Genome-wide identification of salinity stress-associated lncRNAs in Nile tilapia

Long noncoding RNAs (lncRNAs) are increasingly recognized as key players in various biological processes, yet their role in fish's response to salinity changes remains largely unexplored. This study undertakes a genome-wide analysis of lncRNAs in Nile tilapia (Oreochromis niloticus), examining their response to salinity stress across a substantial dataset of 98 RNA-seq samples from nine different tissues. We identified 28,819 high-confidence lncRNA candidates, which are characterized by a shorter average length of 788 nucleotides and fewer exons (average 1.84) compared to mRNAs. Specifically, in the gills exposed to salinity 27 for three and a half months, we found 846 differentially expressed lncRNAs (DElncRNAs), including 342 upregulated and 504 downregulated transcripts. The study also highlighted 220 significant DElncRNA-mRNA pairs, indicating potential regulatory interactions. Notably, in response to acute salinity stress, we identified 989 DElncRNAs, with 414 upregulated and 575 downregulated in gills. An analysis of these DElncRNAs revealed 348 high-confidence pairs, with Gene Ontology (GO) and KEGG pathway analyses indicating a prominent role in immune-inflammatory responses for most target genes, such as trim7, trim35, trim47, cd225. Crucially, two DElncRNAs (ENSONIT00000076723 and MSTRG.18195.2) were found to co-localize with QTL intervals associated with salinity tolerance, situated near three significant SNPs. Additionally, a notable cis-acting pair, consisting of mRNA ENSONIT00000087370 (apold1a) and lncRNA ENSONIT00000076723, demonstrated a strong correlation under both acute and chronic hypo-osmotic stress. Our findings significantly broaden the understanding of lncRNAs in salinity stress adaptation and suggest their novel roles as key regulators in the osmoregulatory mechanisms of Nile tilapia.