Community-led comparative genomic and phenotypic analysis of the aquaculture pathogen Pseudomonas baetica a390T sequenced by Ion semiconductor and Nanopore technologies
2018
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
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.
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