Phylogenomic and metabolomic approaches to provide insight for species delimitation of cultivated <i>Ferula</i> species in Xinjiang, China

The genus <i>Ferula</i> is an important medicinal group within the Apiaceae family, valued globally for its health and culinary uses. Recently, it has gained significant attention because of its cultivation and use to meet growing demands for food and medicine. However, in the Xinjiang production region, farmers often cultivate multiple <i>Ferula</i> species together. In the market, leaves from different species are frequently bundled and sold, leading to inconsistent product quality. This issue greatly reduces the economic value of <i>Ferula</i> as a food resource and affects the efficacy and safety of its clinical applications. Correctly identifying species is essential for the sustainable use and conservation of these plants. Traditional methods mainly rely on floral and fruit traits, but the monocarpic or polycarpic nature of these plants makes species identification difficult, especially since flowering or fruiting specimens are hard to obtain in cultivated conditions. In this study, leaf samples from 30 <i>Ferula</i> specimens collected from ten cultivated locations in Xinjiang were analyzed using phylogenetic methods and ultraperformance liquid chromatography coupled with tandem mass spectrometry (UPLC-MS/MS) to provide insight for species identification and discrimination. Phylogenomic analysis based on the complete plastome was used to clarify relationships among species. The plastome super-barcoding results showed that cultivated <i>Ferula</i> species clustered into three distinct clades: <i>F. sinkiangensis</i>, <i>F. teterrima</i>, and <i>F. fukanensis</i>. Untargeted metabolomic profiling detected 7,169 metabolites, and multivariate analyses (PCA, PLS-DA and HCA) revealed clear chemotaxonomic separation among the three species, with clustering patterns consistent with the phylogenetic tree. Our findings demonstrate that the integration of plastome super-barcoding with metabolomic fingerprinting offers a robust strategy to species discrimination in cultivated <i>Ferula</i>. This combined approach provides complementary chemotaxonomic evidence for differentiating species, with direct implications for ensuring appropriate use in distinct culinary, medicinal, and pharmaceutical applications.