Small RNA, transcriptome, and degradome sequencing to identify salinity stress responsive miRNAs and target genes in Dunaliella salina

Dunaliella salina is known as the most salinity-tolerant unicellular eukaryote. To explore its molecular response mechanisms to high salinity concentrations, D. salina transcriptomes, small RNA groups and degradomes were analyzed under salinity stress conditions, by high throughput sequencing. A total of 1008 microRNA (miRNA) sequences were identified, including 998 known conserved miRNAs and 10 novel miRNAs. Further analysis of miRNA expression in D. salina under salinity stress found that 49miRNAs showed significant differences in expression. For the first time in D. salina, 745 target genes, regulated by 194 miRNAs, were validated by degradome sequencing. Gene ontology (GO) enrichment analysis and KEGG analysis showed that these miRNA target genes are involved in a variety of molecular biological regulation processes, such as signal transduction, material transport, transcriptional regulation and protein processing. In combination with transcriptome sequencing results, 14 differentially expressed miRNAs and 87 differentially expressed target genes were found to negatively correlate in expression. Further analysis showed that mmu-miR-466, dme-miR-2493, mmu-mir-669h, dre-mir-29a and dme-mir-9388 play an important role in osmoregulation in response to high salinity stress in D. salina. These results enrich existing hypotheses, while providing new insights into the molecular mechanism of salinity tolerance in D. salina.