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Genome-based evolutionary history of Pseudomonas spp
Cedar Hesse1, Frederik Schulz2, Carolee T Bull3
1US Department of Agriculture, Agricultural Research Service, Horticultural Crops Research Laboratory, Corvallis, OR, USA.
Environmental Microbiology
|April 11, 2018
Summary
This study establishes a phylogenetic framework for Pseudomonas bacteria, revealing thirteen distinct groups and highlighting significant genomic diversity beyond type strains. The core genome comprises 794 housekeeping genes.
Area of Science:
- Microbiology
- Genomics
- Evolutionary Biology
Background:
- Pseudomonas is a diverse genus of Gammaproteobacteria.
- Understanding evolutionary and taxonomic relationships is crucial for this group.
Purpose of the Study:
- To establish a phylogenetic framework for the Pseudomonas genus.
- To assess the genomic diversity within Pseudomonas.
Main Methods:
- Genome comparison of 166 Pseudomonas type strains and 1224 public genomes.
- Phylogenetic analysis using 100 single-copy orthologous genes.
- Calculation of average nucleotide identities and alignment fractions.
Main Results:
- Identified thirteen distinct groups within the Pseudomonas genus.
- Discovered 394 genomes distinct from any type strain, indicating vast genomic diversity.
- Determined the core genome consists of 794 genes, primarily for housekeeping functions.
Conclusions:
- The study provides a robust phylogenetic framework for Pseudomonas.
- Future research can leverage this framework to explore classification, gene functions, and ecological potential.
- Type strains represent only a portion of the genus's genomic diversity.
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