| Summary: | Salinity is a crucial environmental factor influencing the survival, growth, development, and reproduction of aquatic animals. However, the underlying molecular mechanisms of the shrimp’s response to salinity stress are not yet fully understood. Therefore, we used the Illumina NovaSeq 6000 platform to perform transcriptome sequencing of the hepatopancreas of <i>Litopenaeus vannamei</i> under high-salinity (30 PSU), medium-salinity (10 PSU), and low-salinity (0.5 PSU) conditions. We obtained 63.23 Gb of high-quality data and identified 3589 differentially expressed genes (DEGs), including 1638 upregulated and 1951 downregulated genes. Notably, a comparison between the control group (30 PSU) and the low-salinity group (0.5 PSU) revealed that the <i>BBOX1</i> and <i>CHE1</i> genes were significantly upregulated, while the <i>ACOX1</i>, <i>MPV</i>, <i>CYP2L1</i>, <i>GCH</i>, <i>MVK</i>, <i>TREt1</i>, and <i>XDH</i> genes were significantly downregulated. These genes are primarily involved in key metabolic pathways, such as fatty acid oxidation, cholesterol metabolism, and hormone synthesis and metabolism. The key genes involved in fatty acid β-oxidation, such as <i>ACOX1</i>, <i>ACAD</i>, <i>HADH</i>, <i>HSD17B4</i>, <i>PECR</i>, <i>CROT</i>, <i>PIPOX</i>, and <i>CG5009</i>, all showed a downward trend, suggesting that <i>L. vannamei</i> may respond to salt stress by regulating fatty acid oxidative metabolism, optimizing energy utilization, and maintaining cell homeostasis under low-salinity conditions. Functional annotation of gene ontology (GO) and KEGG pathway enrichment analysis highlighted the roles of these significant DEGs in the adaptation of <i>L. vannamei</i> to environments of varying salinity, underscoring the importance of metabolic pathways in their adaptive physiological responses. This study provides a crucial molecular biological basis for understanding the molecular mechanisms and physiological protection strategies of <i>L. vannamei</i> under salinity stress.
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