Northwest Fisheries Science Center

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Document Type: Journal Article
Center: NWFSC
Document ID: 8341
Title: Identifying copy number variation of the dominant virulence factor msa within genomes of the fish pathogen Renibacterium salmoninarum
Author: Ola Brynildsrud, Snorre Gulla, Edward J. Feil, Simen F. Nørstebø, Linda D. Rhodes
Publication Year: 2016
Journal: Microbial Genomics
Volume: MGen 2016 2
DOI: 10.1099/mgen.0.000055
Keywords: bacterial kidney disease,Genetics,phylogeny,virulence,salmonids

 Renibacterium salmoninarum is the causative agent of bacterial kidney disease (BKD), an important disease of farmed and wild salmonid fish worldwide. In spite of the wide spatiotemporal distribution for this disease and habitat pressures ranging from natural environment to aquaculture and rivers to marine environments, little variation has been observed in the R. salmoninarum genome. Here we use the coverage depth from genomic sequencing and real-time quantitative PCR to detect copy number variation (CNV) among the genes of R. salmoninarum. CNV was limited to the known dominant virulence factors msa and p22. Among 68 isolates representing the United Kingdom, Norway, and North America, the msa gene ranged from two to five identical copies and the p22 gene 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 United Kingdom or Norway. Although both phylogenetic relationship and geographic origin were found to correlate with CNV status, geographic origin was a much stronger predictor than phylogeny, suggesting a role for local selection pressures in the repeated emergence and maintenance of this trait.