Whole-transcriptome RNA sequencing of skin reveals innate immunity differences between wild-type and yellow mutant rainbow trout

Rainbow trout (Oncorhynchus mykiss) is an important aquaculture fish species that is farmed worldwide, and it is also the most widely cultivated cold water fish in China. This species, a member of the salmonidae family, is an ideal model organism for studying the immune system in fish. Two phenotypes of rainbow trout are widely cultured; wild-type rainbow trout with black skin (WR_S) and yellow mutant rainbow trout with yellow skin (YR_S). Fish skin is an important immune organ, however, little is known about the differences in skin immunity between WR_S and YR_S in a natural flowing water pond aquaculture environment, and very few studies were conducted to investigate the ceRNA mechanism for fish skin. Overall design: In the present study, whole-transcriptome sequencing was performed to uncover global molecular expression differences of skin immunity between WR_S and YR_S in a natural flowing water pond culture environment at both mRNAs and ncRNAs levels.