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Cultivating all-female seedlings can significantly improve breeding efficiency. To accelerate the cultivation process of all female seedlings of this species, it is necessary to deeply understand the regulatory mechanisms of sexual differentiation and gonadal development. This study used Illumina high-throughput sequencing to sequence the transcriptome of the testes and ovaries of Nao-zhou stock large yellow croaker to identify genes and molecular functions related to sex determination. A total of 10,536 differentially expressed genes were identified between males and females, including 5682 upregulated and 4854 downregulated genes. Functional annotation screened out 70 important candidate genes related to sex, including 34 genes highly expressed in the testis (including dmrt1, foxm1, and amh) and 36 genes highly expressed in the ovary (including gdf9, hsd3b1, and sox19b). Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis found that differentially expressed genes were significantly enriched in nine signaling pathways related to sex determination and gonadal development, including steroid hormone biosynthesis, MAPK signaling pathway, and the TGF-beta signaling pathway. By screening sex-related differentially expressed genes and mapping protein\u2013protein interaction networks, hub genes such as dmrt1, amh, and cyp19a1a were found to be highly connected. The expression levels of 15 sex-related genes, including amh, dmrt1, dmrt2a, foxl1, and zp3b, were determined by qRT\u2013PCR and RNA sequencing. This study screened for differentially expressed genes related to sex determination and differentiation of Nao-zhou stock large yellow croaker and revealed the signaling pathways involved in gonad development of male and female individuals. The results provide important data for future research on sex determination and differentiation mechanisms, thereby providing a scientific basis for the cultivation of all-female seedlings.<\/jats:p>","DOI":"10.3390\/ani14223261","type":"journal-article","created":{"date-parts":[[2024,11,13]],"date-time":"2024-11-13T06:23:16Z","timestamp":1731478996000},"page":"3261","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":11,"title":["Comparative Transcriptome Analysis of Sexual Differentiation in Male and Female Gonads of Nao-Zhou Stock Large Yellow Croaker (Larimichthys crocea)"],"prefix":"10.3390","volume":"14","author":[{"given":"Haojie","family":"Wang","sequence":"first","affiliation":[{"name":"Fishery College, Guangdong Ocean University, Zhanjiang 524025, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zirui","family":"Wen","sequence":"additional","affiliation":[{"name":"Fishery College, Guangdong Ocean University, Zhanjiang 524025, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8991-8368","authenticated-orcid":false,"given":"Eric","family":"Amenyogbe","sequence":"additional","affiliation":[{"name":"Department of Water Resources and Aquaculture Management, University of Environment and Sustainable Development, PMB, Somanya, Ghana"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jinghui","family":"Jin","sequence":"additional","affiliation":[{"name":"Fishery College, Guangdong Ocean University, Zhanjiang 524025, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yi","family":"Lu","sequence":"additional","affiliation":[{"name":"Fishery College, Guangdong Ocean University, Zhanjiang 524025, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhongliang","family":"Wang","sequence":"additional","affiliation":[{"name":"Fishery College, Guangdong Ocean University, Zhanjiang 524025, China"},{"name":"Guangdong Provincial Key Laboratory of Aquatic Animal Disease Control and Healthy Culture, Zhanjiang 524088, China"},{"name":"Guangdong Marine Fish Science and Technology Innovation Center, Zhanjiang 524088, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jiansheng","family":"Huang","sequence":"additional","affiliation":[{"name":"Fishery College, Guangdong Ocean University, Zhanjiang 524025, China"},{"name":"Guangdong Provincial Key Laboratory of Aquatic Animal Disease Control and Healthy Culture, Zhanjiang 524088, China"},{"name":"Guangdong Marine Fish Science and Technology Innovation Center, Zhanjiang 524088, China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2024,11,13]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","unstructured":"Hayashida, T., Soma, S., Nakamura, Y., Higuchi, K., Kazeto, Y., and Gen, K. 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