Revisiting the intrageneric structure of the genusPseudomonaswith complete whole genome sequence information: Insights into Diversity and Host-related Genetic Determinants

Abstract

Genomic structure of the genus Pseudomonas 2 Abstract:Pseudomonas spp. exhibit considerable differences in virulence, host specificity, and colonization.Many severe clinical infections are caused by Pseudomonas spp., and these bacteria are also responsible for many plant diseases. Interestingly, a variety of Pseudomonas spp. may actually promote plant growth at the same time. Understanding genome variations that generate the tremendous diversity in Pseudomonas biology is important in reducing and controlling the incidence of diseases, and can also help predict the pathogenic potential of newly discovered strains. In this study, we aimed to elucidate the genome-wide population structure of Pseudomonas. With a data set of 704 Pseudomonas whole genome sequences representing 186 species, we calculated a genus wide pan-genome composed of 62,202 genes. The genomic structure of the genus Pseudomonas was explored by hierarchical clustering based on average nucleotide identity, and also by phylogeny analysis based on concatenated core-gene alignment. Interestingly, most species that may act as opportunistic human pathogen appear closely related and fall into one clade. Further comparative functional analyses indicate that Pseudomonas species that only live in natural habitats lack multiple functions involved in stress response, which are predominantly present in species that may act as opportunistic human pathogen. In summary, this study provided detailed insights into the dynamics of genome diversity of Pseudomonas, and revealed hostrelated genetic determinants, which might help the development of more targeted antibiotics for the treatment of clinical Pseudomonas infections.