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ARS Home » Pacific West Area » Corvallis, Oregon » Horticultural Crops Disease and Pest Management Research Unit » Research » Publications at this Location » Publication #357689

Research Project: Development of Knowledge-based Approaches for Disease Management in Small Fruit and Nursery Crops

Location: Horticultural Crops Disease and Pest Management Research Unit

Title: Genome-based evolutionary history of Pseudomonas spp

item Hesse, Cedar
item SCHULZ, FREDERIK - Joint Genome Institute
item BULL, CAROLEE - Pennsylvania State University
item Shaffer, Brenda
item YAN, QING - Oregon State University
item SHAPIRO, NICOLE - Joint Genome Institute
item HASSAN, KARL - University Of Newcastle
item VARGHESE, NEHA - Joint Genome Institute
item ELBOURNE, LIAM - Macquarie University
item PAULSEN, IAN - Macquarie University
item KYRPIDES, NIKOS - Joint Genome Institute
item WOYKE, TANJA - Joint Genome Institute
item LOPER, JOYCE - Oregon State University

Submitted to: Environmental Microbiology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/3/2018
Publication Date: 8/17/2018
Citation: Hesse, C.N., Schulz, F., Bull, C.T., Shaffer, B.T., Yan, Q., Shapiro, N., Hassan, K.A., Varghese, N., Elbourne, L.D., Paulsen, I.T., Kyrpides, N., Woyke, T., Loper, J.E. 2018. Genome-based evolutionary history of Pseudomonas spp. Environmental Microbiology. 20(6):2142–2159.

Interpretive Summary: We analyzed the type strain genomes of 163 species of the agronomically important bacterial genus Pseudomonas. 118 type strain genomes were sequenced and assembled as part of this work. nalysis of these genomes provided the most comprehensive evolutionary understanding of the genus to date. Additionally, 394 potential new species of Pseudomonas were identified from complete genome sequences of non-type strain isolates. Comparative analysis of type strain genomes revealed genes associated with the production of the Pyoluteorin antibiotic were more prevalent than previously thought and are not constrained to the P. fluorescens group. Taken together, this work provides a comprehensive evolutionary framework for subsequent studies in the genus and contributes a wealth of new genomes to the public domain.

Technical Abstract: Pseudomonas is a large and diverse genus of Gammaproteobacteria. To provide a framework for discovery of evolutionary and taxonomic relationships of these bacteria, we compared the genomes of type strains of 163 species and 3 additional subspecies of Pseudomonas, including 118 genomes sequenced herein. A maximum likelihood phylogeny of the 166 type strains based on protein sequences of 100 single-copy orthologous genes revealed thirteen groups of Pseudomonas, composed of two to sixty three species each. Pairwise average nucleotide identities and alignment fractions were calculated for the data set of the 166 type strains and 1224 genomes of Pseudomonas available in public databases. Results revealed that 394 of the 1224 genomes were distinct from any type strain, suggesting that the type strains represent only a fraction of the genomic diversity of the genus. The core genome of Pseudomonas was determined to contain 794 genes conferring primarily housekeeping functions. The results of this study provide a phylogenetic framework for future studies aiming to resolve the classification and phylogenetic relationships, identify new gene functions and phenotypes, and explore the ecological and metabolic potential of the Pseudomonas spp.