Qian Xiao

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.

The increasing salinization and alkalization of inland waters in China pose a growing threat to the early developmental stages of fish. This study investigated the survival rates and transcriptomic response mechanisms of pond smelt (Hypomesus nipponensis) embryos, a species naturally adapted to brackish water, under different salinity stresses. Fertilized eggs were exposed to four salinity gradients: freshwater (0‰, experimental control) and 7‰, 14‰, and 21‰ for 7 days. The results showed that the upper salinity tolerance limit for embryos was between 21‰ and 28‰; hatching rates were zero in the 28‰ and 35‰ groups, and the hatching rate in the 21‰ group decreased to 40.3 ± 6.1%. Transcriptome sequencing analysis of the 0‰, 7‰, 14‰, and 21‰ groups revealed that salinity stress induced extensive differential gene expression in a non-monotonic response pattern. In the 7‰ and 14‰ groups, the number of downregulated genes (approximately 10,000) was significantly higher than that of upregulated genes (approximately 3300). In contrast, in the high-salinity 21‰ group, upregulated genes increased to 4535. Functional enrichment analysis revealed that the calcium signaling pathway, axon guidance, and glutamatergic synapse pathway were significantly enriched across all salinity groups. Changes in the expression of key differential genes (e.g., sparc, hspa4a, aldob, and csmd1a) further confirmed molecular events such as dysregulation of calcium homeostasis, stress protein activation, metabolic inhibition, and neurodevelopmental regulation. The qRT-PCR validation results were highly consistent with the transcriptome data. This study is the first to systematically reveal the molecular regulatory network of pond smelt embryos in response to increasing salinity relative to a freshwater reference point. Our findings indicate their potential for proliferation in moderate saline–alkaline waters (≤14‰), while high salinity (≥21‰) significantly reduces hatching success and triggers a strong stress response. These results provide an important molecular basis and theoretical reference for the enhancement and aquaculture of this species in saline–alkaline waters.

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.

Digestive tract structure is a key indicator of fish health and environmental adaptation, while seasonal dynamics of the gut microbiota reflect host responses to environmental changes. In this study, the digestive tract microstructure of Hypomesus nipponensis from Bosten Lake was characterized using H&E staining and scanning electron microscopy, followed by 16S rDNA gene V3-V4 region sequencing and analysis of the gut microbiota in spring, summer, and autumn. The results showed that the esophageal mucosa of H. nipponensis is a stratified columnar epithelium, with abundant gastric glands, and the circular muscle layer of the stomach caeca is significantly thickened (244.84 ± 49.01 μm). The pyloric caeca resemble the gut in structure; both are covered with dense microvilli on the luminal surface. Collectively, these features constitute the structural basis for its carnivorous diet. Microbiota analysis revealed that the diversity of gut microbiota fluctuated significantly with season: the Chao, Ace, and Sob indices in spring (144.63 ± 30.27) were significantly higher than in summer (82.13 ± 21.45) and autumn (83.25 ± 15.30) (p < 0.001), with no significant difference between summer and autumn (p > 0.05). The dominant marker genera of H. nipponensis in spring, summer, and autumn were Bacillus (31.60%), Clostridium (32.20%), and Sarcina (29.32%), respectively. This study describes the adaptive characteristics of the digestive tract structure and feeding habits of H. nipponensis and reveals the seasonal changes in its gut microbiota. Importantly, since the digestive tract structure data were collected only in summer, the direct relationship between the structure and seasonal microbial dynamics cannot be determined, and multi-season histological sampling is needed for further investigation. Nevertheless, these findings provide preliminary morphological and microbiological references for the ecological adaptation of this species in Bosten Lake and offer a scientific basis for water resource management in this area.

To investigate the effect of epigenetic modifications on sex determination and differentiation in northern pike (Esox lucius), we employed Whole-Genome Bisulfite Sequencing (WGBS) to analyze the DNA methylation patterns in gonadal tissues of females, males, and neomales. First, we obtained high-quality sequencing data, including a total of 410.16 Gb of raw reads and 361.48 Gb of clean reads, with an 86% unique mapping rate, and a bisulfite conversion efficiency of 99.6%. Subsequently, comparative analysis revealed that 66,581 differentially methylated CG regions (i.e., DNA regions with a high frequency of CG dinucleotides), 1215 differentially methylated CHG regions (i.e., DNA regions where CG is followed by another nucleotide), and 3185 differentially methylated CHH regions (i.e., regions where cytosine is methylated in a CHH sequence, with ‘H’ representing A, T, or C) were identified among the three groups. Furthermore, we identified four key differentially methylated candidate genes (Rspo1, hsd11b2, CYP27A1 and smad3) associated with sex determination and differentiation processes in E. lucius. Finally, by integrating GO and KEGG enrichment analyses, we explored the role of epigenetic modification regulatory networks in the sex determination and differentiation of E. lucius and identified multiple metabolic pathways related to sex determination and differentiation processes (Notch signaling pathway, Wnt signaling pathway and Ovarian steroidogenesis). This study thereby lays a foundation for subsequent functional verification.