Integration analysis of microRNAs and mRNA reveals a regulatory mechanism in gonadal differentiation of sea cucumber Apostichopus japonicus

Apostichopus japonicus is a significant aquaculture species in the eastern coastal regions of China. A. japonicus is a dioecious species, but it lacks secondary sexual characteristics that aid in sex identification in the sea cucumber breeding industry. An integrated comparative analysis of microRNAs and mRNA in female and male gonadal whole transcriptome datasets was conducted to identify female gonad- and male gonad-specific genes or microRNAs, particularly molecular networks between protein-coding genes and non-coding microRNAs. We identified 7613 differentially expressed genes (DEGs) and 225 differentially expressed miRNAs (DEmiRs) in total by analyzing male gonad and female gonad transcriptomes. In total, 754 DEGs were considered sex-related genes within Gene Ontology terms associated with reproductive processes or gonadal differentiation by means of GO and KEGG enrichment analysis. Among these, twenty hub genes in the female gonad (e.g., mcm5, mov10l1) and seven hub genes (e.g., tent4b, msh5) in the male gonad potentially contribute to gonadal function or reproductive processes in A. japonicus within protein–protein interaction networks. There were 140 potential miRNA-mRNA negative correlation pairs identified when predicting target genes for differentially expressed microRNA. The integrated mRNA-miRNA analysis identified 16 DEmiRs with negative regulatory relationships with key genes in the PPI network, primarily targeting five DEGs (cct2, sdr16c5, act5c, fnip1, and pla2g6). This study could provide insights into regulatory mechanisms on gonadal differentiation in A. japonicus and the molecular foundation of sexual development and reproductive biology in echinoderms.