Journal Article

Integrated metabolomic and transcriptomic profiling reveals leaf-specific flavonoid biosynthesis in Paris polyphylla Sm

Yang, Wang, Ke, Changhu, Wu, Lun, Li, Zhihao, Huang, Huilin, Lin, Juncheng, Liu, Huimin, Li, Peng, Ren, Fangling, Liu, Jingjian, Wang, Pengju, Ming, Tingwen

2025

Overview

Background  Paris polyphylla Sm. is a precious medicinal plant rich in various active ingredients. In addition to the well-known saponins, the flavonoids it contains have unique pharmacological potential in antioxidant, neuroprotective, and metabolic regulation. However, the flavonoids in Paris polyphylla Sm. have not been fully researched and developed yet. In this work, we conducted a comprehensive metabolomics and transcriptomics analysis to reveal the metabolic differences and biosynthetic mechanisms of flavonoids in the leaves, stems, and roots of Paris polyphylla Sm. Results Non-targeted metabolomics analysis detected a total of 332 metabolites in Paris polyphylla Sm., among which flavonoids accounted for 19.49%. The diversity and abundance of flavonoids in leaves are the highest, followed by stems and roots. By comparing the metabolites of the roots, stems, and leaves in Paris polyphylla Sm., it was found that there were 45 differential metabolites (DMs) between the leaves and roots, of which flavonoids accounted for 35%. There are 38 DMs between leaves and stems, of which flavonoids account for 45.45%. And there are 52 DMs in stems and roots, among which flavonoids account for 25.53%. A total of 62,766 genes were detected by transcriptomics, and pairwise comparison showed that there were tens of thousands of differentially expressed genes (DEGs) between each group. Afterwards, we selected 39 flavonoids and related metabolites (e.g., kaempferol-3-O-glucoside, quercetin 3-β-D-glucoside, rutin) for targeted metabolomics validation and performed RT-qPCR validation on 29 key flavonoid synthesis genes (e.g., C4H, CHS, FLS, F3’H) to verify the reliability of non-targeted metabolomics and transcriptomics. Conclusions This work indicated that leaves are the main site for the biosynthesis of flavonoids in Paris polyphylla Sm. Among them, kaempferol-3-O-glucoside, quercetin 3-β-D-glucoside, rutin, and other flavonoids are present in higher contents in leaves ( P  < 0.05). Further research on its biosynthetic mechanism indicates that naringenin chalcone is converted to naringenin by chalcone isomerase (CHI). Among them, CHI may be the rate-limiting enzyme in the biosynthesis of flavonoids in Paris polyphylla Sm. The expression of FLS is higher in leaves ( P  < 0.05) and tends to promote the synthesis of flavonols. This work promotes the utilization of non-medicinal parts of Paris polyphylla Sm. and enhances the sustainable development of this precious traditional Chinese medicine resource.

• Publisher: BioMed Central,BioMed Central Ltd,Springer Nature B.V,BMC
• Subject: Agriculture / Analysis / Antioxidants / Bioflavonoids / Biomedical and Life Sciences / Biosynthesis / chalcone / Chalcone isomerase / Chemical properties / Flavones / Flavonoids / Flavonoids - biosynthesis / Flavonols / Gene Expression Profiling / gene expression regulation / Gene Expression Regulation, Plant / Genes / Genetic aspects / Glucosides / Herbal medicine / Identification and classification / Isoflavones / Kaempferol / Leaves / Life Sciences / Liliaceae / Liliaceae - genetics / Liliaceae - metabolism / Lilies / Mass spectrometry / Medicinal plants / Medicine, Botanic / Medicine, Chinese / Medicine, Herbal / Melanthiaceae - genetics / Melanthiaceae - metabolism / Metabolites / Metabolome / Metabolomics / Methods / Naringenin / Neuroprotection / Oriental traditional medicine / Paris polyphylla / Paris polyphylla sm / Physiological aspects / Plant Leaves - genetics / Plant Leaves - metabolism / Plant Roots - metabolism / Plant Sciences / Plant Stems - metabolism / Quercetin / RNA sequencing / Roots / Rutin / Saponins / Scientific imaging / Stems / Sustainable development / Traditional Chinese medicine / Transcriptome / Transcriptomics / Tree Biology