Asparagus cochinchinensis is a well-known medicinal herb native to East Asia, appreciated for its therapeutic effects, nutritional value, and cosmetic uses

Evodia rutaecarpa is a valuable medicinal plant, yet its non-medicinal tissues remain largely underexplored. Here, we integrated ultra-performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS)-based widely targeted metabolomics and RNA sequencing (RNA-seq) transcriptomics to systematically profile the metabolic and transcriptional landscapes of roots, stems, leaves, and flowers of Evodia rutaecarpa (Juss.) Benth. Our aim was to characterize tissue-specific metabolic differentiation and its underlying transcriptional regulatory mechanisms. Metabolomic analysis, employing principal component analysis (PCA) and orthogonal partial least squares-discriminant analysis (OPLS-DA) with robust model parameters (R²Y > 0.9, Q² > 0.5), identified 3090 differential metabolite features (variable importance in projection, VIP > 1.0; p < 0.05) across the four tissues, which exhibited distinct tissue-specific clustering patterns. Integrated Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis and weighted gene co-expression network analysis (WGCNA) revealed that roots specifically accumulated quinolone alkaloids and flavonoid glycosides, accompanied by the coordinated upregulation of genes involved in flavonoid and phenylpropanoid biosynthetic pathways. In contrast, stems, leaves, and flowers were enriched in indole alkaloids (evodiamine and rutaecarpine) and volatile oil precursors, with concurrent upregulation of genes involved in tryptophan metabolism and indole alkaloid biosynthesis (e.g., tryptophan decarboxylase, TDC; s N-methyltransferase, NMT). Notably, leaves and flowers displayed particularly high accumulation levels of these bioactive alkaloids, suggesting their potential as alternative sources for industrial and pharmaceutical applications. WGCNA further identified multiple transcription factors and structural gene modules tightly correlated with evodiamine accumulation, offering promising candidate regulators for future biosynthetic pathway engineering. Collectively, this multi-omics integration study systematically elucidates the tissue-partitioned secondary metabolism of Evodia rutaecarpa (Juss.) Benth. and provides a solid scientific foundation for full-plant resource utilization, targeted development of non-medicinal tissues, and future metabolic engineering of indole alkaloid production.

Background/Objectives: Tropane alkaloids (TAs) and phenylpropanoid polyamine alkaloids (PPAs) are major alkaloid constituents of solanaceous plants; however, the tissue-specific distribution of these compounds in Anisodus luridus, a medicinal plant native to southeastern Xizang, remains incompletely characterized. Methods: A biosynthesis-informed putative annotation workflow was developed using ultra-performance liquid chromatography–high-resolution mass spectrometry (UPLC-HRMS) to characterize alkaloid profiles across seven tissues (root, stem, leaf, calyx, corolla, ovary, and seed). Putative annotations were guided by substrate–product structural relationships, predicted enzyme-catalyzed modifications, and diagnostic tandem mass spectrometry (MS/MS) fragmentation patterns. Results: Eighteen alkaloid features were characterized, comprising 6 TAs and 12 PPAs. Hyoscyamine and scopolamine were identified using authentic standards, and the remaining 16 features were putatively annotated, including dihydroanisodamine, hexosylhyoscyamine, and several PPAs not previously reported in A. luridus. TAs were predominantly enriched in roots and ovaries, whereas PPAs accumulated in floral tissues and leaves. Orthogonal partial least squares discriminant analysis (OPLS-DA) identified scopolamine (variable importance in projection (VIP) = 1.30) as a principal variable associated with separation among tissue metabolic profiles. Conclusions: This workflow supports the putative annotation of alkaloids in non-model medicinal plants. The observed tissue-specific distribution patterns provide a basis for future comparative studies with A. belladonna and for evaluating cultivation, tissue-selective harvesting, and extraction strategies.