title: Identifying copy number variation of the dominant virulence factorsmsaandp22within genomes of the fish pathogenRenibacterium salmoninarum.
abstract: Renibacterium salmoninarumis the causative agent of bacterial kidney disease, an important disease of farmed and wild salmonid fish worldwide. Despite the wide spatiotemporal distribution of this disease and habitat pressures ranging from the natural environment to aquaculture and rivers to marine environments, little variation has been observed in theR. salmoninarumgenome. Here we use the coverage depth from genomic sequencing corroborated by real-time quantitative PCR to detect copy number variation (CNV) among the genes ofR. salmoninarum. CNV was primarily limited to the known dominant virulence factorsmsaandp22. Among 68 isolates representing the UK, Norway and North America, themsagene ranged from two to five identical copies and thep22gene ranged from one to five copies. CNV for these two genes co-occurred, suggesting they may be functionally linked. Isolates carrying CNV were phylogenetically restricted and originated predominantly from sites in North America, rather than the UK or Norway. Although both phylogenetic relationship and geographical origin were found to correlate with CNV status, geographical origin was a much stronger predictor than phylogeny, suggesting a role for local selection pressures in the repeated emergence and maintenance of this trait.
authors.affiliation: 1​Department of Bacteriology and Immunology Lovisenberggata 8, Norwegian Institute of Public Health/Department of Food Safety and Infection Biology, Norwegian University of Life Sciences (NMBU),Oslo,Norway.
authors.forename: Ola
authors.initials: O
authors.lastname: Brynildsrud
authors.affiliation: 2​Department of Bacteriology - Aquatic and Terrestrial Animals, Norwegian Veterinary Institute (NVI), Oslo, Norway.
authors.forename: Snorre
authors.initials: S
authors.lastname: Gulla
authors.affiliation: 3​Department of Biology and Biochemistry, University of Bath,Claverton Down, Bath,United Kingdom.
authors.forename: Edward J
authors.initials: EJ
authors.lastname: Feil
authors.affiliation: 4​Department of Food Safety and Infection Biology, Norwegian University of Life Sciences (NMBU),Oslo,Norway.
authors.forename: Simen Foyn
authors.initials: SF
authors.lastname: Nørstebø
authors.affiliation: 5​Northwest Fisheries Science Center, National Marine Fisheries Service, NOAA,Seattle, WA,United States.
authors.forename: Linda D
authors.initials: LD
authors.lastname: Rhodes
mesh_terms: D000818:Animals; D001426:Bacterial Proteins / Q000235:genetics*; D056915:DNA Copy Number Variations; D008835:Micrococcaceae / Q000235:genetics*; D009656:North America; D009664:Norway; D010802:Phylogeny; D037521:Virulence Factors / Q000235:genetics*
chemical_list: D001426:Bacterial Proteins; D037521:Virulence Factors
keywords: copy number variation; gene duplication-amplification; major soluble antigen; p22; renibacterium salmoninarum