Integrating gonadal RNA-seq and small RNA-seq to analyze mRNA and miRNA changes in medaka sex differentiation

MicroRNAs are important post-transcriptional regulators, yet the molecular crosstalk between miRNAs and their target genes during sex differentiation remains poorly understood. Medaka (Oryzias latipes), the first fish in which the sex determination gene was identified, serves as an ideal model for studying this process. Here, we generated gonadal RNA-seq and small RNA-seq data from XY^DMY- females, wild-type females and males to explore this crosstalk. A total of twenty-seven RNA-seq datasets, comprising 188 Gb of raw reads, and twenty-seven small RNA-seq datasets, totaling 18 Gb of raw reads, were collected, covering 10, 30 and 120 days. After optimizing the mapping and normalizing, we conducted transcriptional and post-transcriptional dynamic analyses of differentially expressed genes and miRNAs between WT females and males, as well as between WT females and XY^DMY- females. Additionally, we integrated the RNA-seq and small RNA-seq data to construct comprehensive interaction networks and performed a detailed analysis of the temporal dynamics in gene and miRNA expression. These resources offer valuable insights into the transcriptional regulation of gonadal differentiation and development in vertebrates.