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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 L. vannamei 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 Fem-1a, Fem-1c, and Sxl were found to produce AS isoforms exclusively in ovarian tissue. We also identified three germ cell development-associated genes\u2014MAD2-like, RAD51-like, and Su(dx)-like\u2014that 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 L. vannamei and provide novel insights into the molecular mechanisms governing sex differentiation and gonadal development.<\/jats:p>","DOI":"10.3390\/ijms26125863","type":"journal-article","created":{"date-parts":[[2025,6,19]],"date-time":"2025-06-19T06:11:07Z","timestamp":1750313467000},"page":"5863","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":4,"title":["Full-Length Transcriptome of Testis and Ovary Provides Insights into Alternative Splicing During Gonadal Development in Litopenaeus vannamei"],"prefix":"10.3390","volume":"26","author":[{"given":"Youyan","family":"Wang","sequence":"first","affiliation":[{"name":"School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao 266109, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yang","family":"Yu","sequence":"additional","affiliation":[{"name":"School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao 266109, China"},{"name":"State Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266000, China"},{"name":"Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao 266071, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yue","family":"Wang","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266000, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8693-600X","authenticated-orcid":false,"given":"Fuhua","family":"Li","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266000, China"},{"name":"Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao 266071, China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2025,6,19]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"277","DOI":"10.1007\/s10126-017-9749-5","article-title":"Identification of Sex-determining Loci in Pacific White Shrimp Litopeneaus vannamei Using Linkage and Association Analysis","volume":"19","author":"Yu","year":"2017","journal-title":"Mar. 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