Ovarian microrna transcriptome of Macrobrachium rosenbergii after eyestalk ablation: unveiling molecular switches in reproductive regulation

Macrobrachium rosenbergii is an economically important freshwater prawn species in China. The X-organ–sinus gland complex in crustacean eyestalks regulates reproduction through neurohormones, with ablation significantly promoting ovarian maturation. However, the miRNA mediated molecular mechanisms underlying this eyestalk ovary regulatory axis remain poorly characterized in M. rosenbergii. RNA sequencing of 9 ovarian samples produced 207 million paired-end reads (62.25 Gb total), averaging > 6 Gb per sample with Q30 scores exceeding 94.42%. The reads showed 84.32% alignment efficiency to the reference transcriptome. Transcriptomic analysis identified 769 differentially expressed genes (DEGs) and 176 differentially expressed miRNAs (DEMs), which were significantly enriched in reproduction related pathways including steroid biosynthesis and Wnt signaling.​ Integration analysis revealed 11 functionally important miRNA-mRNA regulatory pairs targeting key ovarian development genes. qRT-PCR validation confirmed the high reliability of sequencing data. Transcriptomic analysis of ovarian mRNA and miRNA in eyestalk-ablated M. rosenbergii revealed the molecular mechanisms of eyestalk mediated ovarian regulation.​​ Eyestalk ablation significantly upregulated vitellogenin genes and ecdysteroid biosynthesis genes, ​​demonstrating its dual regulatory role in reproduction and molting.​​ The findings indicate potential roles of the eyestalk in reproductive regulation via specific pathways, with the identified DEGs and DEMs serving as a valuable resource for future investigations.