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

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

16 Citations (Scopus)

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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 language	English
Article number	fny069
Number of pages	12
Journal	FEMS Microbiology Letters
Volume	365
Issue number	9
Early online date	22 Mar 2018
DOIs	https://doi.org/10.1093/femsle/fny069
Publication status	E-pub ahead of print - 22 Mar 2018

Keywords

pseudomonas
aquaculture
whole genome sequencing
pathogenic organisms

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10.1093/femsle/fny069Licence: CC BY 4.0

Beaton-etal-FEMS-ML-2018-Community-led-comparative-genomic-and-phenotypic-analysis-of-the-aquaculture-pathogen-Pseudomonas-baetica-a390TFinal published version, 3.44 MBLicence: CC BY 4.0

Cite this

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., da Silva, A. C., ... 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), Article fny069. Advance online publication. https://doi.org/10.1093/femsle/fny069

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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",

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doi = "10.1093/femsle/fny069",

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

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 - 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

C2 - 29579234

SN - 0378-1097

VL - 365

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

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Accelerating clinical introduction of novel antibacterial drugs

The differing biological fates of DNA minor groove-binding (MGB) antibiotics in Gram-negative and Gram-Positive bacteria.

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

Abstract

Keywords

Access to Document

Other files and links

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Projects

Accelerating clinical introduction of novel antibacterial drugs

The differing biological fates of DNA minor groove-binding (MGB) antibiotics in Gram-negative and Gram-Positive bacteria.

Cite this