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

FEMS Microbiol Lett. 2018 May 1;365(9):fny069. doi: 10.1093/femsle/fny069.


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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Fish Diseases / microbiology*
  • Genome, Bacterial
  • Genomics / instrumentation
  • Genomics / methods*
  • Nanopores
  • Phenotype
  • Phylogeny
  • Pseudomonas / classification
  • Pseudomonas / genetics*
  • Pseudomonas / isolation & purification
  • Pseudomonas Infections / microbiology
  • Pseudomonas Infections / veterinary*
  • Semiconductors
  • Sequence Analysis, DNA / instrumentation
  • Sequence Analysis, DNA / methods*