Genomic identification and multi-tissue transcriptomic profiling of vitamin D3-related genes in Atlantic salmon (Salmo salar)

The metabolic pathway of vitamin D3 is well characterized in mammals, but its genetic basis in teleost fish remains poorly defined. We identified 16 vitamin D3-related genes in Atlantic salmon (Salmo salar), 14 orthologs of pathway genes and two albumins as candidate carriers, and profiled their expression in a 14-tissue atlas and in seven independent RNA-seq studies. Phylogenetic analysis resolved seven paralog pairs from the salmonid whole-genome duplication. Atlantic salmon and three other euteleost fishes lacked a gc gene, and the genes that flank gc in other fishes were adjacent in their genomes. The proteins annotated as GC in three Oncorhynchus species were albumins. Skin expression of dhcr7, which converts the precursor 7-dehydrocholesterol to cholesterol, was low and differed between studies. The activating enzyme cyp27b1 was barely expressed in five kidney and 21 head kidney samples, including those of the atlas, whereas cyp27b1.a was expressed in the brain and cyp27b1.b in the liver. In northern pike, which lacks this duplication, cyp27b1 was not detected in the kidney either. The catabolic enzyme cyp24a1 was only weakly expressed in the kidney and the head kidney. These transcript data suggest that vitamin D3 activation in Atlantic salmon may not depend on renal cyp27b1 expression under the conditions sampled, and that albumins or lipoproteins may carry vitamin D metabolites. Both hypotheses need to be tested with protein, enzyme activity, and metabolite measurements. The curated gene set provides a basis for studies of vitamin D3 metabolism and dietary vitamin D3 requirements in salmonids.