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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 Laboratory (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:
Journal Article: 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. 2018. "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},
url = {https://www.osti.gov/biblio/1529110}, journal = {Environmental Microbiology},
issn = {1462-2912},
number = 6,
volume = 20,
place = {United States},
year = {Fri Apr 06 00:00:00 EDT 2018},
month = {Fri Apr 06 00:00:00 EDT 2018}
}

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Works referenced in this record:

Full-Genome Sequence of the Plant Growth-Promoting Bacterium Pseudomonas protegens CHA0
journal, March 2014


On the molecular mechanism of GC content variation among eubacterial genomes
journal, January 2012


DNA sequence-based analysis of the Pseudomonas species
journal, March 2010


What It Takes to Be a Pseudomonas aeruginosa? The Core Genome of the Opportunistic Pathogen Updated
journal, May 2015


Real-Time DNA Sequencing from Single Polymerase Molecules
journal, January 2009


Dynamic Evolution of Pathogenicity Revealed by Sequencing and Comparative Genomics of 19 Pseudomonas syringae Isolates
journal, July 2011


Evidence for Diversifying Selection at the Pyoverdine Locus of Pseudomonas aeruginosa
journal, March 2005


1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life
journal, June 2017


An Improved General Amino Acid Replacement Matrix
journal, April 2008


Correction for Bartoli et al., Whole-Genome Sequencing of 10 Pseudomonas syringae Strains Representing Different Host Range Spectra: TABLE 1
journal, June 2015


Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data
journal, May 2013


High-quality draft assemblies of mammalian genomes from massively parallel sequence data
journal, December 2010


Pangenome-wide and molecular evolution analyses of the Pseudomonas aeruginosa species
journal, January 2016


Deciphering the Rhizosphere Microbiome for Disease-Suppressive Bacteria
journal, May 2011


ExaML version 3: a tool for phylogenomic analyses on supercomputers
journal, March 2015


Pseudomonas rhizosphaerae sp. nov., a novel species that actively solubilizes phosphate in vitro
journal, November 2003


Pseudomonas silesiensis sp. nov. strain A3 T isolated from a biological pesticide sewage treatment plant and analysis of the complete genome sequence
journal, January 2018


Solexa Ltd
journal, June 2004


Characterization of the core and accessory genomes of Pseudomonas aeruginosa using bioinformatic tools Spine and AGEnt
journal, January 2014


Complete Genome Sequence of the Type Strain Pseudomonas stutzeri CGMCC 1.1803
journal, October 2011


High quality draft genome sequence of the type strain of Pseudomonas lutea OK2T, a phosphate-solubilizing rhizospheric bacterium
journal, August 2016


The Aerobic Pseudomonads a Taxonomic Study
journal, May 1966


FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments
journal, March 2010


Iron uptake and metabolism in pseudomonads
journal, March 2010


Phytopathogen Genome Announcement: Draft Genome Sequences of 62 Pseudomonas syringae Type and Pathotype Strains
journal, April 2016


Genomic Encyclopedia of Type Strains, Phase I: The one thousand microbial genomes (KMG-I) project
journal, December 2013


Alternative Pathways of Carbohydrate Utilization in Pseudomonads
journal, October 1984


Metagenomics of petroleum muck: revealing microbial diversity and depicting microbial syntrophy
journal, May 2014


Microbial species delineation using whole genome sequences
journal, July 2015


Genomic and Genetic Diversity within the Pseudomonas fluorescens Complex
journal, February 2016


MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability
journal, January 2013


Analysis of the core genome and pangenome of P seudomonas putida : The
journal, September 2015


Velvet: Algorithms for de novo short read assembly using de Bruijn graphs
journal, February 2008


ETE 3: Reconstruction, Analysis, and Visualization of Phylogenomic Data
journal, February 2016


Phylogenomics and systematics in Pseudomonas
journal, March 2015


Taxonomic heterogeneity, as shown by siderotyping, of strains primarily identified as Pseudomonas putida
journal, November 2007


Defining the Pseudomonas Genus: Where Do We Draw the Line with Azotobacter?
journal, August 2011


Pseudomonas caeni sp. nov., a denitrifying bacterium isolated from the sludge of an anaerobic ammonium-oxidizing bioreactor
journal, July 2009


Complete genome sequence of the entomopathogenic and metabolically versatile soil bacterium Pseudomonas entomophila
journal, May 2006


Azotobacter vinelandii: a Pseudomonas in disguise?
journal, May 2004


Phylogeny of the genus Pseudomonas: intrageneric structure reconstructed from the nucleotide sequences of gyrB and rpoD genes
journal, October 2000


Accelerated Profile HMM Searches
journal, October 2011


Thiopseudomonas denitrificans gen. nov., sp. nov., isolated from anaerobic activated sludge
journal, October 2014


trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses
journal, June 2009


Chemistry and Biology of Pyoverdines, Pseudomonas Primary Siderophores
journal, December 2014


Pyoverdine siderophores: from biogenesis to biosignificance
journal, January 2007


Oblitimonas alkaliphila gen. nov., sp. nov., in the family Pseudomonadaceae, recovered from a historical collection of previously unidentified clinical strains
journal, August 2016


The rhizosphere microbiome and plant health
journal, August 2012


Pseudomonas helleri sp. nov. and Pseudomonas weihenstephanensis sp. nov., isolated from raw cow's milk
journal, March 2016


Nucleic Acid Homologies in the Genus Pseudomonas
journal, October 1973


Unearthing the genomes of plant-beneficial Pseudomonas model strains WCS358, WCS374 and WCS417
journal, July 2015


Green Fluorescent Pigment Accumulated by a Mutant of Cellvibrio Gilvus
journal, January 1964


Clarification of Taxonomic Status within the Pseudomonas syringae Species Group Based on a Phylogenomic Analysis
journal, December 2017


Probable synonymy of the nitrogen-fixing genus Azotobacter and the genus Pseudomonas
journal, December 2007


Genomics of secondary metabolite production by Pseudomonas spp.
journal, January 2009


antiSMASH 3.0—a comprehensive resource for the genome mining of biosynthetic gene clusters
journal, May 2015


Proteinortho: Detection of (Co-)orthologs in large-scale analysis
journal, April 2011


Identification of Novel Non-Metal Haloperoxidases from the Marine Metagenome
journal, June 2014


The current status on the taxonomy of Pseudomonas revisited: An update
journal, January 2018


Pseudomonas aeruginosa: all roads lead to resistance
journal, August 2011


IMG/M: integrated genome and metagenome comparative data analysis system
journal, October 2016


Erratum to: Diversity of Endosymbiotic Nostoc in Gunnera magellanica from Tierra del Fuego, Chile
journal, June 2013


Systematic discovery of pseudomonad genetic factors involved in sensitivity to tailocins
journal, March 2021


Full-Genome Sequence of the Plant Growth-Promoting Bacterium Pseudomonas protegens CHA0
text, January 2014


Dynamic Evolution of Pathogenicity Revealed by Sequencing and Comparative Genomics of 19 Pseudomonas syringae Isolates
text, January 2011


Works referencing / citing this record:

Biological Control Agents Against Fusarium Wilt of Banana
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A Rare Thioquinolobactin Siderophore Present in a Bioactive Pseudomonas sp. DTU12.1
journal, December 2019


Genomic and metabolic differences between Pseudomonas putida populations inhabiting sugarcane rhizosphere or bulk soil
journal, October 2019


Narrative of a versatile and adept species Pseudomonas putida
journal, March 2020


Convergent gain and loss of genomic islands drive lifestyle changes in plant-associated Pseudomonas
journal, February 2019


A Rare Thioquinolobactin Siderophore Present in a Bioactive Pseudomonas sp. DTU12.1
journal, December 2019


Genomic and metabolic differences between Pseudomonas putida populations inhabiting sugarcane rhizosphere or bulk soil
journal, October 2019


Genome-Based Analysis Reveals the Taxonomy and Diversity of the Family Idiomarinaceae
journal, October 2018


In silico and Genetic Analyses of Cyclic Lipopeptide Synthetic Gene Clusters in Pseudomonas sp. 11K1
journal, March 2019


Biological Control Agents Against Fusarium Wilt of Banana
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