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 Smith & 8 others Nathan Smits, Ryan Thomson, Stuart Woodcock, Martin Welch, Pierre Cornelis, Rob Lavigne, Vera van Noort, Nicholas P Tucker

Research output: Contribution to journalArticle

3 Citations (Scopus)

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.

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

Fingerprint

Nanopores
Aquaculture
Semiconductors
Pseudomonas
Genome
Ions
Technology
Pseudomonas fluorescens
Oxytetracycline
Osmotic Pressure
Liver Diseases
Fishes

Keywords

  • pseudomonas
  • aquaculture
  • whole genome sequencing
  • pathogenic organisms

Cite this

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 ; da Silva, Ana C ; Smith, Brian A ; Smits, Nathan ; Thomson, Ryan ; Woodcock, Stuart ; Welch, Martin ; Cornelis, Pierre ; Lavigne, Rob ; van Noort, Vera ; Tucker, Nicholas P. / Community-led comparative genomic and phenotypic analysis of the aquaculture pathogen Pseudomonas baetica a390T sequenced by Ion semiconductor and Nanopore technologies. In: FEMS Microbiology Letters . 2018 ; Vol. 365, No. 9.
@article{983c612f0411436f99ff2cc14346babb,
title = "Community-led comparative genomic and phenotypic analysis of the aquaculture pathogen Pseudomonas baetica a390T sequenced by Ion semiconductor and Nanopore technologies",
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.",
keywords = "pseudomonas, aquaculture, whole genome sequencing, pathogenic organisms",
author = "Ainsley Beaton and C{\'e}dric Lood and Edward Cunningham-Oakes and Alison MacFadyen and Mullins, {Alex J} and Bestawy, {Walid El} and Jo{\~a}o Botelho and Sylvie Chevalier and Shannon Coleman and Chloe Dalzell and Dolan, {Stephen K} and Alberto Faccenda and Ghequire, {Maarten G K} and Steven Higgins and Alexander Kutschera and Jordan Murray and Martha Redway and Talal Salih and {da Silva}, {Ana C} and Smith, {Brian A} and Nathan Smits and Ryan Thomson and Stuart Woodcock and Martin Welch and Pierre Cornelis and Rob Lavigne and {van Noort}, Vera and Tucker, {Nicholas P}",
year = "2018",
month = "3",
day = "22",
doi = "10.1093/femsle/fny069",
language = "English",
volume = "365",
journal = "FEMS Microbiology Letters",
issn = "0378-1097",
number = "9",

}

Beaton, A, Lood, C, Cunningham-Oakes, E, MacFadyen, A, Mullins, AJ, Bestawy, WE, Botelho, J, Chevalier, S, Coleman, S, Dalzell, C, Dolan, SK, Faccenda, A, Ghequire, MGK, Higgins, S, Kutschera, A, Murray, J, Redway, M, Salih, T, da Silva, AC, Smith, BA, Smits, N, Thomson, R, Woodcock, S, Welch, M, Cornelis, P, Lavigne, R, van Noort, V & Tucker, NP 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 , vol. 365, no. 9, fny069. https://doi.org/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. / 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; da Silva, Ana C; Smith, Brian A; Smits, Nathan; Thomson, Ryan; Woodcock, Stuart; Welch, Martin; Cornelis, Pierre; Lavigne, Rob; van Noort, Vera; Tucker, Nicholas P.

In: FEMS Microbiology Letters , Vol. 365, No. 9, fny069, 22.03.2018.

Research output: Contribution to journalArticle

TY - JOUR

T1 - Community-led comparative genomic and phenotypic analysis of the aquaculture pathogen Pseudomonas baetica a390T sequenced by Ion semiconductor and Nanopore technologies

AU - Beaton, Ainsley

AU - Lood, Cédric

AU - Cunningham-Oakes, Edward

AU - MacFadyen, Alison

AU - Mullins, Alex J

AU - Bestawy, Walid El

AU - Botelho, João

AU - Chevalier, Sylvie

AU - Coleman, Shannon

AU - Dalzell, Chloe

AU - Dolan, Stephen K

AU - Faccenda, Alberto

AU - Ghequire, Maarten G K

AU - Higgins, Steven

AU - Kutschera, Alexander

AU - Murray, Jordan

AU - Redway, Martha

AU - Salih, Talal

AU - da Silva, Ana C

AU - Smith, Brian A

AU - Smits, Nathan

AU - Thomson, Ryan

AU - Woodcock, Stuart

AU - Welch, Martin

AU - Cornelis, Pierre

AU - Lavigne, Rob

AU - van Noort, Vera

AU - Tucker, Nicholas P

PY - 2018/3/22

Y1 - 2018/3/22

N2 - 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.

AB - 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.

KW - pseudomonas

KW - aquaculture

KW - whole genome sequencing

KW - pathogenic organisms

UR - https://academic.oup.com/femsle

U2 - 10.1093/femsle/fny069

DO - 10.1093/femsle/fny069

M3 - Article

VL - 365

JO - FEMS Microbiology Letters

T2 - FEMS Microbiology Letters

JF - FEMS Microbiology Letters

SN - 0378-1097

IS - 9

M1 - fny069

ER -