Differentially expressed miRNAs offer new perspective into cave adaptation of Astyanax mexicanus

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 gene expression changes between morphs under even 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. Our analysis identified 683 mature miRNAs, establishing 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 cave milieu. Furthermore, we performed in silico target prediction of these miRNAs, revealing possible roles in developmental and metabolic pathways pivotal for thriving in nutrient-limited cave conditions. Interestingly, we also observed that Molino, which is the “youngest” of the three cavefish analyzed in this study, exhibited the most abundant number of differentially expressed mature miRNAs among the cave morphs. The comprehensive miRNA catalog generated, along with the insight into their differential expression across different morphs, will guide future investigations into the intricate world of miRNA-mediated evolution of complex traits.