Integrating gonadal RNA-seq and small RNA-seq to analyze mRNA and miRNA changes in medaka sex differentiation
2025-05-12
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.