Abstract

The spotted scat ( Scatophagus argus ), an economically valuable aquaculture species in southern China, exhibits a pronounced sexual dimorphism in growth performance, with females growing significantly faster than males. Nevertheless, progress in sex-controlled breeding remains limited due to limited understanding of its sex determination and differentiation mechanisms. To investigate sex-biased gene expression in this species, a comprehensive transcriptomic analysis was performed. A total of 62 transcriptomic libraries were analyzed, comprising 18 newly sequenced libraries derived from female gill, muscle, stomach, heart, and adipose tissue, and male adipose tissue, integrated with 44 publicly available libraries covering the brain, pituitary gland, liver, kidney, gonads, and other tissues. The analysis identified 33,214 unigenes, including 8958 novel genes, with 1724 receiving functional annotation. Principal component analysis (PCA) and heatmap clustering revealed distinct expression profiles in gonadal (ovary and testis) and somatic tissues. Differential expression analysis identified 2951 ovary-highly expressed and 1660 testis-highly expressed genes. Functional annotation revealed genes essential for folliculogenesis, spermatogenesis, and meiosis, including figla , gdf9 , mos , amhr2 , spata22 , and dmc1 . Additionally, 23 ovary-specific and 75 testis-specific genes were identified. KEGG enrichment analysis revealed significantly enriched pathways in the gonads, including oocyte meiosis, cell cycle, and DNA replication. RT-PCR and qRT-PCR validations confirmed the RNA-seq results, demonstrating consistent tissue-specific expression patterns of these genes. These findings advance the understanding of the molecular mechanisms of sex differentiation and gametogenesis in spotted scat and provided a foundation for studies of reproductive regulation and gonadal development in this species.