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Title: Genome-based evolutionary history of Pseudomonas spp

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. Here, 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.

Authors:
 [1]; ORCiD logo [2];  [3];  [1];  [4];  [2];  [5];  [2];  [6];  [6];  [2];  [2]; ORCiD logo [7]
  1. US Dept. of Agriculture (USDA), Corvallis OR (United States). Agricultural Research Service, Horticultural Crops Research Lab.
  2. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
  3. Pennsylvania State Univ., University Park, PA (United States). Dept. of Plant Pathology and Environmental Microbiology
  4. Oregon State Univ., Corvallis, OR (United States). Dept. of Botany and Plant Pathology
  5. Univ. of Newcastle, Callaghan NSW (Australia). School of Environmental and Life Sciences
  6. Macquarie Univ., NSW (Australia). Dept. of Molecular Sciences
  7. US Dept. of Agriculture (USDA), Corvallis OR (United States). Agricultural Research Service, Horticultural Crops Research Lab.; Oregon State Univ., Corvallis, OR (United States). Dept. of Botany and Plant Pathology
Publication Date:
Research Org.:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). National Energy Research Scientific Computing Center (NERSC)
Sponsoring Org.:
USDOE Office of Science (SC)
OSTI Identifier:
1529110
Alternate Identifier(s):
OSTI ID: 1461210
Grant/Contract Number:  
AC02-05CH11231
Resource Type:
Accepted Manuscript
Journal Name:
Environmental Microbiology
Additional Journal Information:
Journal Volume: 20; Journal Issue: 6; Journal ID: ISSN 1462-2912
Publisher:
Wiley
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES

Citation Formats

Hesse, Cedar, Schulz, Frederik, Bull, Carolee T., Shaffer, Brenda T., Yan, Qing, Shapiro, Nicole, Hassan, Karl A., Varghese, Neha, Elbourne, Liam D. H., Paulsen, Ian T., Kyrpides, Nikos, Woyke, Tanja, and Loper, Joyce E. Genome-based evolutionary history of Pseudomonas spp. United States: N. p., 2018. Web. doi:10.1111/1462-2920.14130.
Hesse, Cedar, Schulz, Frederik, Bull, Carolee T., Shaffer, Brenda T., Yan, Qing, Shapiro, Nicole, Hassan, Karl A., Varghese, Neha, Elbourne, Liam D. H., Paulsen, Ian T., Kyrpides, Nikos, Woyke, Tanja, & Loper, Joyce E. Genome-based evolutionary history of Pseudomonas spp. United States. https://doi.org/10.1111/1462-2920.14130
Hesse, Cedar, Schulz, Frederik, Bull, Carolee T., Shaffer, Brenda T., Yan, Qing, Shapiro, Nicole, Hassan, Karl A., Varghese, Neha, Elbourne, Liam D. H., Paulsen, Ian T., Kyrpides, Nikos, Woyke, Tanja, and Loper, Joyce E. Fri . "Genome-based evolutionary history of Pseudomonas spp". United States. https://doi.org/10.1111/1462-2920.14130. https://www.osti.gov/servlets/purl/1529110.
@article{osti_1529110,
title = {Genome-based evolutionary history of Pseudomonas spp},
author = {Hesse, Cedar and Schulz, Frederik and Bull, Carolee T. and Shaffer, Brenda T. and Yan, Qing and Shapiro, Nicole and Hassan, Karl A. and Varghese, Neha and Elbourne, Liam D. H. and Paulsen, Ian T. and Kyrpides, Nikos and Woyke, Tanja and Loper, Joyce E.},
abstractNote = {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. Here, 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.},
doi = {10.1111/1462-2920.14130},
journal = {Environmental Microbiology},
number = 6,
volume = 20,
place = {United States},
year = {2018},
month = {4}
}

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