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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.

Published version
Peer-reviewed

Type

Article

Change log

Authors

Beaton, Ainsley 
Lood, Cédric 
Cunningham-Oakes, Edward 
MacFadyen, Alison 
Mullins, Alex J 

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.

Description

Keywords

Animals, Fish Diseases, Genome, Bacterial, Genomics, Nanopores, Phenotype, Phylogeny, Pseudomonas, Pseudomonas Infections, Semiconductors, Sequence Analysis, DNA

Journal Title

FEMS Microbiol Lett

Conference Name

Journal ISSN

0378-1097
1574-6968

Volume Title

365

Publisher

Oxford University Press (OUP)
Sponsorship
Rosetrees Trust (A1318)
Evelyn Trust (17/51)