Comparative Transcriptomic Analysis of Male and Female Gonads in Hemibagrus guttatus (Lacepède)

<i>Hemibagrus guttatus</i> is a commercially valuable freshwater fish in the Pearl River Basin, renowned as the "King of Freshwater Fish." Due to habitat degradation and overfishing, its wild population has declined sharply, leading to its listing as a National Key Protected Wild Animal of Class II in China. Artificial breeding is therefore crucial for conservation, yet progress is hindered by the lack of clear sexual dimorphism and poor understanding of its sex differentiation mechanism. In this study, we performed high-throughput RNA sequencing (RNA-seq) to compare gonadal transcriptomes of male and female <i>H. guttatus</i>. A total of 3245 differentially expressed genes (DEGs) were identified, including 3122 male-biased and 123 female-biased DEGs, which clustered into three distinct expression patterns. Enrichment analysis revealed that genes associated with the TGF-β (Transforming Growth Factor-beta) and GnRH (Gonadotropin-Releasing Hormone) signaling pathways were significantly enriched in the female gonads, suggesting their potential roles in gonadal differentiation. From the DEG set, we further highlighted five genes with pronounced sex-biased expression: <i>rbm46</i> (RNA Binding Motif Protein 46) exhibited gonad-specific expression, whereas <i>myc</i> (v-myc avian myelocytomatosis viral oncogene homolog), <i>angptl4</i> (Angiopoietin-Like 4), <i>sox9</i> (SRY-Related HMG-Box Gene 9), and <i>fzd2</i> (Frizzled Class Receptor 2) showed marked expression differences between male and female gonads. These findings provide insights into the molecular mechanisms underlying sex differentiation in <i>H. guttatus</i>, offer potential molecular markers for sex identification, and establish a scientific basis for germplasm conservation and the optimization of breeding techniques.