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. 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.

Diversity of phytobeneficial traits revealed by whole‐genome analysis of worldwide‐isolated phenazine‐producing Pseudomonas spp.

“…This species complex is characterized by its wide phenotypic, ecological and genomic diversity (Loper et al, 2012;Garrido-Sanz et al, 2016). Based on multisequence analysis (MLSA) and phylogenomic analysis, the P. fluorescens species complex has been divided into nine or ten subgroups (Mulet et al, 2010;Garrido-Sanz et al, 2016;Hesse et al, 2018). While most plant-beneficial phenazine-producing strains belong to the P. fluorescens and P. chlororaphis subgroups, strains from at least two other subgroups within the P. fluorescens species complex have also been isolated (Parejko et al, 2013;Arnau et al, 2015;Flury et al, 2016;Garrido-Sanz et al, 2016).…”

Phenazines in plant‐beneficial Pseudomonas spp.: biosynthesis, regulation, function and genomics

“…Numerous genomes of the P. fluorescens species complex have been sequenced (Garrido-Sanz et al, 2016;Hesse et al, 2018) in the last decade, including several phenazine-producing Pseudomonas spp. genomes (Loper et al, 2012;Shen et al, 2012;Flury et al, 2016).…”

Comparative genomics identified a genetic locus in plant-associated Pseudomonas spp. that is necessary for induced systemic susceptibility

“…as previously described [14]. To more easily visualize this tree, we collapsed 368 monophyletic clades with strong support (as determined by FastTree's local Hasegawa test) that correspond with major taxonomic divisions identified by Hesse et al (2018). 370…”