Potential role of microRNAs in regulating transcriptional profile, and sculpting development and metabolism in cavefish.

Astyanax mexicanus, a species with both surface-dwelling and multiple cave-dwelling populations, offers a unique opportunity to study repeated adaptation to dark and resource-scarce environments. While previous work has identified large-scale changes in gene expression between morphs even under identical laboratory conditions, the regulatory basis of these expression differences remains largely unexplored. In this study, we focus on microRNAs (miRNAs) as key regulators of gene expression to understand cavefish adaptation nuances. Our analysis identified 683 miRNAs, which not only surpasses the number documented in related species but also provides the first comprehensive catalog of miRNAs for this species. We identified a unique subset of differentially expressed miRNAs common to all studied cave-dwelling populations, potentially orchestrating the nuanced gene expression patterns required for survival in the challenging cave milieu. Gene Ontology analysis of the predicted miRNA targets revealed involvement in developmental and metabolic pathways that are pivotal for thriving in nutrient-limited environments, such as the regulation of neuromast migration. Moreover, our study provides evidence for miRNA influence on circadian rhythm and oxidative stress response, both essential adaptations for the cave-dwelling lifestyle. The comprehensive miRNA catalog generated will guide future investigations into the intricate world of miRNA-mediated evolution of complex traits.