Integrated Analyses of miRNome and Transcriptome Reveal the Critical Role of miRNAs Toward Heat Stress Response in Isochrysis galbana

Isochrysis galbana is widely used in aquaculture as a bait microalgal species. High temperature (HT) can severely impair the development of I. galbana , exerting adverse effects on its yield. MicroRNAs (miRNAs) play an essential role in modulating stress-responsive genes. However, the role of miRNAs in response to HT in microalgae remains largely unexplored. In the present study, we identified several conserved and novel miRNAs in I. galbana through miRNome sequencing. Among these identified miRNAs, 22 miRNAs were differentially expressed in response to heat stress, and their target genes were predicted accordingly. Moreover, a comprehensive and integrated analysis of miRNome and transcriptome was performed. We found that six potential reversely correlated differentially expressed miRNA (DEM) and differentially expressed gene (DEG) pairs were associated with heat stress response (HSR) in I. galbana . The expressions of DEMs and DEGs were further verified using real-time quantitative PCR (RT-qPCR). Integrated analyses showed that miRNAs played fundamental roles in the regulatory network of HSR in I. galbana mainly by regulating some heat-responsive genes, including heat shock proteins (HSPs), reactive oxygen species (ROS) signaling-related genes, and specific key genes in the ubiquitination pathway. Our current study identified the first set of heat-responsive miRNAs from I. galbana and helped elucidate the miRNA-mediated HSR and resistance mechanisms in I. galbana . This new knowledge could provide ways to enhance its heat stress tolerance.