Full-Length Transcriptome Comparison of Male and Female Gonads in Scatophagus argus Reveals Alternative Splicing Events

Spotted scat (Scatophagus argus) is an economically important fish species with an XX/XY sex determination (SD) system and the candidate sex-determining gene Dmrt1Y. Alternative splicing (AS) contributes to transcript diversity and post-transcriptional regulation, but its role in fish gonadal function remains unclear. In this study, we conducted a comprehensive analysis of AS events in adult ovaries (n = 3) and testes (n = 3) of S. argus using ONT-based full-length transcriptome sequencing. An average of 7.30 Gb of clean data per sample was obtained, with a mean N50 length of 1502 bp. A total of 3333 differentially expressed genes (DEGs) were identified, including 2064 ovary-upregulated and 1269 testis-upregulated genes. Additionally, 9417 and 17,216 AS events were detected in the ovary and testis, respectively. Notably, no AS events were detected in the Dmrt1Y gene. A total of 2253 differential alternative splicing (DAS) events involving 1300 genes were identified between ovaries and testes. Of these, only 213 genes were also differentially expressed. Sex-biased AS patterns were observed in genes potentially associated with gonadal function and germ-cell regulation, including Ncoa5, Tp53, and Fancl. Male-biased AS events in Tp53 and Fancl were predicted to alter coding regions corresponding to the DNA-binding and UBC-like domains, respectively. Furthermore, male-biased Ncoa5 isoforms lacking exons 3 and 4 (381 bp) were predicted to result in partial loss of the RNA recognition motif (RRM). Collectively, this study provides insights into AS regulation in adult gonads of S. argus and highlights the potential contribution of AS to reproduction.