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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. 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, and Loper, Joyce E. Fri . "Genome-based evolutionary history of Pseudomonas spp". United States. doi: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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    Works referencing / citing this record:

    Alternative Pathways of Carbohydrate Utilization in Pseudomonads
    journal, October 1984


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

    • Huerta-Cepas, Jaime; Serra, François; Bork, Peer
    • Molecular Biology and Evolution, Vol. 33, Issue 6
    • DOI: 10.1093/molbev/msw046

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


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

    • Gomila, Margarita; Busquets, Antonio; Mulet, Magdalena
    • Frontiers in Microbiology, Vol. 8
    • DOI: 10.3389/fmicb.2017.02422

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

    • Berendsen, Roeland L.; van Verk, Marcel C.; Stringlis, Ioannis A.
    • BMC Genomics, Vol. 16, Issue 1
    • DOI: 10.1186/s12864-015-1632-z

    In-silico Taxonomic Classification of 373 Genomes Reveals Species Misidentification and New Genospecies within the Genus Pseudomonas
    journal, July 2017


    Pyoverdine siderophores: from biogenesis to biosignificance
    journal, January 2007


    Taxonomic Profiling and Metagenome Analysis of a Microbial Community from a Habitat Contaminated with Industrial Discharges
    journal, June 2013


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

    • Udaondo, Zulema; Molina, Lázaro; Segura, Ana
    • Environmental Microbiology, Vol. 18, Issue 10
    • DOI: 10.1111/1462-2920.13015

    The Aerobic Pseudomonads a Taxonomic Study
    journal, May 1966

    • Stanier, R. Y.; Palleroni, N. J.; Doudoroff, M.
    • Journal of General Microbiology, Vol. 43, Issue 2
    • DOI: 10.1099/00221287-43-2-159

    Prospects of a new antistaphylococcal drug batumin revealed by molecular docking and analysis of the complete genome sequence of the batumin-producer Pseudomonas batumici UCM B-321
    journal, January 2016


    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

    • Kaminski, Michał A.; Furmanczyk, Ewa M.; Sobczak, Adam
    • Systematic and Applied Microbiology, Vol. 41, Issue 1
    • DOI: 10.1016/j.syapm.2017.09.002

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    Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees
    journal, April 2016

    • Letunic, Ivica; Bork, Peer
    • Nucleic Acids Research, Vol. 44, Issue W1
    • DOI: 10.1093/nar/gkw290

    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

    • Peix, A.
    • INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 53, Issue 6
    • DOI: 10.1099/ijs.0.02703-0

    An Improved General Amino Acid Replacement Matrix
    journal, April 2008


    Reclassification of Serpens flexibilis Hespell 1977 as Pseudomonas flexibilis comb. nov., with Pseudomonas tuomuerensis Xin et al. 2009 as a later heterotypic synonym
    journal, December 2015

    • Shin, Su-Kyoung; Hwang, Chung Yeon; Cho, Yong-Joon
    • Systematic and Applied Microbiology, Vol. 38, Issue 8
    • DOI: 10.1016/j.syapm.2015.09.007

    High quality draft genome sequences of Pseudomonas fulva DSM 17717T, Pseudomonas parafulva DSM 17004T and Pseudomonas cremoricolorata DSM 17059T type strains
    journal, September 2016

    • Peña, Arantxa; Busquets, Antonio; Gomila, Margarita
    • Standards in Genomic Sciences, Vol. 11, Issue 1
    • DOI: 10.1186/s40793-016-0178-2

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

    • Gross, Harald; Loper, Joyce E.
    • Natural Product Reports, Vol. 26, Issue 11
    • DOI: 10.1039/b817075b

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

    • Breidenstein, Elena B. M.; de la Fuente-Núñez, César; Hancock, Robert E. W.
    • Trends in Microbiology, Vol. 19, Issue 8
    • DOI: 10.1016/j.tim.2011.04.005

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


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


    The rhizosphere microbiome and plant health
    journal, August 2012

    • Berendsen, Roeland L.; Pieterse, Corné M. J.; Bakker, Peter A. H. M.
    • Trends in Plant Science, Vol. 17, Issue 8
    • DOI: 10.1016/j.tplants.2012.04.001

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


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


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

    • Xiao, Y. -P.; Hui, W.; Wang, Q.
    • INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 59, Issue 10
    • DOI: 10.1099/ijs.0.005108-0

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

    • Mosquera-Rendón, Jeanneth; Rada-Bravo, Ana M.; Cárdenas-Brito, Sonia
    • BMC Genomics, Vol. 17, Issue 1
    • DOI: 10.1186/s12864-016-2364-4

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

    • Gnerre, S.; MacCallum, I.; Przybylski, D.
    • Proceedings of the National Academy of Sciences, Vol. 108, Issue 4
    • DOI: 10.1073/pnas.1017351108

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

    • von Neubeck, M.; Huptas, C.; Glück, C.
    • International Journal of Systematic and Evolutionary Microbiology, Vol. 66, Issue 3
    • DOI: 10.1099/ijsem.0.000852

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

    • Drobish, Adam M.; Emery, Brian D.; Whitney, Anne M.
    • International Journal of Systematic and Evolutionary Microbiology, Vol. 66, Issue 8
    • DOI: 10.1099/ijsem.0.001147

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

    • Katoh, K.; Standley, D. M.
    • Molecular Biology and Evolution, Vol. 30, Issue 4
    • DOI: 10.1093/molbev/mst010

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