Transcriptomic analysis reveals coordinated carotenoid and oil metabolism during sea buckthorn (Hippophae rhamnoides L.) fruit ripening

Sea buckthorn ( Hippophae rhamnoides L.) is a plant used as both food and medicine, possessing diverse metabolites including carotenoids and fatty acids. However, the fundamental relationship between carotenoid and fatty acid components during sea buckthorn fruit ripening remains not clear. This study integrated phenotypic, physiological, and transcriptomic analyses to explore their accumulation patterns across six developmental stages. Fruit horizontal and longitudinal diameters, and hundred-grain weight, increased progressively during fruit ripening. Total carotenoid, lutein, zeaxanthin, and β-carotene consistently accumulated. Oil content and the relative proportion of monounsaturated fatty acids increased, whereas the relative proportion of polyunsaturated fatty acids decreased. Key structural genes associated with these metabolic shifts were identified: Z-ISO (Sph_LG4G000363), ZDS (Sph_LG4G000989), and BCH (Sph_LG11G000128) were participated in carotenoid metabolism, while NCED-1 (Sph_LG0G002915) and CYP707A4 (Sph_LG1G001039), played roles in abscisic acid metabolism. In addition, SAD5-3 (Sph_LG10G002328), FAD2 (Sph_LG1G001317), FAD3 (Sph_LG3G000182), and GPAT6 (Sph_LG11G002235) also contributed to fatty acid metabolism. Co-expression network analysis indicated that carotenoid and fatty acid biosynthesis were may regulated by transcription factors such as bHLH93 (Sph_LG1G000917) and MYB79 (Sph_LG7G000293), which significantly correlated with carotenoids and oil accumulation, as well as their structural genes. This study identified key metabolites, structural genes, and transcription factors related to carotenoids, oil, and fatty acids in sea buckthorn pulp during fruit ripening. These findings may provide a theoretical foundation for improving the color of sea buckthorn fruit and the nutritional quality of sea buckthorn pulp oil.