Genome-based evolutionary history of Pseudomonas spp

Cedar Hesse, Frederik Schulz, Carolee Theresa Bull, Brenda T. Shaffer, Qing Yan, Nicole Shapiro, Karl A. Hassan, Neha Varghese, Liam D.H. Elbourne, Ian T. Paulsen, Nikos Kyrpides, Tanja Woyke, Joyce E. Loper

Research output: Contribution to journalArticle

7 Citations (Scopus)

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.

Original languageEnglish (US)
Pages (from-to)2142-2159
Number of pages18
JournalEnvironmental microbiology
Volume20
Issue number6
DOIs
StatePublished - Jun 1 2018

Fingerprint

Pseudomonas
genome
Genome
history
gene
phylogeny
phylogenetics
Genes
Gammaproteobacteria
Housekeeping
genes
gamma-Proteobacteria
subspecies
Phylogeny
phenotype
genomics
amino acid sequences
Nucleotides
nucleotides
bacterium

All Science Journal Classification (ASJC) codes

  • Microbiology
  • Ecology, Evolution, Behavior and Systematics

Cite this

Hesse, C., Schulz, F., Bull, C. T., Shaffer, B. T., Yan, Q., Shapiro, N., ... Loper, J. E. (2018). Genome-based evolutionary history of Pseudomonas spp. Environmental microbiology, 20(6), 2142-2159. https://doi.org/10.1111/1462-2920.14130
Hesse, Cedar ; Schulz, Frederik ; Bull, Carolee Theresa ; 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. In: Environmental microbiology. 2018 ; Vol. 20, No. 6. pp. 2142-2159.
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Hesse, C, Schulz, F, Bull, CT, Shaffer, BT, Yan, Q, Shapiro, N, Hassan, KA, Varghese, N, Elbourne, LDH, Paulsen, IT, Kyrpides, N, Woyke, T & Loper, JE 2018, 'Genome-based evolutionary history of Pseudomonas spp', Environmental microbiology, vol. 20, no. 6, pp. 2142-2159. https://doi.org/10.1111/1462-2920.14130

Genome-based evolutionary history of Pseudomonas spp. / Hesse, Cedar; Schulz, Frederik; Bull, Carolee Theresa; 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.

In: Environmental microbiology, Vol. 20, No. 6, 01.06.2018, p. 2142-2159.

Research output: Contribution to journalArticle

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AU - Shapiro, Nicole

AU - Hassan, Karl A.

AU - Varghese, Neha

AU - Elbourne, Liam D.H.

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AU - Kyrpides, Nikos

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AU - Loper, Joyce E.

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Hesse C, Schulz F, Bull CT, Shaffer BT, Yan Q, Shapiro N et al. Genome-based evolutionary history of Pseudomonas spp. Environmental microbiology. 2018 Jun 1;20(6):2142-2159. https://doi.org/10.1111/1462-2920.14130