Integrated transcriptome and metabolome analyses revealed regulatory mechanisms of flavonoid biosynthesis in Radix Ardisia

Identification and biological characterization of pathogen causing sooty blotch of Ardisia crispa (Thunb.) A.DC

Sooty blotch, a primary leaf disease affecting Ardisia crispa (Thunb.) A.DC. (A. crispa, AC), significantly impacts both the yield and quality of this medicinal plant. However, the specific species of pathogenic fungi responsible for this disease and their mechanisms of pathogenesis remain unclear. To elucidate the etiology of sooty blotch, it is essential to investigate effective prevention and treatment methods, and provide a theoretical basis for the effective protection of AC. Initially, the alterations in internal organelles that result in sooty blotch were examined using transmission electron microscopy (TEM) and scanning electron microscopy (SEM). Additionally, differential genes were analyzed using differential display reverse transcriptase-PCR (DDRT-PCR) in both healthy and diseased leaves of AC. Moreover, the pathogenic fungi were separated, purified and identified from leaves infected with sooty blotch of AC, and subsequently, their pathogenicity and biological characteristics were tested. Furthermore, the inhibitory effect of pathogens was measured using the water extract of traditional Chinese medicine, based on the growth rate of the mycelium. The findings indicated that the photosynthesis rate of diseased leaves was slower than that of healthy leaves, as revealed by TEM and SEM analyses. Additionally, DDRT-PCR results demonstrated that the differentially expressed genes primarily included those related to zinc finger proteins, acyl-CoA-transferases, and chloroplasts. The phylogenetic tree and pathogenicity test results showed that the pathogens causing sooty blotch of AC were Annulohypoxylon stygium and Diaporthe angelicae. Microscopic observation revealed that Annulohypoxylon stygium and Diaporthe angelicae exhibited distinct microscopic characteristics, and a pH range of 7-10 along with a subdued light environment were more conducive to the growth of pathogens. Additionally, the water extract of Lonicera fulvotomentosa Hsu et S. C. Cheng and A. crispa (Thunb.) A.DC. had a strong antifungal action on the two pathogens of sooty blotch, and the water extract of Ardisia crenate Sims had a better antifungal action on the Diaporthe angelicae. In this study, Annulohypoxylon stygium and Diaporthe angelicae were reported as pathogenic fungi causing sooty blotch for the first time, and affected the photosynthesis of AC leaf, and these study provides a theoretical basis for the diagnosis and prevention of A. crispa (Thunb.) A.DC. sooty blotch.

Combined transcriptome and widely targeted metabolome analysis reveals the potential mechanism of HupA biosynthesis and antioxidant activity in Huperzia serrata

Introduction

Huperzia serrata is a traditional Chinese herb that has gained much attention for its production of Huperzine A (HupA). HupA has shown promise on treating Alzheimer's disease (AD). However, the biosynthetic pathway and molecular mechanism of HupA in H. serrata are still not well understood.

Methods

Integrated transcriptome and metabolome analysis was performed to reveal the molecular mechanisms related to HupA biosynthesis and antioxidant activity in Huperzia serrata.

Results

HT (in vitro H. serrata thallus) exhibits higher antioxidant activity and lower cytotoxicity than WH (wild H. serrata). Through hierarchical clustering analysis and qRT-PCR verification, 7 important enzyme genes and 13 transcription factors (TFs) related to HupA biosynthesis were detected. Among them, the average |log2FC| value of CYP (Cytochrome P450) and CAO (Copper amine oxidase) was the largest. Metabolomic analysis identified 12 metabolites involved in the HupA biosynthesis and 29 metabolites related to antioxidant activity. KEGG co-enrichment analysis revealed that tropane, piperidine and pyridine alkaloid biosynthesis were involved in the HupA biosynthesis pathway. Furthermore, the phenylpropanoid, phenylalanine, and flavonoid biosynthesis pathway were found to regulate the antioxidant activity of H. serrata. The study also identified seven important genes related to the regulation of antioxidant activity, including PrAO (primary-amine oxidase). Based on the above joint analysis, the biosynthetic pathway of HupA and potential mechanisms of antioxidant in H. serrata was constructed.

Discussion

Through differential transcriptome and metabolome analysis, DEGs and DAMs involved in HupA biosynthesis and antioxidant-related were identified, and the potential metabolic pathway related to HupA biosynthesis and antioxidant in Huperzia serrata were constructed. This study would provide valuable insights into the HupA biosynthesis mechanism and the H. serrata thallus medicinal value.

Unraveling the Molecular Basis of Color Variation in Dioscorea alata Tubers: Integrated Transcriptome and Metabolomics Analysis

Dioscorea alata L. (Dioscoreaceae) is a widely cultivated tuber crop with variations in tuber color, offering potential value as health-promoting foods. This study focused on the comparison of D. alata tubers possessing two distinct colors, white and purple, to explore the underlying mechanisms of color variation. Flavonoids, a group of polyphenols known to influence plant color and exhibit antioxidant properties, were of particular interest. The total phenol and total flavonoid analyses revealed that purple tubers (PTs) have a significantly higher content of these metabolites than white tubers (WTs) and a higher antioxidant activity than WTs, suggesting potential health benefits of PT D. alata. The transcriptome analysis identified 108 differentially expressed genes associated with the flavonoid synthesis pathway, with 57 genes up-regulated in PTs, including CHS, CHI, DFR, FLS, F3H, F3'5'H, LAR, ANS, and ANR. The metabolomics analysis demonstrated that 424 metabolites, including 104 flavonoids and 8 tannins, accumulated differentially in PTs and WTs. Notably, five of the top ten up-regulated metabolites were flavonoids, including 6-hydroxykaempferol-7-O-glucoside, pinocembrin-7-O-(6″-O-malonyl)glucoside, 6-hydroxykaempferol-3,7,6-O-triglycoside, 6-hydroxykaempferol-7-O-triglycoside, and cyanidin-3-O-(6″-O-feruloyl)sophoroside-5-O-glucoside, with the latter being a precursor to anthocyanin synthesis. Integrating transcriptome and metabolomics data revealed that the 57 genes regulated 20 metabolites within the flavonoid synthesis pathway, potentially influencing the tubers' color variation. The high polyphenol content and antioxidant activity of PTs indicate their suitability as nutritious and health-promoting food sources. Taken together, the findings of this study provide insights into the molecular basis of tuber color variation in D. alata and underscore the potential applications of purple tubers in the food industry and human health promotion. The findings contribute to the understanding of flavonoid biosynthesis and pigment accumulation in D. alata tubers, opening avenues for future research on enhancing the nutritional quality of D. alata cultivars.