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In-silico taxonomic classification of 373 genomes reveals species misidentification and new genospecies within the genus Pseudomonas

Tran, Phuong N., Savka, Michael A. and Gan, Han Ming 2017, In-silico taxonomic classification of 373 genomes reveals species misidentification and new genospecies within the genus Pseudomonas, Frontiers in microbiology, vol. 8, pp. 1-7, doi: 10.3389/fmicb.2017.01296.

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Title In-silico taxonomic classification of 373 genomes reveals species misidentification and new genospecies within the genus Pseudomonas
Formatted title In-silico taxonomic classification of 373 genomes reveals species misidentification and new genospecies within the genus Pseudomonas
Author(s) Tran, Phuong N.
Savka, Michael A.
Gan, Han MingORCID iD for Gan, Han Ming orcid.org/0000-0001-7987-738X
Journal name Frontiers in microbiology
Volume number 8
Article ID 1296
Start page 1
End page 7
Total pages 7
Publisher Frontiers Research Foundation
Place of publication Lausanne, Switzerland
Publication date 2017-07-12
ISSN 1664-302X
Keyword(s) pseudomonas
taxonomy
phylogenomics
in-silico genome-genome hybridization
comparative genomics
average nucleotide identity
genospecies
Summary The genus Pseudomonas has one of the largest diversity of species within the Bacteria kingdom. To date, its taxonomy is still being revised and updated. Due to the non-standardized procedure and ambiguous thresholds at species level, largely based on 16S rRNA gene or conventional biochemical assay, species identification of publicly available Pseudomonas genomes remains questionable. In this study, we performed a large-scale analysis of all Pseudomonas genomes with species designation (excluding the well-defined P. aeruginosa) and re-evaluated their taxonomic assignment via in silico genome-genome hybridization and/or genetic comparison with valid type species. Three-hundred and seventy-three pseudomonad genomes were analyzed and subsequently clustered into 145 distinct genospecies. We detected 207 erroneous labels and corrected 43 to the proper species based on Average Nucleotide Identity Multilocus Sequence Typing (MLST) sequence similarity to the type strain. Surprisingly, more than half of the genomes initially designated as Pseudomonas syringae and Pseudomonas fluorescens should be classified either to a previously described species or to a new genospecies. Notably, high pairwise average nucleotide identity (>95%) indicating species-level similarity was observed between P. synxantha-P. libanensis, P. psychrotolerans–P. oryzihabitans, and P. kilonensis- P. brassicacearum, that were previously differentiated based on conventional biochemical tests and/or genome-genome hybridization techniques.
Language eng
DOI 10.3389/fmicb.2017.01296
Field of Research 060309 Phylogeny and Comparative Analysis
060102 Bioinformatics
HERDC Research category C1 Refereed article in a scholarly journal
ERA Research output type C Journal article
Copyright notice ©2017, The Authors
Free to Read? Yes
Use Rights Creative Commons Attribution licence
Persistent URL http://hdl.handle.net/10536/DRO/DU:30098039

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Every reasonable effort has been made to ensure that permission has been obtained for items included in DRO. If you believe that your rights have been infringed by this repository, please contact drosupport@deakin.edu.au.