Functional Diets Modulate lncRNA-Coding Genes Interactions in the Intestine of Rainbow Trout Oncorhynchus mykiss

Along with the advent of functional genomics, there is a growing interest in inferring the function of non-coding regions from the transcriptome in non-model species. However, there are still numerous biological processes that have not been studied under this perspective, such as the intestinal immunity in farmed fish. The aim of this study was to infer long non-coding RNAs (lncRNAs) expression profiles in rainbow trout fed with functional diets based on pre- and probiotics. For 30 days fish were fed with one of the four diets (control, supplemented with prebiotic, probiotic, or with the mix of both), after which the intestines of freshwater-cultures juvenile fishes were extracted for RNA-sequencing. Then, lncRNAs were mined through a specific bioinformatics pipeline to evaluate the transcriptional activity in each condition. Correlation in expression levels and genome co-localization with known coding genes were also analyzed. 880 novel lncRNAs were thus found in the trout transcriptome, and 9,067 described lncRNAs were used to detect differentially expressed transcripts. Strong differences in gene expression were highlighted, specially in the probiotic diet which had twice the number of down-regulated lncRNAs in respect to the other treatments. Great differences were also found regarding correlation with coding genes, having high correlation index with genes related to distinct processes according to each diet. In contrast, genome co-localization of lncRNAs with coding genes were similar for all the diets. This study contributes with novel knowledge regarding lncRNAs function in salmon species.