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; Nathan Smits; Ryan Thomson; Stuart Woodcock; Martin Welch; Pierre Cornelis; Rob Lavigne; Vera van Noort; Nicholas P. Tucker

doi: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

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^*

^*Corresponding author for this work

Research output: Contribution to journal › Article › peer-review

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.

Original language	English
Article number	fny069
Pages (from-to)	1-12
Number of pages	12
Journal	FEMS Microbiology Letters
Volume	365
Issue number	9
DOIs	https://doi.org/10.1093/femsle/fny069
Publication status	Published - May 2018
Externally published	Yes

Keywords

Pseudomonas
Aquaculture
Whole genome sequencing
Oxford Nanopore MinIon
Ion torrent
Pseudomonas baetica

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

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10.1093/femsle/fny069Licence: CC BY

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Beaton, A., Lood, C., Cunningham-Oakes, E., MacFadyen, A., Mullins, A. J., Bestawy, W. E., Botelho, J., Chevalier, S., Coleman, S., Dalzell, C., Dolan, S. K., Faccenda, A., Ghequire, M. G. K., Higgins, S., Kutschera, A., Murray, J., Redway, M., Salih, T., Silva, A. C. D., ... Tucker, N. 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), 1-12. Article fny069. https://doi.org/10.1093/femsle/fny069

@article{63556aaafeea47459070b45ce4e9648d,

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 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.",

keywords = "Pseudomonas, Aquaculture, Whole genome sequencing, Oxford Nanopore MinIon, Ion torrent, Pseudomonas baetica",

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 Silva, {Ana C. da} 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.}",

note = "Publisher Copyright: {\textcopyright} FEMS 2018.",

year = "2018",

month = may,

doi = "10.1093/femsle/fny069",

language = "English",

volume = "365",

pages = "1--12",

journal = "FEMS Microbiology Letters",

issn = "0378-1097",

publisher = "Oxford University Press",

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, Silva, ACD, 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, pp. 1-12. 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 et al.
In: FEMS Microbiology Letters, Vol. 365, No. 9, fny069, 05.2018, p. 1-12.

Research output: Contribution to journal › Article › peer-review

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 - Silva, Ana C. da

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 - 2018/5

Y1 - 2018/5

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 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.

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 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.

KW - Pseudomonas

KW - Aquaculture

KW - Whole genome sequencing

KW - Oxford Nanopore MinIon

KW - Ion torrent

KW - Pseudomonas baetica

U2 - 10.1093/femsle/fny069

DO - 10.1093/femsle/fny069

M3 - Article

C2 - 29579234

SN - 0378-1097

VL - 365

SP - 1

EP - 12

JO - FEMS Microbiology Letters

JF - FEMS Microbiology Letters

IS - 9

M1 - fny069

ER -

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

Abstract

Keywords

UN SDGs

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