Physiological, transcriptomic, and metabolomic analyses reveal the adaptation mechanism of Gracilaria tenuistipitata var. liui under long-term salt stress

Salinity is a critical ecological factor influencing the composition, growth, and reproduction of macroalgae. Gracilaria tenuistipitata var. liui is a key cultivated species of Gracilaria in southern China, with both economic and ecological significance. It inhabits in intertidal zones, estuaries, brackish ponds, and lagoons, with an optimal growth salinity range of 15–30 psu and long-term tolerance to salinities of 5–75 psu. Although G. tenuistipitata demonstrates long-term adaptability to a broad range of salinities, the molecular mechanisms underlying its salinity tolerance remain poorly understood.To explore these mechanisms, we investigated the physiological responses of G. tenuistipitata to varying salinities (5–70 psu) and analyzed its transcriptomic and metabolomic profiles at salinities of 5 psu (S5), 60 psu (S60), and 30 psu (S30, control). Physiological data indicated that growth, photosynthesis, and total soluble protein content were significantly affected by salinity levels. Transcriptome sequencing generated a total of 85,894 unigenes, with 42,503 successfully annotated. Comparative analysis revealed 1480 differentially expressed genes (DEGs) in the S30 vs S5 group (759 upregulated; 721 downregulated) and 2451 DEGs in the S30 vs S60 group (1255 upregulated; 1196 downregulated). Nitrogen metabolism, Betalain biosynthesis, Biosynthesis of amino acids and Carotenoid biosynthesis pathways were significantly enriched in the S5. In the S60, ABC transporters pathway enrichment was relatively significant. A total of 25 metabolites were detected, the metabolite profiles of S5 were more similar to those of S30. Salinity variation had a significant impact on the regulation of energy metabolism, photosynthesis, and antioxidant systems in G. tenuistipitata. Overall, G. tenuistipitata exhibited stronger tolerance to hypo-saline conditions. These findings provide valuable insights into the molecular basis of salinity adaptation in G. tenuistipitata, contributing to a better understanding of its ecological and economic potential.