Sweet potato is the sixth most important crop widely cultivated around the world with abundant varieties. Different varieties gain different phenolic profiles which has drawn researchers’ attention for its unique health benefits. Our study evaluated the phenolic profiles, total and cellular antioxidant activities, antiproliferative activities, and cytotoxicity in 10 cultivated varieties of sweet potato in different colours. Among fourteen metabolites detected in our study, hyperoside, ferulic acid and caffeic acid were considered as prominent in SPSRs. According to the principle component analysis, phytochemical composition of HX22, YS15 and YS7 was quite similar. The results also evidenced that purple-fleshed varieties, such as YS43, YZ7 and YY153, have higher total phenolics content and corresponding stronger total antioxidant capacities as well as cellular antiproliferative activities against human liver cancer HepG2 cells than other varieties. The extremely significant correlation between phenolics and total antioxidant activity was also revealed by Pearson correlation analysis (p < 0.05). However, no significant relevance was found between intracellular antioxidant activity and total phenolic content or flesh colour of sweet potatoes.

Flavonoids are essential secondary metabolites that predominantly affect flower pigmentation in plants. Understanding the molecular mechanisms underlying flower color divergence is crucial for ornamental plant breeding. This study aimed to elucidate the factors responsible for the differences in color between white-petaled Cosmos bipinnatus and orange-petaled Cosmos sulphureus. We employed an integrated approach combining untargeted LC–MS/MS metabolomics and high-throughput transcriptome sequencing of fresh petals to analyze pigment composition and differential gene expression. Petal pigment extraction, total flavonoid quantification, and metabolomic profiling consistently revealed that differences in flavonoid abundance are responsible for flower color divergence between the two species. In contrast, carotenoids, previously considered potential contributors to flower coloration, were neither evident in the oil phase of the pigment extracts nor detected by metabolomic analysis. Flavonoid compounds accumulated at relatively high levels in the orange petals of C. sulphureus, reaching 11.36 times that of C. bipinnatus, contributing to its bright appearance. Transcriptomic analysis revealed differences in gene expression patterns between the two species, highlighting key candidate genes involved in the flavonoid biosynthesis pathway, such as chalcone synthase. These findings indicate that the orange coloration of C. sulphureus may be associated with CHS-regulated accumulation of naringenin chalcone and downstream compounds in the flavonoid metabolic pathway after CHS, providing valuable theoretical support for a deeper understanding of the causes underlying the differences in flower color between C. bipinnatus and the orange-petaled C. sulphureus.