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.

Background Inter-specific hybridizations were common and can easily take place in Buddleja , and it was an important way for evolution and rapid speciation. The F1 hybrid in this study was a newly identified inter-specific hybridization between B. crispa and B. offic inalis in Sino-Himalayan region. In the natural hybrid zones, F1 hybrids always occupy different habitats from their parents. The objective of this study was to explore environmental acclimatization of F1 hybrids and their parents at physiological and biochemical levels.Results The results showed that F1 hybrids performed as an intermediate in adaptation to their parents, with divergent gas-exchange and chlorophyll fluorescence features. F1 hybrids showed the parallel light compensation point and light saturation point with their parents, but low utilization efficiency to low-light density. They synthesized the greatest total chlorophyll content (10.41 ± 0.56 mg•g -1 ) in leaves than their parents. During the diurnal variation of photosynthesis, F1 hybrids markedly decreased and preserved the stomatal conductance and leaf transpiration rate at a low level. However, they kept high carbon assimilation rate and water-use efficiency with markedly increased vapor pressure deficit. In F1 hybrids, the maximum net photosynthetic rate, maximum water-use efficiency and maximum vapor pressure deficit were 10.48 ± 0.50 mmol CO 2 •mmol -1 photo, 21.52 ± 2.20 µmol•mmol -1 and 4.18 ± 0.55 kPa, respectively. In addition, all Buddleja species performed well and grow healthy with high level of the maximum photochemical efficiency of PSII and low non-photochemical quenching, 0.83 ± 0.004 - 0.85 ± 0.004, and 1.22 ± 0.15 - 1.97 ± 0.08, respectively. In F1 hybrids, they showed great photochemical activity compared to their parental species with high photochemical quenching. Furthermore, the effective quantum yield and electron transport rate presented a similar behavior.Conclusions The results indicated that F1 hybrids have great photochemical activities and growth acclimatization compared to their parents. Associated with the growth performance of F1 hybrids in the homogenous garden, our results suggested that the divergent gas-exchange and chlorophyll fluorescence patterns may facilitate F1 hybrids to respond to different habitats, and to improve growth performance.