Angelica sinensis is a traditional Chinese medicinal plant that has been primarily used as a blood tonic. It largely relies on its bioactive metabolites, which include ferulic acid, volatile oils, polysaccharides and flavonoids. In order to improve the yield and quality of A. sinensis, the two cultivars Mingui 1 (M1), with a purple stem, and Mingui 2 (M2), with a green stem, have been selected in the field. Although a higher root yield and ferulic acid content in M1 than M2 has been observed, the differences of flavonoid biosynthesis and stem-color formation are still limited. In this study, the contents of flavonoids and anthocyanins were determined by spectrophotometer, the differences of flavonoids and transcripts in M1 and M2 were conducted by metabolomic and transcriptomic analysis, and the expression level of candidate genes was validated by qRT-PCR. The results showed that the contents of flavonoids and anthocyanins were 1.5- and 2.6-fold greater in M1 than M2, respectively. A total of 26 differentially accumulated flavonoids (DAFs) with 19 up-regulated (UR) and seven down-regulated (DR) were obtained from the 131 identified flavonoids (e.g., flavonols, flavonoid, isoflavones, and anthocyanins) in M1 vs. M2. A total 2210 differentially expressed genes (DEGs) were obtained from the 34,528 full-length isoforms in M1 vs. M2, and 29 DEGs with 24 UR and 5 DR were identified to be involved in flavonoid biosynthesis, with 25 genes (e.g., CHS1, CHI3, F3H, DFR, ANS, CYPs and UGTs) mapped on the flavonoid biosynthetic pathway and four genes (e.g., RL1, RL6, MYB90 and MYB114) belonging to transcription factors. The differential accumulation level of flavonoids is coherent with the expression level of candidate genes. Finally, the network of DAFs regulated by DEGs was proposed. These findings will provide references for flavonoid production and cultivars selection of A. sinensis.

Introduction: Cistanche deserticola is an important traditional Chinese herbal medicine. The fresh cistanche squamous stem is typically yellow-white and brown after drying. Oil cistanche is a cistanche variant with a purple squamous stem that turns black after drying. The color difference between oil cistanche and cistanche is obvious, and the former has a higher market price. However, the mechanism underlying the color difference of oil cistanche and cistanche remains unclear.Methods: This study evaluated the total flavone contents in oil cistanche and cistanche and compared the differential metabolites and differentially expressed genes (DEGs) and the contents of iridoid of dried oil cistanche and cistanche samples were determined by high-performance liquid chromatography, and finally the polysaccharides contents of them were determined to comprehensively analyze the formation mechanism of color difference between oil cistanche and cistanche.Results: The results showed that the total flavonoid content in oil cistanche was significantly higher than that in cistanche. Metabolomic analysis identified 50 differentially accumulated metabolites (DAMs) (34 up-regulated and 16 down-regulated), including carbohydrates, terpenoids, and flavonoids. Moreover, 3,376 DEGs were selected, among which significant up-regulated of IGS1 and CYP84A1 and down-regulated of 4CLL1, F6H2-2-1 and 5MAT1 genes jointly regulated flavonoid biosynthesis and affected the accumulation of differentially accumulated metabolites. Significant up-regulated of the CCD7 gene affected carotenoid component production, and significant up-regulated of the UGT85A24 gene promoted the accumulation of geniposidic acid. In addition, the contents of iridoid and polysaccharide in oil cistanche were significantly higher than those in cistanche.Discussion: The differential expression of flavonoids and terpenoid differential metabolites and CYP84A1, 5MAT1, FLS, UGT85A24 and CCD7 mainly caused the purple color of fresh oil cistanche. Dried samples of oil cistanche were darker in color than those of cistanche, due to the higher content of iridoids and polysaccharides in the former. This study preliminarily revealed the causes of the color differences between oil cistanche and cistanche, and provided references for the systematic study of cistanche and its germplasm resources, as well as for the breeding of C. deserticola.