Identification of miRNAs in sea urchin Strongylocentrotus purpuratus larvae response to pH stress

MicroRNAs (miRNAs) are a class of small, endogenous, non-coding RNAs that regulate gene expression through transcriptional repression of messenger RNA. They play significant roles in many physiological and biochemical processes in eukaryotes. Ocean acidification can impact the development, survival, growth and physiology of many marine organisms. Here, we performed miRNA transcriptome analysis of the sea urchin Strongylocentrotus purpuratus larvae exposed to CO2-driven seawater acidification. We generated 10.6 and 10.8 million clean reads from the malformed S. purpuratus larva after CO2 treatment and the larvae with the normal bone development respectively. A total of 682 conserved and 17 novel miRNAs were identified. Target genes of the differential expression miRNAs were also predicted, which contained growth-related genes (collagenase, collagen and HSP70-binding protein 1), spicule formation-related gene (carbonic anhydrase transcript variant X1) and skeletogenesis-related genes (breast carcinoma amplified sequence 2). Target genes of the differentially expressed miRNAs were used to perform KEGG pathway analysis and were found to be involved in the proteasome and oxidative phosphorylation. These results provide a relatively large number of miRNAs transcriptome resource and provide a foundation for further analyses on the functional and molecular mechanisms of S. purpuratus larvae impacted by ocean acidification.