Comparative genomics of the Pseudomonas corrugata subgroup reveals high species diversity and allows the description of Pseudomonas ogarae sp. nov.

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Type
Article: article from journal or magazin.
Collection
Publications
Institution
Title
Comparative genomics of the Pseudomonas corrugata subgroup reveals high species diversity and allows the description of Pseudomonas ogarae sp. nov.
Journal
Microbial genomics
Author(s)
Garrido-Sanz D., Redondo-Nieto M., Martin M., Rivilla R.
ISSN
2057-5858 (Electronic)
ISSN-L
2057-5858
Publication state
Published
Issued date
06/2021
Peer-reviewed
Oui
Volume
7
Number
6
Pages
000593
Language
english
Notes
Publication types: Journal Article ; Research Support, Non-U.S. Gov't
Publication Status: ppublish
Abstract
Pseudomonas corrugata constitute one of the phylogenomic subgroups within the Pseudomonas fluorescens species complex and include both plant growth-promoting rhizobacteria (PGPR) and plant pathogenic bacteria. Previous studies suggest that the species diversity of this group remains largely unexplored together with frequent misclassification of strains. Using more than 1800 sequenced Pseudomonas genomes we identified 121 genomes belonging to the P. corrugata subgroup. Intergenomic distances obtained using the genome-to-genome blast distance (GBDP) algorithm and the determination of digital DNA-DNA hybridization values were further used for phylogenomic and clustering analyses, which revealed 29 putative species clusters, of which only five correspond to currently named species within the subgroup. Comparative and functional genome-scale analyses also support the species status of these clusters. The search for PGPR and plant pathogenic determinants showed that approximately half of the genomes analysed could have a pathogenic behaviour based on the presence of a pathogenicity genetic island, while all analysed genomes possess PGPR traits. Finally, this information together with the characterization of phenotypic traits, allows the reclassification proposal of Pseudomonas fluorescens F113 as Pseudomonas ogarae sp. nov., nom rev., type strain F113 <sup>T</sup> (=DSM 112162 <sup>T</sup> =CECT 30235 <sup>T</sup> ), which is substantiated by genomic, functional genomics and phenotypic differences with their closest type strains.
Keywords
Base Sequence, DNA, Bacterial/genetics, Genes, Bacterial/genetics, Genome, Bacterial, Genomics, Nucleic Acid Hybridization, Phylogeny, Plant Diseases/microbiology, Pseudomonas/classification, Pseudomonas/genetics, Sequence Analysis, DNA, PGPR, Pseudomonas corrugata, Pseudomonas ogarae, comparative genomics, phylogenomics
Pubmed
Open Access
Yes
Create date
06/07/2021 11:27
Last modification date
23/01/2024 8:26
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