Multidimensional molecular differences between artificial and wild Artemisia rupestris L.

Different ecological environments affect the active ingredients and molecular content of medicinal plants. Artemisia rupestris L. is a kind of traditional medicinal plant, and the shortages of the wild resource have led to increased use of artificial varieties. However, there have few investigations referring to molecular differences between them in a systematic manner. In the present study, artificial and wild Artemisia rupestris L. plants were collected in the Altay-Fuyun region, Xinjian, China. Untargeted metabolomics method based on liquid chromatography-mass spectrometry (LC-MS) technology was applied to profile flower, stem, and leaf samples, respectively, and levels of a panel of representative known metabolites in this plant were simultaneously analyzed. The genetic basis of these samples was explored using a de novo transcriptomics approach to investigate differentially expressed genes (DEGs) and their pathway annotations. Results indicated metabolic differences between the two varieties mainly reflected in flavonoids and chlorogenic acid/caffeic acid derivatives. 34 chemical markers (CMs) belonging to these two structural categories were discovered after validation using another batch of samples, including 19 potentially new compounds. After correlation analysis, total of six DEGs in different organs relating to 24 CMs were confirmed using quantitative real-time PCR (qPCR). These findings provided novel insight into the molecular landscape of this medicinal plant through metabolomics-transcriptomics integration strategy, and reference information of its quality control and species identification. ONE SENTENCE SUMMARYA metabolomics-transcriptomics research on Artemisia rupestris L. to discover metabolite differences and the genetic basis between artificial and wild varieties in systematic and novel manner.