Identification of salinity-responsive microRNAs in Dunaliella salina and their regulatory influence on carotenogenic genes

Carotenoid biosynthesis in Dunaliella species is regulated by a complex network of molecular mechanisms, which remain largely unexplored. MicroRNAs (miRNAs) function as post-transcriptional regulators, acting as molecular switches that modulate gene expression. However, their role in the regulation of carotenogenesis pathway genes (Crt genes) in D. salina has not been investigated. This study aimed to identify and characterize miRNAs involved in the regulation of Crt genes in D. salina using publicly available Sequence Read Archive (SRA) data and a homology-based mapping approach. A total of 30 miRNAs were mapped from the D. salinaSRA dataset, and their potential targets among Crt genes were predicted using psRNATarget. The miRNA-target interactions were validated through RNA hybridization analysis using RNAHybrid. Five miRNAs—dsa-miR1163.2, dsa-miR917, dsa-miR1145.1, dsa-miR166a-3p, and dsa-miR414—were identified in D. salinaas putative regulators of Crt genes and were further analyzed for differential expression under salinity stress using reverse transcription quantitative PCR (RT-qPCR) was performed to confirm their expression profiles. This study represents the first report of miRNAs from a D. salina strain isolated from Sambhar Lake, India, providing novel insights into miRNA-mediated regulation of Crt genes. These findings pave the way for future research on engineering D. salina strains with enhanced carotenoid production for commercial applications.