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oa Identifying copy number variation of the dominant virulence factors msa and p22 within genomes of the fish pathogen Renibacterium salmoninarum
- Authors: Ola Brynildsrud1 , Snorre Gulla2 , Edward J. Feil3 , Simen Foyn Nørstebø4 , Linda D. Rhodes5
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1 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 2 2 Department of Bacteriology - Aquatic and Terrestrial Animals, Norwegian Veterinary Institute (NVI), Oslo, Norway 3 3 Department of Biology and Biochemistry, University of Bath,Claverton Down, Bath,United Kingdom 4 4 Department of Food Safety and Infection Biology, Norwegian University of Life Sciences (NMBU),Oslo,Norway 5 5 Northwest Fisheries Science Center, National Marine Fisheries Service, NOAA,Seattle, WA,United States
- Correspondence Ola Brynildsrud ([email protected])
- First Published Online: 29 April 2016, Microbial Genomics , 2016 2, doi: 10.1099/mgen.0.000055
- Subject: Research Paper - Genomic Methodologies: Genome variation detection
- Received:
- Accepted:
- Cover date:
- This is an open access article published by the Microbiology Society under the Creative Commons Attribution License




Identifying copy number variation of the dominant virulence factors msa and p22 within genomes of the fish pathogen Renibacterium salmoninarum, Page 1 of 1
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Renibacterium salmoninarum is 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 the R. salmoninarum genome. Here we use the coverage depth from genomic sequencing corroborated by real-time quantitative PCR to detect copy number variation (CNV) among the genes of R. salmoninarum. CNV was primarily limited to the known dominant virulence factors msa and p22. Among 68 isolates representing the UK, 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 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.
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All supporting data, code and protocols have been provided within the article or through supplementary data files.
- Keyword(s): renibacterium salmoninarum, gene duplication-amplification, copy number variation, major soluble antigen, p22
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Abbreviations: BKD bacterial kidney disease CNV copy number variation msa major soluble antigen IS Insertion sequence
© 2016 The Authors | Published by the Microbiology Society
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1. Brynildsrud, O., Feil, E. J., Bohlin, J., Castillo-Ramirez, S., Colquhoun, D., McCarthy, U., Matejusova, I. M., Rhodes, L. D. & Wiens, G. D. (2014). NCBI Sequence Read Archive. http://trace.ncbi.nlm.nih.gov/Traces/study/?acc=ERP003780.

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