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

Ainsley Beaton, Cédric Lood, Edward Cunningham-Oakes, Alison MacFadyen, Alex J Mullins, Walid El Bestawy, João Botelho, Sylvie Chevalier, Shannon Coleman, Chloe Dalzell, Stephen K Dolan, Alberto Faccenda, Maarten G K Ghequire, Steven Higgins, Alexander Kutschera, Jordan Murray, Martha Redway, Talal Salih, Ana C da Silva, Brian A SmithNathan Smits, Ryan Thomson, Stuart Woodcock, Martin Welch, Pierre Cornelis, Rob Lavigne, Vera van Noort, Nicholas P Tucker

Research output: Contribution to journalArticle

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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.

Original languageEnglish
Article numberfny069
Number of pages12
JournalFEMS Microbiology Letters
Volume365
Issue number9
Early online date22 Mar 2018
DOIs
Publication statusE-pub ahead of print - 22 Mar 2018

Keywords

  • pseudomonas
  • aquaculture
  • whole genome sequencing
  • pathogenic organisms

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