Multidimensional molecular differences between artificial cultivated and wild Artemisia rupestris L. based on metabolomics–transcriptomics integration strategy

Various ecological environments affect the active ingredients and molecular content of medicinal plants. Artemisia rupestris L. is a traditional medicinal plant, and shortages of the wild resource has led to the increased use of artificial cultivated varieties. However, few investigations have studied the molecular differences between the cultivated and wild varieties in a systematic manner. In this study, two A. rupestris varieties were collected in the Altay–Fuyun region, Xinjiang, China. We used a liquid chromatography-mass spectrometry based untargeted metabolomics approach to profile the metabolome in the flower, stem, and leaf samples respectively, and simultaneously analyzed the levels of a panel of representative known metabolites in the plant. The genetic basis of these samples was explored using a de novo transcriptomics approach to investigate differentially expressed genes and their pathway annotations. The results indicated that the metabolic differences between the two varieties were mainly reflected in flavonoids and chlorogenic acid/caffeic acid derivatives. Thirty-four chemical markers, including 19 potentially new compounds, of these two structural categories were identified after validation using another batch of samples. Correlation analysis combined with quantitative real-time polymerase chain reaction revealed that six differentially expressed genes in different organs were closely correlated with 24 chemical markers. This study provides novel insight into the molecular landscape of this medicinal plant.