Metabolomics and Transcriptomics Studies of the Differential Accumulation of Flavonoids in Different Organs in Emilia sonchifolia

Integration of Transcriptomics and Metabolomics Reveals Organ-Specific Biosynthesis and Accumulation of Pharmacologically Active Flavonoids in Rhododendron yedoense var. poukhanense

These findings collectively support flavanone 3-hydroxylase (F3H) as a candidate regulatory node governing organ-specific flavonoid partitioning in Rhododendron yedoense var.

Widely Targeted Metabolomic Analysis of Metabolic Differences Among Various Organs of Clematis huchouensis from the Huzhou Production Region

Background/Objectives: Clematis huchouensis Tamura, a genuine medicinal herb endemic to Huzhou, Zhejiang Province. However, its secondary metabolic profile and organ-specific distribution of bioactive constituents remain largely uncharacterized. This study aims to systematically characterize the metabolic profile of its roots, stems, and leaves, and to elucidate organ-specific accumulation patterns of pharmacologically relevant constituents, thereby providing a scientific basis for resource evaluation and quality control of this regional germplasm. Methods: A widely targeted metabolomics approach was employed to profile metabolites in the roots, stems, and leaves of C. huchouensis. Comprehensive annotation and relative quantification were performed using ultra-performance liquid chromatography–tandem mass spectrometry (UPLC-MS/MS) combined with database matching. Cluster analysis and pathway enrichment were conducted to compare metabolic profiles across organs. Results: A total of 1561 metabolites were identified, exhibiting distinct organ-specific accumulation patterns. Flavonoids, alkaloids, and most phenolic acids were predominantly enriched in the aerial parts, whereas the roots accumulated high levels of glutathione and its related peptides, reflecting their significant antioxidant activity. Amino acids displayed complementary tissue-specific distribution, with peptides enriched in leaves and sulfur-containing amino acids such as L-methionine in stems. Organ-specific metabolic differences were significantly associated with pathways including flavonoid biosynthesis and linoleic acid metabolism. Notably, numerous pharmacologically active compounds, such as hispidulin, diosmetin, trigonelline, colchicoside, and oleanolic acid-3-O-xylosyl(1→3)glucuronide—exhibited marked tissue-selective accumulation. Conclusions: This first metabolomic study of C. huchouensis reveals organ-specific accumulation of bioactive compounds, providing a metabolic foundation for its quality control and rational utilization.

Integrated Metabolomic and Transcriptomic Analysis Reveals Tissue-Specific Secondary Metabolic Differentiation and Indole Alkaloid Accumulation in Evodia rutaecarpa

Simple Summary Evodia rutaecarpa (Juss.) Benth. is a classic traditional Chinese medicinal plant with significant pharmacological activities, and its dried fruits are the officially recognized medicinal part. While most existing research focuses on the fruit, the metabolic and transcriptional characteristics of non-medicinal tissues (roots, stems, leaves, and flowers) remain underexplored, which hinders the full utilization of E. rutaecarpa plant resources. To address this gap, we conducted an integrated analysis combining widely targeted metabolomics and transcriptomics to profile the metabolic and transcriptional landscapes across four tissues of E. rutaecarpa. Our results revealed pronounced tissue-specific secondary metabolic differentiation: roots specifically accumulated quinolone alkaloids and flavonoid glycosides, whereas leaves, stems, and flowers preferentially accumulated bioactive indole alkaloids (evodiamine and rutaecarpine). Notably, leaves and flowers exhibited particularly high accumulation levels of these active alkaloids, indicating their potential as alternative sources for industrial and pharmaceutical production. We further identified key candidate structural genes and regulatory gene modules associated with indole alkaloid biosynthesis. Collectively, our findings provide a systematic foundation for the comprehensive utilization of E. rutaecarpa resources and lay a solid groundwork for future metabolic engineering of bioactive indole alkaloids.

Integrative analyses of metabolome and transcriptome reveal differences in terpenoids and identify the genes involved in the synthesis of terpenoids in Magnoliae Flos from different varieties

The molecular basis of terpenoid diversity in MF is revealed, and theoretical references for germplasm discrimination, quality evaluation and genetic improvement of medicinal magnolia resources are provided.

Multi-omics dissection of metabolic pathways for differential flavonoid accumulation in Solanum pennellii and S. lycopersicum

Single-Cell Transcriptomic Profiling of the O -Methyltransferase Characteristics of Flavonoid Biosynthesis in Ziziphus jujuba var. spinosa Fruit

Sour jujube (Ziziphus jujuba var. spinosa) is a valuable medicinal and edible fruit owing to its health-promoting properties. Methoxylated flavonoids enhance their value by improving stability and bioavailability. However, the cellular basis of their biosynthesis remains unclear. We constructed a single-nucleus transcriptomic atlas of sour jujube fruit. Parenchyma cells were identified as the primary sites for flavonoid biosynthesis and their O-methylation, characterized by high expression of phenylpropanoid pathway genes and O-methyltransferases (OMTs). Among the 48 identified OMTs, four (ZjOMT1–4) exhibited high expression, phylogenetically clustered with known functional OMTs, and localized to the cytoplasm; they were further characterized by enzyme activity assays. Notably, ZjOMT1 demonstrates moderate substrate promiscuity, catalyzing the methylation of various substrates, including quercetin, quercitrin, and rutin. Our findings reveal the cellular architecture of flavonoid metabolism in sour jujube fruit, providing genetic resources for breeding varieties with enhanced flavonoid profiles to develop functional foods and nutraceuticals.