Metabolomic and transcriptomic analyses reveal the monoterpenoid indole alkaloid biosynthesis in Neolamarckia cadamba

Transcriptomic landscape of Cestrum diurnum: elucidating pathways of medicinally important terpenoids and toxic alkaloids

Amaryllidaceae Alkaloids and Isoquinoline Alkaloids: A Perspective on Historical Approaches to Pathway Elucidation

This review compares the historical and methodological trajectories that have shaped IA and AA pathway elucidation, from compound isolation, radiotracer experiments, and biochemical inference to transcriptomics, metabolomics, functional enzymology, isotope-guided active-tissue identification, regulatory studies, and heterologous pathway reconstruction.

Whole transcriptome sequencing and metabolism analysis reveal new insight into Ginkgo biloba terpene trilactones biosynthesis

Integrated Metabolomic and Transcriptomic Analyses of Tuberous Root Enlargement in Mirabilis himalaica (Edgew.) Heimerl

Mirabilis himalaica is a Tibetan medicinal plant whose tuberous root is its principal medicinal organ. To characterise molecular and metabolic differences associated with root enlargement, we integrated untargeted metabolomic and transcriptomic analyses of enlarged and non-enlarged roots. We identified 1465 metabolites, including 336 differentially accumulated metabolites, and 4058 differentially expressed genes. Flavonoids and phenolic acids were predominantly less abundant in enlarged roots, whereas several alkaloids showed higher relative abundance. Three gibberellin-related metabolites were lower in enlarged roots, while 1-Aminocyclopropanecarboxylic acid (ACC), L-tryptophan, tryptamine, and several cytokinin-related metabolites showed higher relative signals. Tryptophan metabolism was a shared enriched pathway in the integrated analysis. L-Tryptophan was positively correlated with Anthranilate synthase beta subunit 2 (ASB2) and negatively correlated with Tryptophan synthase alpha chain (TSA) and Probable indole-3-pyruvate monooxygenase (YUC) across the six samples; these exploratory correlations do not establish regulatory relationships. The observed patterns are consistent with coordinated changes in hormone-related metabolites, secondary metabolism, and gene expression during root enlargement. Because Indole-3-acetic acid (IAA) and lignin were not directly quantified, the study does not infer their concentrations or deposition. These findings provide a multi-omics resource for investigating tuberous-root development and for guiding future functional and targeted validation studies in this endangered medicinal species.

Integrated Transcriptomic Profiling Reveals Candidate Genes for Huperzine A Biosynthesis in Huperzia serrata

Huperzine A (HupA) is a natural Lycopodium alkaloid known for its potent neuroprotective properties through the inhibition of acetylcholinesterase. Nevertheless, the limited understanding of its biosynthesis restricts its broader application. This study integrates full-length and second-generation transcriptomes with the quantification of HupA and its precursor, huperzine B, across various tissues of Huperzia serrata, the primary source plant. By employing phylogenetic clustering, expression profiling, and correlation analysis between gene expression and metabolite abundance, we identified 71 candidate genes from seven enzyme families potentially involved in the synthesis of the HupA backbone, including lysine/ornithine decarboxylases, copper amine oxidases (CAOs), chalcone synthases, and cytochrome P450 monooxygenases. Additionally, 28 genes from two families were identified for modification reactions, specifically 2-oxoglutarate/Fe(II)-dependent dioxygenases and caffeoyl shikimate esterases. Comparative analysis between young and mature leaves revealed 3801 genes with higher expression in young leaves, with 84 showing a high correlation with HupA content across seven families. Protein–protein interaction network analysis indicated possible interactions with transcription factors from the MYB, NF-YC, GRAS, ERF, BHLH, and SAP families. Functional validation of two candidate CAOs in planta confirmed their catalytic roles in amine/alkaloid metabolism. This study provides a theoretical foundation and a set of candidate genes for elucidating the biosynthetic pathway of HupA and related alkaloids in H. serrata.

Identification and Transcription Analysis of Phenolic Acid Biosynthesis Pathway in Pseudotaxus chienii.

This study clarifies the molecular basis and transcriptional regulation of phenolic acid glycosylation in P. chienii, providing a framework for exploiting its medicinal resources and guiding conservation-oriented breeding.