Full-Length Transcriptome of Testis and Ovary Provides Insights into Alternative Splicing During Gonadal Development in Litopenaeus vannamei

The Pacific white shrimp, <i>Litopenaeus vannamei</i> (<i>L. vannamei</i>), is an important aquaculture species, yet the molecular mechanisms underlying its sex differentiation and gonadal development remain poorly understood. A deeper understanding of these processes is critical for advancing broodstock quality and enabling unisex breeding strategies. While previous studies have focused on gene expression differences between females and males, structural differences in transcriptomic regulation between sexes have been largely overlooked. Here, we present a comprehensive full-length transcriptome analysis of <i>L. vannamei</i> testis and ovary, identifying 830 and 690 novel genes, respectively, and over 6000 new isoforms. Notably, we discovered extensive alternative splicing (AS) events, with the cartilage oligomeric matrix protein-like gene exhibiting over 300 AS isoforms in the ovary compared to only 2 in the testis, suggesting a potential role in ovarian development. Furthermore, sex-determining genes such as <i>Fem-1a</i>, <i>Fem-1c</i>, and <i>Sxl</i> were found to produce AS isoforms exclusively in ovarian tissue. We also identified three germ cell development-associated genes-<i>MAD2-like</i>, <i>RAD51-like</i>, and <i>Su(dx)-like</i>-that undergo distinct AS events in gonadal tissues, leading to sex-specific structural domain alterations. These findings highlight the complexity of AS-mediated post-transcriptional regulation in <i>L. vannamei</i> and provide novel insights into the molecular mechanisms governing sex differentiation and gonadal development.