J
authors.lastname: Yue
mesh_terms: D001426:Bacterial Proteins / Q000235:genetics; D019143:Evolution, Molecular; D051456:Gene Flow; D014644:Genetic Variation; D016680:Genome, Bacterial; D016905:Gram-Negative Bacterial Infections / Q000382:microbiology; D006801:Humans; D009894:Opportunistic Infections / Q000382:microbiology; D010802:Phylogeny; D011995:Recombination, Genetic; D012641:Selection, Genetic; D020615:Stenotrophomonas maltophilia / Q000145:classification / Q000235:genetics*
chemical_list: D001426:Bacterial Proteins
keywords: Stenotrophomonas maltophilia; diversité génétique; gain de gènes; gene gain; gene loss; genetic diversity; perte de gènes; positive selection; recombinaison; recombination; sélection positive