Abstract
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.
Highlights
Renibacterium salmoninarum is the causative agent of bacterial kidney disease (BKD) in cultured and wild salmonid fish
R. salmoninarum is a highly clonal bacterium with a very limited accessory genome, and duplication of msa is already known as a concept, this study extends the finding to p22, the other major surface protein
Duplicates of genes encoding ribosomal and transfer RNA subunits are well known in bacteria, other gene duplication–amplification events are only gaining attention and have probably been underreported in the literature (Andersson & Hughes, 2009; Elliott et al, 2013)
Summary
Renibacterium salmoninarum is the causative agent of bacterial kidney disease (BKD) in cultured and wild salmonid fish. BKD can result in acute morbidity or mortality, or it can be a slowly progressive disease causing an often dramatic decline in growth. BKD is economically important in aquaculture, where it can spread horizontally throughout sea pens of juvenile and subadult Atlantic salmon (Salmo salar) (Murray et al, 2012) or vertically through transferred broodstock or eggs (Evelyn et al, 1986).
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