Agarwood is an expensive resinous portion derived from Aquilaria plants and has been widely used as medicine, incense, and perfume. The factors involved in steady agarwood accumulation remain elusive.

The aim of the present study was to investigate the effect of wound location on the fungal communities and volatile distribution of agarwood in Aquilaria sinensis . Two-dimensional gas chromatography with high-resolution time-of-flight mass spectrometry revealed 60 compounds from the NIST library, including 25 sesquiterpenes, seven monoterpenes, two diterpenes, nine aromatics, nine alkanes and eight others. Of five agarwood types, Types IV and II contained the greatest number and concentration of sesquiterpenes, respectively. The fungal communities of the agarwood were dominated by the phylum Ascomycota and were significantly affected by the type of wound tissue. Community richness indices (observed species, Chao1, PD whole tree, ACE indices) indicated that Types I and IV harboured the most and least species-rich fungal communities, and the fungal communities of Types V, I, III and IV/II were dominated by Lasiodiplodia , Hydnellum , Phaeoisaria and Ophiocordyceps species, respectively. Correlations between fungal species and agarwood components revealed that the chemical properties of A. sinensis were associated with fungal diversity. More specifically, the dominant fungal genera of Types V, I and III ( Lasiodiplodia , Hydnellum and Phaeoisaria , respectively) were strongly correlated with specific terpenoid compounds. The finding that wound location affects the fungal communities and volatile distribution of agarwood provides insight into the formation of distinct agarwood types.

Adventitious root branching is vital to plant growth and regeneration, but the regulation of this process remains unclear. We therefore investigated how ginsenosides regulate adventitious root branching in Panax ginseng. Cell proliferation and adventitious root branching were decreased in the presence of ginsenoside Rb1 and a high concentration of ginsenoside Re, but increased when treating with a low concentration of Re. Moreover, the exogenous application of a synthetic dodeca-amino acid peptide that has a CLAVATA3/EMBRYO SURROUNDING REGION-related (CLE) motif corresponding to PgCLE45 retarded root growth in both ginseng and Arabidopsis. The root Re levels and the expression of the DDS, CYP716A47, and CYP716A53 genes that encode enzymes involved in ginsenoside synthesis were decreased in the presence of PgCLE45. The expression profiles of PgWOX and PgCLE genes were determined to further investigate the CLE–WOX signaling pathway. The levels of PgWOX11 transcripts showed an inverse pattern to PgCLE45 transcripts. Using yeast one-hybrid assay, EMSA, and ChIP assay, we showed that PgWOX11 bound to the PgCLE45 promoter, which contained the HD motif. Transient expression assay showed that PgWOX11 induced the expression of PgCLE45 in adventitious roots, while PgCLE45 suppressed the expression of PgWOX11. These results suggest that there is a negative feedback regulation between PgCLE45 and PgWOX11. Taken together, these data show that ginsenosides regulate adventitious root branching via a novel PgCLE45–PgWOX11 regulatory loop, providing a potential mechanism for the regulation of adventitious root branching.

Medicinal plants have garnered significant attention in ethnomedicine and traditional medicine due to their potential antitumor, anti-inflammatory and antioxidant properties. Recent advancements in genome sequencing and synthetic biology have revitalized interest in natural products. Despite the availability of sequenced genomes and transcriptomes of these plants, the absence of publicly accessible gene annotations and tabular formatted gene expression data has hindered their effective utilization. To address this pressing issue, we have developed IMP (Integrated Medicinal Plantomics), a freely accessible platform at https://www.bic.ac.cn/IMP. IMP curated a total of 8 565 672 genes for 84 high-quality genome assemblies, and 2156 transcriptome sequencing samples encompassing various organs, tissues, developmental stages and stimulations. With the integrated 10 analysis modules, users could simply examine gene annotations, sequences, functions, distributions and expressions in IMP in a one-stop mode. We firmly believe that IMP will play a vital role in enhancing the understanding of molecular metabolic pathways in medicinal plants or plants with medicinal benefits, thereby driving advancements in synthetic biology, and facilitating the exploration of natural sources for valuable chemical constituents like drug discovery and drug production.

Lonicera japonica (honeysuckle) is an important herb with various pharmaceutically active secondary metabolites. MicroRNAs (miRNAs) are a class of small endogenous noncoding RNAs (sRNA), which play vital regulatory roles in plant secondary metabolism. Although sufficient data is available on the identification and functions of plant miRNAs, research on miRNA regulation of secondary metabolism in different varieties and producing areas of medical herbs has been scarce. In this study, we identified 28 conserved and 2517 novel miRNAs in honeysuckle using deep-sequencing analysis. The variety-specific regulation of miRNA expression was comparatively analysed by Cluster 3.0 algorithm. A total of 37 miRNAs showed differential expression among the three samples including two varieties of honeysuckle at two locations. The Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses indicated that 19 miRNAs with significantly different expression were putatively involved in the response against various factors and plant development. Additionally, the identification of target transcripts revealed that some of the miRNAs, namely U436803, U977315, U805963, U3938865, and U4351355, could be involved in fatty acid and secondary metabolite biosynthesis. To our knowledge, this is the first report on differentially expressed miRNAs in different varieties of honeysuckle. The results from this study can further facilitate the discovery of functional regulatory miRNAs involved in the secondary metabolism in L. japonica.

Background: Syringa pinnatifolia Hemsl. is a shrub belonging to the Oleaceae family. The peeled woody stems and roots of S. pinnatifolia are used in Chinese traditional medicine. This plant has been used for centuries, and modern pharmacological research has revealed its medicinal value. However, the wild populations of S. pinnatifolia have been decreasing, and it has been listed as an endangered plant in China. To elucidate the molecular mechanism leading to the synthesis of the major components of S. pinnatifolia for its further development and sustainable use, this study compared peeled stems and twigs at the metabolic and molecular levels. Results: Peeled stems with the purple substance visible (SSP) and peeled twigs without the purple substance (TSP) were compared at different levels. Microscopic observation showed resin-like fillers in SSP and wood fiber cell walls approximately 1.0 μm thicker than those in TSP (wood fiber cell thickness approximately 2.7 μm). In addition, 104 volatile organic compounds and 870 non-volatile metabolites were detected in the non-targeted and widely-targeted metabolome analyses, respectively. Among the 76 differentially accumulated metabolites (DAMs) detected, 62 were up-accumulated in SSP. Most of these DAMs were terpenes, of which 90% were identified as sesquiterpenes in the volatile organic compound analysis. In the analysis of the non-volatile metabolites, 21 differentially accumulated lignans were identified, of which 18, including five subtypes, were accumulated in SSP. RNA sequencing revealed 4,421 upregulated differentially expressed genes (DEGs) and 5,522 downregulated DEGs in SSP compared with TSP, as well as 33,452 genes that were not differentially expressed. Analysis of the DEGs suggested that sesquiterpenes and lignans were mostly biosynthesized via the mevalonate and phenylpropanoid pathways, respectively. Additionally, in SSP, the enriched Gene Ontology terms included response to biotic stimulus and defense response, while the enriched Kyoto Encyclopedia of Genes and Genomes pathways included plant–pathogen interaction and many other pathways related to plant immunity. Conclusions: This study provides metabolome and transcriptome information for S. pinnatifolia, suggesting that biotic stimuli, including pathogens, are potential and valuable approaches to promoting the biosynthesis of the metabolites linked to the medicinal properties of this plant.