The northern pike (Esox lucius) is an economically important cold-water fish species in northern China. It exhibits pronounced sexual dimorphism, yet the molecular mechanism underlying its sex differentiation remains unclear, which hinders the development of aquaculture. Whole-transcriptome sequencing is a powerful approach for screening sex-related genes; however, no such study has been reported for this species to date. In this study, gonadal tissues from three female and three male E. lucius were collected for whole-transcriptome sequencing. A total of 14,941 differentially expressed messengerRNAs, 119 differentially expressed microRNAs, 229 differentially expressed circularRNAs, and 2055 differentially expressed long non-codingRNAs were identified. Functional enrichment analysis revealed that the differentially expressed genes were significantly enriched in pathways closely associated with sex differentiation, such as steroid hormone biosynthesis and oocyte meiosis. Several key sex-biased genes were identified, including female-biased genes (FANCL, DDX5, SRSF5B) and male-biased genes (STAR, FDX1B, ITGA2B). Furthermore, a competing endogenous RNA (ceRNA) regulatory network involving dre-miR-107b was constructed, which may represent a candidate for further investigation into sex differentiation in E. lucius. This study provides the first comprehensive whole-transcriptome dataset of female and male gonads in E. lucius, identifies key sex-biased genes and core pathways involved in its sex differentiation, and thereby identifies the dre-miR-107b-centered ceRNA network and key sex-biased genes (FANCL, DDX5, SRSF5B, STAR, FDX1B, ITGA2B) as core molecular players in sex differentiation of this species.

Northern pike (Esox lucius) exhibits significant sexual growth dimorphism, yet the molecular basis of this sex-biased trait remains largely unexplored. In this study, we performed an integrative analysis of whole-genome DNA methylation (WGBS) and whole-transcriptome (RNA-seq) data from female and male gonadal tissues of E. lucius. Promoter methylation exhibited sexually dimorphic associations with gene expression: in females, promoter hypermethylation showed a positive correlation with elevated expression, whereas no such association was observed in males; gene body methylation was not correlated with expression in either sex. Integrative analysis identified a total of 508 methylation-associated differentially expressed genes (mDEGs), comprising 377 Hyper-Down (hypermethylated with downregulated expression) and 131 Hypo-Up (hypomethylated with upregulated expression) genes, from which 13 candidate genes were prioritized. Pathway enrichment analyses implicated TGF-β signaling, Wnt signaling, and progesterone-mediated oocyte maturation pathways, suggesting crosstalk between sex differentiation and metabolic regulation/signal transduction. Collectively, this study provides an exploratory perspective on the epigenetic landscape associated with sex differentiation in E. lucius. Our results reveal associations between promoter methylation and the expression of core sex-related genes, including dmrt1 (male-biased) and rspo1 (female-biased), which may be relevant to sex differentiation. The potential link between these epigenetic patterns and sexual growth dimorphism remains speculative and requires direct validation using growth-related phenotypic data and tissues.