Full-length transcriptome of <i>Micropterus salmoides</i> gonads and muscle insights into alternative splicing during gonadal development

The largemouth bass ( Micropterus salmoides ) is a commercially important freshwater aquaculture species. Understanding the molecular mechanisms of gonadal development is critical for improving broodstock quality and enabling monosex culture. However, transcriptional regulatory mechanisms, particularly alternative splicing (AS) events during gonadal differentiation, remain poorly characterized. In this study, Oxford Nanopore Technology (ONT) was employed to generate high-quality full-length transcriptomes from largemouth bass testis, ovary, and muscle tissues. A total of 37,788 unique transcripts were identified, corresponding to 22,273 genes, including 10,065 novel transcripts. Functional annotation revealed distinct transcriptional profiles between gonadal and muscle tissues, with gonadal transcripts enriched in reproductive pathways such as spermatogenesis and steroid hormone biosynthesis, while muscle transcripts displayed functional divergence in non-reproductive processes. Comparative analysis identified 14,112 differentially expressed genes between testes and ovaries, and after refining with muscle tissue controls, 939 testis-specific and 1,353 ovary-specific genes were confirmed. Notably, AS events in gonadal tissues were characterized, uncovering 581 multi-isoform genes in testes and 787 in ovaries. Key genes including dazl (testis-specific) and hsd17b1 (ovary-specific) exhibited differential transcript usage (DTU) and differential transcript expression (DTE), suggesting their roles in sex-specific functional specialization. These findings establish a comprehensive full-length transcriptomic resource for largemouth bass, demonstrate AS as a critical regulatory mechanism in gonadal differentiation, and provide a robust methodological framework for transcriptome studies in aquatic species.