Genome-based evolutionary history of Pseudomonas spp

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.

doi:10.1111/1462-2920.14130

Title: Genome-based evolutionary history of Pseudomonas spp

Journal Article · 06 April 2018 · Environmental Microbiology

DOI: https://doi.org/10.1111/1462-2920.14130 · OSTI ID:1529110

Hesse, Cedar ^[1];

^[2]; Bull, Carolee T. ^[3]; Shaffer, Brenda T. ^[1]; Yan, Qing ^[4]; Shapiro, Nicole ^[2]; Hassan, Karl A. ^[5]; Varghese, Neha ^[2]; Elbourne, Liam D. H. ^[6]; Paulsen, Ian T. ^[6]; Kyrpides, Nikos ^[2]; Woyke, Tanja ^[2];

^[7]

US Dept. of Agriculture (USDA), Corvallis OR (United States). Agricultural Research Service, Horticultural Crops Research Lab.
USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
Pennsylvania State Univ., University Park, PA (United States). Dept. of Plant Pathology and Environmental Microbiology
Oregon State Univ., Corvallis, OR (United States). Dept. of Botany and Plant Pathology
Univ. of Newcastle, Callaghan NSW (Australia). School of Environmental and Life Sciences
Macquarie Univ., NSW (Australia). Dept. of Molecular Sciences
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

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.

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Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States). National Energy Research Scientific Computing Center (NERSC)

Sponsoring Organization:: USDOE Office of Science (SC)

Grant/Contract Number:: AC02-05CH11231

OSTI ID:: 1529110

Alternate ID(s):: OSTI ID: 1461210

Journal Information:: Environmental Microbiology, Vol. 20, Issue 6; ISSN 1462-2912

Publisher:: WileyCopyright Statement

Country of Publication:: United States

Language:: English

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Cited by: 116 works

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A Rare Thioquinolobactin Siderophore Present in a Bioactive Pseudomonas sp. DTU12.1 Sazinas, Pavelas; Hansen, Morten Lindqvist; Aune, May Iren Genome Biology and Evolution, Vol. 11, Issue 12 https://doi.org/10.1093/gbe/evz267	journal	December 2019
Genomic and metabolic differences between Pseudomonas putida populations inhabiting sugarcane rhizosphere or bulk soil Lopes, Lucas Dantas; Weisberg, Alexandra J.; Davis, Edward W. PLOS ONE, Vol. 14, Issue 10 https://doi.org/10.1371/journal.pone.0223269	journal	October 2019
Genome-Based Analysis Reveals the Taxonomy and Diversity of the Family Idiomarinaceae Liu, Yang; Lai, Qiliang; Shao, Zongze Frontiers in Microbiology, Vol. 9 https://doi.org/10.3389/fmicb.2018.02453	journal	October 2018
In silico and Genetic Analyses of Cyclic Lipopeptide Synthetic Gene Clusters in Pseudomonas sp. 11K1 Zhao, Hui; Liu, Yan-Ping; Zhang, Li-Qun Frontiers in Microbiology, Vol. 10 https://doi.org/10.3389/fmicb.2019.00544	journal	March 2019
Biological Control Agents Against Fusarium Wilt of Banana Bubici, Giovanni; Kaushal, Manoj; Prigigallo, Maria Isabella Frontiers in Microbiology, Vol. 10 https://doi.org/10.3389/fmicb.2019.00616	journal	April 2019

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