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

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

Open Access

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

Author(s) -

Ainsley Beaton,

Cédric Lood,

Edward Cunningham-Oakes,

Alison C. MacFadyen,

Alex J. Mullins,

Walid El Bestawy,

João Botelho,

Sylvie Chevalier,

Shan R. Coleman,

Chloe Dalzell,

Stephen K. Dolan,

Alberto Faccenda,

Maarten G. K. Ghequire,

Steven Higgins,

Alexander Kutschera,

Jordan Murray,

Martha Redway,

Talal Sabhan Salih,

Ana C. da Silva,

Brian A. Smith,

Nathan Smits,

Ryan Thomson,

Stuart Daniel Woodcock,

Martin Welch,

Pierre Cornélis,

Rob Lavigne,

Vera van Noort,

Nicholas P. Tucker

Publication year - 2018

Publication title -

fems microbiology letters

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 0.899

H-Index - 151

eISSN - 1574-6968

pISSN - 0378-1097

DOI - 10.1093/femsle/fny069

Subject(s) - ion semiconductor sequencing , biology , genome , phylogenetic tree , strain (injury) , nanopore sequencing , clade , genetics , evolutionary biology , dna sequencing , gene , anatomy

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.

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