Background: Traditional Chinese medicine uses various herbs for the treatment of various diseases for thousands of years and it is now time to assess the characteristics and effectiveness of these medicinal plants based on modern genetic and molecular tools. The herb Flos Lonicerae Japonicae (FLJ or Lonicera japonica Thunb.) is used as an anti-inflammatory agent but the chemical quality of FLJ and its medicinal efficacy has not been consistent. Here, we analyzed the transcriptomes and metabolic pathways to evaluate the active medicinal compounds in FLJ and hope that this approach can be used for a variety of medicinal herbs in the future.

The content of flavonoids especially baicalin and baicalein determined the medical quality of Scutellaria baicalensis which is a Chinese traditional medicinal plant. Here, we investigated the mechanism responsible for the content and composition of flavonoids in S. baicalensis under water deficit condition. The transcription levels of several genes which are involved in flavonoid biosynthesis were stimulated by water deficit. Under water deficit condition, fifteen up-regulated proteins, three down-regulated proteins and other six proteins were detected by proteomic analysis. The identified proteins include three gibberellin (GA)- or indoleacetic acid (IAA)-related proteins. Decreased endogenous GAs level and increased IAA level were observed in leaves of S. baicalensis which was treated with water deficit. Exogenous application of GA or α-naphthalene acelic acid (NAA) to plants grown under water deficit conditions led to the increase of endogenous GAs and the decrease of IAA and flavonoids, respectively. When the synthesis pathway of GA or IAA in plants was inhibited by application with the inhibitors, flavonoid levels were recovered. These results indicate that water deficit affected flavonoid accumulation might through regulating hormone metabolism in S. baicalensis Georgi.

Spatholobus suberectus Dunn ( S . suberectus ), which belongs to the Leguminosae, is an important medicinal plant in China. Owing to its long growth cycle and increased use in human medicine, wild resources of S . suberectus have decreased rapidly and may be on the verge of extinction. De novo assembly of the whole S . suberectus genome provides us a critical potential resource towards biosynthesis of the main bioactive components and seed development regulation mechanism of this plant. Utilizing several sequencing technologies such as Illumina HiSeq X Ten, single-molecule real-time sequencing, 10x Genomics, as well as new assembly techniques such as FALCON and chromatin interaction mapping (Hi-C), we assembled a chromosome-scale genome about 798 Mb in size. In total, 748 Mb (93.73%) of the contig sequences were anchored onto nine chromosomes with the longest scaffold being 103.57 Mb. Further annotation analyses predicted 31,634 protein-coding genes, of which 93.9% have been functionally annotated. All data generated in this study is available in public databases.

The useful information of Lamiophlomis rotata (Benth.) Kudo was summarized, which provided a basis for the development of new therapeutic drugs for this plant.

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Drought stress affects the normal growth and development of Mesona chinensis Benth (MCB), which is an important medicinal and edible plant in China. To investigate the physiological and molecular mechanisms of drought resistance in MCB, different concentrations of polyethylene glycol 6000 (PEG6000) (0, 5, 10, and 15%) were used to simulate drought conditions in this study. Results showed that the growth of MCB was significantly limited under drought stress conditions. Drought stress induced the increases in the contents of Chla, Chlb, Chla + b, soluble protein, soluble sugar, and soluble pectin and the activities of superoxide dismutase (SOD), catalase (CAT), total antioxidant capacity (TAC), hydrogen peroxide (H2O2), and malondialdehyde (MDA). Transcriptome analysis revealed 3,494 differentially expressed genes (DEGs) (1,961 up-regulated and 1,533 down-regulated) between the control and 15% PEG6000 treatments. These DEGs were identified to be involved in the 10 metabolic pathways, including “plant hormone signal transduction,” “brassinosteroid biosynthesis,” “plant–pathogen interaction,” “MAPK signaling pathway-plant,” “starch and sucrose metabolism,” “pentose and glucuronate interconversions,” “phenylpropanoid biosynthesis,” “galactose metabolism,” “monoterpenoid biosynthesis,” and “ribosome.” In addition, transcription factors (TFs) analysis showed 8 out of 204 TFs, TRINITY_DN3232_c0_g1 [ABA-responsive element (ABRE)-binding transcription factor1, AREB1], TRINITY_DN4161_c0_g1 (auxin response factor, ARF), TRINITY_DN3183_c0_g2 (abscisic acid-insensitive 5-like protein, ABI5), TRINITY_DN28414_c0_g2 (ethylene-responsive transcription factor ERF1b, ERF1b), TRINITY_DN9557_c0_g1 (phytochrome-interacting factor, PIF3), TRINITY_DN11435_c1_g1, TRINITY_DN2608_c0_g1, and TRINITY_DN6742_c0_g1, were closely related to the “plant hormone signal transduction” pathway. Taken together, it was inferred that these pathways and TFs might play important roles in response to drought stress in MCB. The current study provided important information for MCB drought resistance breeding in the future.