Diversity of Pseudomonas Genomes, Including Populus-Associated Isolates, as Revealed by Comparative Genome Analysis

作者：Se‐Ran Jun, Trudy M. Wassenaar, Intawat Nookaew, Loren Hauser, Visanu Wanchai, Miriam Land, Collin M. Timm, Tse-Yuan S. Lu, Christopher W. Schadt, Mitchel J. Doktycz, Dale A. Pelletier, David Wayne Ussery · 发表于：Applied and Environmental Microbiology · 年份：2015 · DOI：10.1128/aem.02612-15 · 被引用次数：91 · 研究领域：Plant-Microbe Interactions and Immunity、Genomics and Phylogenetic Studies、Legume Nitrogen Fixing Symbiosis

The Pseudomonas genus contains a metabolically versatile group of organisms that are known to occupy numerous ecological niches, including the rhizosphere and endosphere of many plants. Their diversity influences the phylogenetic diversity and heterogeneity of these communities. On the basis of average amino acid identity, comparative genome analysis of >1,000 Pseudomonas genomes, including 21 Pseudomonas strains isolated from the roots of native Populus deltoides (eastern cottonwood) trees resulted in consistent and robust genomic clusters with phylogenetic homogeneity. All Pseudomonas aeruginosa genomes clustered together, and these were clearly distinct from other Pseudomonas species groups on the basis of pangenome and core genome analyses. In contrast, the genomes of Pseudomonas fluorescens were organized into 20 distinct genomic clusters, representing enormous diversity and heterogeneity. Most of our 21 Populus-associated isolates formed three distinct subgroups within the major P. fluorescens group, supported by pathway profile analysis, while two isolates were more closely related to Pseudomonas chlororaphis and Pseudomonas putida. Genes specific to Populus-associated subgroups were identified. Genes specific to subgroup 1 include several sensory systems that act in two-component signal transduction, a TonB-dependent receptor, and a phosphorelay sensor. Genes specific to subgroup 2 contain hypothetical genes, and genes specific to subgroup 3 were annotated with hydrol...