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FEMS Microbiol Lett. 2018 May 1;365(9). doi: 10.1093/femsle/fny069.

Community-led comparative genomic and phenotypic analysis of the aquaculture pathogen Pseudomonas baetica a390T sequenced by Ion semiconductor and Nanopore technologies.

Author information

1
Strathclyde Institute of Pharmacy and Biomedical Science, University of Strathclyde, 161 Cathedral Street, Glasgow, G4 0RE, UK.
2
Centre of Microbial and Plant Genetics, KU Leuven, Kasteelpark Arenberg 20, bus 2460, Leuven B-3001, Belgium.
3
Laboratory of Gene Technology, KU Leuven, Kasteelpark Arenberg 20, bus 2460, Leuven B-3001, Belgium.
4
Cardiff School of Biosciences, Cardiff University, Sir Martin Evans Building, Park Place, Cardiff CF10 3AX, UK.
5
Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, Midlothian EH25 9RG, Scotland, UK.
6
UCIBIO/REQUIMTE, Laboratório de Microbiologia, Faculdade de Farmácia, Universidade do Porto, Rua de Jorge Viterbo Ferreira no. 228 Porto 4050-313, Portugal.
7
Laboratoire Microbiologie Signaux et Microenvironnement (LMSM), Université de Rouen, 55, rue St Germain, Evreux 27000, France.
8
Lower Mall Research Station, University of British Columbia, 2259 Lower Mall, Vancouver, BC V6T 1Z4, Canada.
9
Department of Biochemistry, University of Cambridge, Hopkins Building, Tennis Court Road, Cambridge CB2 1QW, UK.
10
Department of Plant and Microbial Biology, University of Zürich, Zürich 8008, Switzerland.
11
Department of Phytopathology, Center of Life and Food Sciences, Technical University of Munich, Weihenstephan D-85354, Germany.
12
Centre for Biomolecular Sciences, School of Life Sciences, University of Nottingham, Nottingham NG7 2RD, UK.
13
School of Plant Sciences, The University of Arizona, P.O. Box 210036, Forbes Building, 303 Tucson, Arizona 85721-0036, USA.
14
Department of Biological Chemistry, John Innes Centre, Colney Lane, Norwich NR4 7UH, UK.

Abstract

Pseudomonas baetica strain a390T is the type strain of this recently described species and here we present its high-contiguity draft genome. To celebrate the 16th International Conference on Pseudomonas, the genome of P. baetica strain a390T was sequenced using a unique combination of Ion Torrent semiconductor and Oxford Nanopore methods as part of a collaborative community-led project. The use of high-quality Ion Torrent sequences with long Nanopore reads gave rapid, high-contiguity and -quality, 16-contig genome sequence. Whole genome phylogenetic analysis places P. baetica within the P. koreensis clade of the P. fluorescens group. Comparison of the main genomic features of P. baetica with a variety of other Pseudomonas spp. suggests that it is a highly adaptable organism, typical of the genus. This strain was originally isolated from the liver of a diseased wedge sole fish, and genotypic and phenotypic analyses show that it is tolerant to osmotic stress and to oxytetracycline.

PMID:
29579234
PMCID:
PMC5909648
DOI:
10.1093/femsle/fny069
[Indexed for MEDLINE]
Free PMC Article

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