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

Beaton, Ainsley, Lood, Cédric, Cunningham-Oakes, Edward, MacFadyen, Alison, Mullins, Alex J., Bestawy, Walid E.l., Botelho, João, Chevalier, Sylvie, Coleman, Shannon, Dalzell, Chloe, Dolan, Stephen K., Faccenda, Alberto, Ghequire, Maarten G. K., Higgins, Steven, Kutschera, Alexander, Murray, Jordan, Redway, Martha, Salih, Talal, da Silva, Ana C., Smith, Brian A., Smits, Nathan, Thomson, Ryan, Woodcock, Stuart, Welch, Martin, Cornelis, Pierre, Lavigne, Rob, van Noort, Vera and Tucker, Nicholas P. 2018. Community-led comparative genomic and phenotypic analysis of the aquaculture pathogen Pseudomonas baetica a390T sequenced by Ion semiconductor and Nanopore technologies. FEMS Microbiology Letters 365 (9) , fny069. 10.1093/femsle/fny069

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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.

Item Type: Article
Date Type: Publication
Status: Published
Schools: Biosciences
Publisher: Oxford University Press (OUP)
ISSN: 0378-1097
Date of First Compliant Deposit: 28 January 2021
Date of Acceptance: 22 March 2018
Last Modified: 28 Jan 2021 11:30
URI: http://orca.cardiff.ac.uk/id/eprint/137975

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