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

Beaton, Ainsley and Lood, Cédric and Cunningham-Oakes, Edward and MacFadyen, Alison and Mullins, Alex J and Bestawy, Walid El and Botelho, João and Chevalier, Sylvie and Coleman, Shannon and Dalzell, Chloe and Dolan, Stephen K and Faccenda, Alberto and Ghequire, Maarten G K and Higgins, Steven and Kutschera, Alexander and Murray, Jordan and Redway, Martha and Salih, Talal and da Silva, Ana C and Smith, Brian A and Smits, Nathan and Thomson, Ryan and Woodcock, Stuart and Welch, Martin and Cornelis, Pierre and Lavigne, Rob and 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. ISSN 0378-1097 (https://doi.org/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 Pseudomonas koreensis clade of the Pseudomonas 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.

ORCID iDs

Beaton, Ainsley, Lood, Cédric, Cunningham-Oakes, Edward, MacFadyen, Alison, Mullins, Alex J, Bestawy, Walid El, 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 ORCID logoORCID: https://orcid.org/0000-0003-2545-7886, 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 ORCID logoORCID: https://orcid.org/0000-0002-6331-3704;
CORE (COnnecting REpositories)