Mechanism of Terpene Formation in Pogostemon cablin cv. Jing Huoxiang Revealed by Metabolome and Transcriptome Analysis

Enhanced terpenoid synthesis in Alternaria alstroemeriae PPL7 via co-fermentation with Paeonia lactiflora roots: integrated metabolomic and transcriptomic analysis

Characterization of terpene synthase from Piper nigrum during biotic stress

The molecular evidence linking a PnTPS-derived gene to caryophyllene biosynthesis in P. nigrum is provided, highlighting its potential role in plant defense and paving the way for functional validation and genetic improvement strategies aimed at enhancing biotic stress resistance in black pepper.

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.

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

This work provides a foundational resource for C. diurnum for future pharmaceutical and biotechnological applications, enables the discovery and functional characterization of candidate genes, supports metabolic engineering strategies to enhance valuable terpenoids, and offers avenues to mitigate toxic alkaloid accumulation.

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.

Integrated metabolome and transcriptome analysis reveals the potential mechanism of anthocyanin biosynthesis in Paeonia lactiflora Pall. flowers

Paeonia lactiflora Pall. (Chinese peony), a perennial plant indigenous to northeastern China, exhibits extensive flower-color variation, but the metabolite-gene relationships underlying anthocyanin accumulation remain incompletely understood. We integrated metabolomic and transcriptomic of petals from three cultivars with pink (cv. ‘Exclusive Memory’, PF), pale pink (cv. ‘Salad’, PPF), and white (cv. ‘Duchess’, WF) flowers. Metabolomic profiling detected 689 metabolites, including 169 flavonoids and six anthocyanins. Pairwise comparisons identified 153, 199, and 137 differentially accumulated metabolites in PF vs. PPF, PF vs. WF, and PPF vs. WF, respectively, with 27 metabolites shared among the three comparisons. The total anthocyanin signal in PF petals was 3.25-fold that in PPF petals and 60.37-fold that in WF petals. By contrast, the abundance of the individual compound cyanidin-3,5-O-diglucoside (cyanin) was 76.85-fold higher in PF than in WF and 23.10-fold higher in PPF than in WF, these values therefore describe compound-specific rather than total-anthocyanin differences. RNA-seq identified 6,777, 8,030, and 6,794 differentially expressed genes in the three pairwise comparisons, including 779 shared genes. Correlation analysis prioritized 21 flavonoid-pathway structural genes and 53 candidate transcription factors associated with anthocyanin abundance. Weighted gene co-expression network analysis identified a turquoise module positively associated with anthocyanins and a DFR-centered subnetwork containing 24 candidate transcription factors, including MYB and bHLH genes. qRT-PCR of 12 selected genes reproduced the RNA-seq expression trends. These results elucidate the metabolic basis of peony petal coloration and identify candidate regulatory networks and key genes potentially involved in anthocyanin biosynthesis, providing a foundation for future functional validation.