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In recent years, extensive experience has been accumulated in the cage farming of T. ovatus, but whether it can adapt to deep-sea environments and grow normally remains a current research focus. This study used RNA-Seq sequencing technology to analyze the gene expression changes in the liver of T. ovatus under three conditions: rest (0 cm\/s), medium flow velocity (54 cm\/s), and high flow velocity (90 cm\/s). Through differential expression analysis, Short Time-series Expression Miner (STEM) analysis and protein\u2013protein interaction (PPI) network analysis, a total of 5107 differentially expressed genes (DEGs), three significantly expressed gene profiles (profile6, profile1, and profile5), and 15 hub genes were identified. The results showed that changes in flow speed significantly impacted key biological processes such as energy metabolism, protein homeostasis, and endoplasmic reticulum (ER) stress response. Under moderate and high flow conditions, glycolysis-related genes were upregulated to meet the energy demands of swimming, while the downregulation of the PPAR\u03b3-RXRG complex and its downstream genes in the lipid metabolism pathway suggested a limitation in its fatty acid \u03b2-oxidation capacity. At the same time, protein synthesis was enhanced, and the unfolded protein response (UPR) was activated to help cope with ER stress. Furthermore, when the flow speed reached 90 cm\/s, the expression of UPR- related genes and the anti-apoptotic factor JNK significantly decreased, suggesting that the stress response was nearing its limit and could potentially trigger cell apoptosis. These findings provide new insights into the molecular adaptation mechanisms of T. ovatus to flow speed stress and offer theoretical support for its rational farming in deep-sea cages, suggesting that the water flow speed in farming should not exceed 90 cm\/s.<\/jats:p>","DOI":"10.3390\/ani15131932","type":"journal-article","created":{"date-parts":[[2025,6,30]],"date-time":"2025-06-30T13:06:17Z","timestamp":1751288777000},"page":"1932","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":3,"title":["Transcriptomic Analysis of Trachinotus ovatus Under Flow Velocity Stress"],"prefix":"10.3390","volume":"15","author":[{"given":"Jing","family":"Zhang","sequence":"first","affiliation":[{"name":"College of Fisheries, Guangdong Ocean University, Zhanjiang 524088, China"},{"name":"Guangdong Provincial Key Laboratory of Aquatic Animal Disease Contril and Healthy Culture, College of Fishery, Guangdong Ocean University, Zhanjiang 524088, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xixi","family":"Liu","sequence":"additional","affiliation":[{"name":"College of Fisheries, Guangdong Ocean University, Zhanjiang 524088, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jiayue","family":"Dai","sequence":"additional","affiliation":[{"name":"College of Fisheries, Guangdong Ocean University, Zhanjiang 524088, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sufang","family":"Niu","sequence":"additional","affiliation":[{"name":"College of Fisheries, Guangdong Ocean University, Zhanjiang 524088, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5399-094X","authenticated-orcid":false,"given":"Xuefeng","family":"Wang","sequence":"additional","affiliation":[{"name":"College of Fisheries, Guangdong Ocean University, Zhanjiang 524088, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Baogui","family":"Tang","sequence":"additional","affiliation":[{"name":"College of Fisheries, Guangdong Ocean University, Zhanjiang 524088, China"},{"name":"Guangdong Provincial Key Laboratory of Aquatic Animal Disease Contril and Healthy Culture, College of Fishery, Guangdong Ocean University, Zhanjiang 524088, China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2025,6,30]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"259","DOI":"10.1007\/s10695-011-9505-0","article-title":"Fish under Exercise","volume":"37","author":"Palstra","year":"2011","journal-title":"Fish Physiol. 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