Integration of Transcriptomics and Metabolomics Reveals Organ-Specific Biosynthesis and Accumulation of Pharmacologically Active Flavonoids in Rhododendron yedoense var. poukhanense
Aug 2026· Plants· Vol 15· 0 citations· 41 references
Medicine
TL;DR
These findings collectively support flavanone 3-hydroxylase (F3H) as a candidate regulatory node governing organ-specific flavonoid partitioning in Rhododendron yedoense var.
Abstract
Rhododendron yedoense var. poukhanense is an important medicinal plant, but still little is known about how its bioactive flavonoids are made in different organs. Comprehensive metabolomic profiling was performed using ultra-performance liquid chromatography–tandem mass spectrometry (UPLC-MS/MS), coupled with reference-based RNA sequencing (RNA-seq), to analyze root, stem, and leaf tissues from three independent biological replicates. Subsequently, we performed two-way orthogonal partial least squares (O2PLS) regression, canonical correlation analysis (CCA), and Pearson correlation analyses. A total of 2182 metabolites were detected. Among these, 1116, 896, and 1264 metabolites exhibited differential accumulation across the three pairwise comparisons. Concurrently, 9836, 5457, and 8007 genes were differentially expressed across the three pairwise comparisons, yielding a total of 13,019 unique differentially expressed genes (DEGs). The bifunctional flavanone 3-hydroxylase/flavonol synthase (F3H/FLS) enzyme exhibited the highest expression level in roots, consistent with root-preferential biosynthesis of flavonoid skeletons and the subsequent accumulation of flavonol glycosides in this tissue. In contrast, dihydroflavonol 4-reductase (DFR) exhibited predominant activity in roots, consistent with its role in farrerol biosynthesis. The multi-omics integration model demonstrated excellent goodness-of-fit to the experimental data. Canonical correlation analysis (CCA) further revealed a robust positive association between dihydrokaempferol accumulation and kaempferol biosynthesis. These findings collectively support flavanone 3-hydroxylase (F3H) as a candidate regulatory node governing organ-specific flavonoid partitioning. However, functional validation is required to substantiate this inference.
Gerbera piloselloides (L.) Cass. is a medicinal and edible plant with diverse pharmacological activities attributed to its abundant metabolites. However, systematic research on the organ-specific metabolite distribution and accumulation patterns in roots, stems, and leaves remains limited. In this study, we performed a comparative metabolomic analysis of roots, stems, and leaves collected from the same population, season, and developmental stage using untargeted metabolomics combined with multivariate statistical methods, with five biological replicates per organ. UHPLC-MS/MS identified 1,221 metabolites, dominated by organooxygen compounds, fatty acyls, carboxylic acid derivatives, prenol lipids, and flavonoids. PCA revealed distinct metabolic profiles among the three organs. Analysis of differential metabolites revealed 562, 588, and 526 significant metabolites between roots and stems, roots and leaves, and stems and leaves, respectively. KEGG enrichment identified flavonoid biosynthesis, phenylpropanoid and linoleic acid metabolism as core pathways. These results reveal its organ-specific metabolism and guide rational medicinal and edible use.
Yan Li, Juan Xue, Yongjia Shu et al.· Natural Product Research· 0 citations
Magnoliae Flos (MF)
, the dried flower buds of
Magnolia denudata
Desr.,
Magnolia biondii
Pamp., and
Magnolia sprengeri
Pamp., is a crucial East Asian medicinal herb used to treat allergic rhinitis and other ailments. However, the molecular basis for its quality differences remains unclear.
This study integrates GC-MS-based volatile metabolomics, high-throughput RNA sequencing, and RT-qPCR validation to elucidate the terpenoid metabolic differences and their regulatory mechanisms among the three
MF
varieties.
The metabolomic analysis screened 55 differential terpenoids (15 key markers) that distinguish the
MF
varieties, with terpenoids being the primary metabolic category and the
M. sprengeri
vs.
M. biondii
group exhibiting the most differential metabolites. The transcriptomic analysis revealed
TPS26
as key candidate genes involved in monoterpene synthesis, while IMPMBI2G0000034954 and IMPMBI2G0000034957 were identified as candidate genes for sesquiterpene synthesis. The expression abundances of these genes exhibited significant linear correlations with the accumulation levels of differential terpenoids, though such coordinated variation does not confirm direct causal regulation.
Collectively, this work reveals the molecular basis of terpenoid diversity in
MF
, and provides theoretical references for germplasm discrimination, quality evaluation and genetic improvement of medicinal magnolia resources.
Rui Ma, Hong-Dan Liu, Weimeng Feng et al.· Frontiers in Plant Science· 0 citations
Emilia sonchifolia (L.) DC is a medicinal and edible herb of Asteraceae with Lingnan characteristics. Flavonoids are its core pharmacodynamic substances, but the molecular regulation mechanism of differential accumulation of flavonoids in different organs of this species is still unclear. In this study, the molecular basis of tissue-specific synthesis of flavonoids was analyzed by integrating UPLC-MS broad-target metabolome and Illumina high-throughput transcriptome with four tissues of Emilia sonchifolia: root, stem, leaf, and flower. The results showed that a total of 73 flavonoid metabolites were identified in the metabolome, including naringenin chalcone, luteolin, quercitrin, and other pharmacologically active substances. Multi-omics joint analysis showed that the floral organ was the core tissue for the synthesis and enrichment of flavonoids, and there were specific characteristic flavonoid subtypes in different tissues. A total of 211 differentially expressed genes related to the flavonoid synthesis pathway were screened by transcriptome analysis, including 16 flavonol synthases, five cinnamic acid 4-hydroxylases, and five chalcone synthases. The WGCNA and gene–metabolite association network showed that the transcription levels of key enzyme genes such as CHS, C4H, F3′H, and F3H were highly positively correlated with the accumulation of downstream flavonols. The qRT-PCR quantitative verification showed that the expression patterns of CHS1, CHI4, F3′H5, F3H, FLS4, and GT in the four tissues were highly consistent with the transcriptome sequencing results, which confirmed that the transcriptome data were reliable. For the first time, this study revealed the molecular regulatory network of tissue-specific accumulation of flavonoids in Emilia sonchifolia, and clarified that the flower organ was the optimal medicinal harvesting site of flavonoids. It provided key theoretical support for the breeding of high-efficacy Emilia sonchifolia germplasm, the development of flavonoid active ingredients, and the study of secondary metabolic evolution of Compositae plants.
Xuemei Jiang, Rongchang Wei, Yanqing Qin et al.· International Journal of Mol...· 0 citations
Background: Dendrobium huoshanense flowers are a potentially valuable medicinal resource, but metabolic variation among different germplasm materials remains incompletely characterized. This study aimed to characterize metabolic and transcriptional differences among three D. huoshanense germplasm materials and to explore gene–metabolite associations related to phenylpropanoid metabolism. Methods: Untargeted LC–MS metabolomics and transcriptome sequencing were used to comparatively profile flowers of three D. huoshanense germplasm materials (DH-1, DH-2, and DH-3). Results: Metabolomic profiling detected 4357 metabolic features putatively assigned to 12 chemical classes and revealed clear separation among the three materials. A total of 1292, 1861, and 2035 differentially accumulated metabolic features were identified in DH-1 vs. DH-2, DH-1 vs. DH-3, and DH-2 vs. DH-3, respectively. Transcriptome analysis identified 33,665 expressed genes, including 3365, 5244, and 5964 DEGs in the respective pairwise comparisons. Phenylpropanoid biosynthesis was recurrently enriched across all three DEG comparisons. Exploratory gene–metabolite analysis identified associations involving phenylpropanoid–related candidate genes, including PAL, C4H, 4CL/4CL–like, HCT–like, CSE–like, COMT/OMT–like, and CAD, with the DH-2 vs. DH-3 comparison showing the most extensive molecular differences. Conclusions: The three D. huoshanense germplasm materials exhibited distinct metabolic and transcriptional profiles, providing candidate genes and metabolic features for subsequent targeted validation.
BACKGROUND
'Rucheng Baimaocha' (RCBMC) is a traditional tea landrace found in Hunan Province, China. Its morphological characteristics differ substantially from those of the other cultivars, featuring larger mature leaves with thicker cuticle layers. Both young buds and leaf undersides are densely covered in silvery-white trichomes, indicating that RCBMC has a distinct metabolite composition compared to other cultivars. To elucidate the metabolic profile differences and their underlying molecular mechanisms, we conducted an integrated metabolomic and transcriptomic analysis of RCBMC and representative cultivars.
RESULTS
Metabolomics revealed that RCBMC accumulated higher levels of non-epicatechins, such as catechin, catechin gallate, and gallocatechin gallate, and the ellagitannin strictinin, whereas flavonoid glycosides were significantly lower. Transcriptomics identified 11,775 differentially expressed genes with key shifts in the flavonoid pathway: upregulated LAR and downregulated ANS gene expression collectively redirected metabolic flux toward non-epicatechin synthesis. The downregulation of multiple UGT genes was correlated with reduced flavonoid glycoside levels. Weighted gene co-expression network analysis further identified transcription factors strongly associated with metabolite accumulation. Quantitative analysis of 607 medium- and small-leaf tea germplasms indicated that strictinin content was genetically influenced and seasonally regulated, with RCBMC exhibiting notably high levels. Correlation analysis identified candidate genes from the SCPL, CXE, and LAC families that are potentially involved in strictinin biosynthesis.
CONCLUSIONS
This study revealed a unique pattern of bioactive compound accumulation in RCBMC and provides valuable germplasm resources and genetic targets for breeding tea cultivars with enhanced functional components.
Furong Qu, Yang Zhao, Peidi Yang et al.· BMC Plant Biology· 0 citations
: Mint is notably rich in phenolic acids, flavonoids, antioxidants and other bioactive components, and is widely used as food, medicine, spices, and flavoring agents. Thus, metabolite composition serves as a critical indicator for assessing mint quality. In this study, two mint genotypes of Mentha canadensis L., were sampled, namely purple mint and green mint. The two genotypes are distinguished by stem color: the purple mint exhibits purple stems, whereas the green mint has green stems. The purple mint exhibited significantly higher anthocyanin and total flavone contents than green mint. Integrated transcriptomic and metabolomic analyses were performed to elucidate the regulatory mechanisms underlying pigment and flavonoid accumulation in mint stems. High-throughput RNA-Seq yielded 167,901 unigenes, of which 34,608 genes were differentially expressed. These differentially expressed genes (DEGs) were mainly involved in the lignin metabolic process and flavonoid biosynthetic process. A total of 143 differentially expressed metabolites (DEMs) were enriched in isoflavonoid, flavonoid biosynthesis, flavone and flavonol biosynthesis, and anthocyanin biosynthesis pathways. Co-analysis of DEGs and DEMs revealed that the flavone and flavonol biosynthesis pathway (ko00944) contained the most DEMs, followed by the flavonoid biosynthesis pathway (ko00941) and the anthocyanin biosynthesis pathway (ko00942). Furthermore, nine key genes and metabolites were identified using the O2PLS model. These findings provide a theoretical basis for understanding the key pathways and genes involved in pigment and flavonoid regulation in mint stems.
Xiang-Dong Wang, Hai-Long An, Yan-Zhi Ma et al.· Phyton· 0 citations