Differentially Expressed miRNAs and mRNAs in Regenerated Scales of Rainbow Trout (Oncorhynchus mykiss) under Salinity Acclimation

SIMPLE SUMMARY: To further understand the molecular mechanism underlying the bone remodeling process, transcriptional information of regenerated scales of rainbow trout under sea water (SW) and fresh water (FW) environments was compared in this study. The miRNA and mRNA expression profiles in regenerated scales were compared to those data collected in ontogenic scales to investigate the effects of salinity acclimation on skeletal growth and development. Gene ontology and KEGG enrichment analysis of the differentially expressed genes and differentially expressed miRNA target genes showed similar expression profiles. These genes were mainly related to ion and energy metabolism. ABSTRACT: In order to explore the potential effects of salinity acclimation on bone metabolism of rainbow trout (Oncorhynchus mykiss), transcriptional information of regenerated scales under salinity acclimation (sea water, SW) was compared to those of fish under fresh water (FW) environments. According to the high-throughput sequencing results, a total of 2620 significantly differentially expressed genes (DEGs) were identified in the data of SW vs. FW. Compared with the FW group, six significantly downregulated and 44 significantly upregulated miRNAs were identified in the SW scales (p < 0.05). Furthermore, a total of 994 significantly differentially expressed target genes (DETGs) were identified from the 50 significantly differentially expressed miRNAs (DE miRNAs). Gene ontology analysis of the aforementioned DETGs was similar to the results of the differentially expressed genes (DEGs) obtained from mRNA-seq data, these genes were mainly related to ion metabolism. KEGG enrichment analysis of the DEGs and DETGs suggested that many significantly enriched pathways were related to the energy metabolism pathway.