Complete Genome Sequence of Flavobacterium psychrophilum Strain OSU THCO2-90, Used for Functional Genetic Analysis

Abstract

We report here the complete annotated genome sequence of Flavobacterium psychrophilum OSU THCO2-90, isolated from Coho salmon (Oncorhynchus kisutch) in Oregon. The genome consists of a circular chromosome with 2,343 predicted open reading frames. This strain has proved to be a valuable tool for functional genomics.

More Than Gliding: Involvement of GldD and GldG in the Virulence of Flavobacterium psychrophilum

“… a Proteins which relative abundance changed at least ±2-fold significantly (p < 0.01) and for which at least 3 spectra have been identified in one of analyzed strain (full data available in Table S2 ) . b Proteins annotation as previously described (Rochat et al, 2017a ) . c CTD type identified by BLASTP analysis .…”

“…The resulting circular molecules were used as a template to amplify by inverse PCR the sequences adjacent to the Tn 4351 insertion site using a specific pair of primers TN-1/IS4351-F (Table 1 ) and the GoTaq DNA polymerase (Promega, France). Sanger sequencing of the PCR amplified products was performed on an ABI PRISM 3100 (Applied Biosystems, CA, USA) and sequences were used to locate the transposon insertion site on the THCO2-90 genome (Rochat et al, 2017a ).…”

“…The genome of F. psychrophilum THCO2-90 (Rochat et al, 2017a ) was searched by the X!TandemPipeline (open source software developed by PAPPSO, version 3.4.3, http://pappso.inra.fr/bioinfo/xtandempipeline/ ). Protein identification was run with a precursor mass tolerance of 10 ppm and a fragment mass tolerance of 0.5 Da.…”

“…Furthermore, the mechanisms of pathogenicity of this microorganism are still poorly understood (Álvarez et al, 2006 , 2008 ; Pérez-Pascual et al, 2011 , 2015 ; Nakayama et al, 2015 ). Several improvements have been reported during the last decades in bacterial physiology (Álvarez et al, 2004 ; Pérez-Pascual et al, 2009 ), molecular diagnosis (Cepeda and Santos, 2000 ; del Cerro et al, 2002 ; Fujiwara-Nagata and Eguchi, 2009 ; Strepparava et al, 2014 ), molecular epidemiology (Nicolas et al, 2008 ; Siekoula-Nguedia et al, 2012 ; Fujiwara-Nagata et al, 2013 ; Avendaño-Herrera et al, 2014 ; Nilsen et al, 2014 ; Van Vliet et al, 2016 ; Ngo et al, 2017 ), genome analysis (Duchaud et al, 2007 ; Wiens et al, 2014 ; Wu et al, 2015 ; Rochat et al, 2017a , b ), and development of genetic tools (Álvarez et al, 2006 ; Pérez-Pascual et al, 2011 ; Gómez et al, 2012 , 2015 ), opening the way for functional genomics studies.…”

“…Analyses of F . psychrophilum genomes revealed that all the above-mentioned gliding genes as well as T9SS-encoding genes studied in F. johnsoniae or P. gingivalis so far are well-conserved (Duchaud et al, 2007 ; Rochat et al, 2017a ). With the aim of achieving a deeper insight into these two intertwined biological processes, as well as their relevance into the pathogenesis of F. psychrophilum , a set of mutants deficient in spreading were isolated using Tn 4351 -mutagenesis in strain THCO2-90.…”