Dracaena cochinchinensis has special defensive reactions against wound stress. Under wound stress, D. cochinchinensis generates a resin that is an important medicine known as dragon’s blood. However, the molecular mechanism underlying the defensive reactions is unclear. Metabolomics and transcriptomics analyses were performed on stems of D. cochinchinensis at different timepoints from the short term to the long term after wounding. According to the 378 identified compounds, wound-induced secondary metabolic processes exhibited three-phase characteristics: short term (0–5 days), middle term (10 days–3 months), and long term (6–17 months). The wound-induced transcriptome profile exhibited characteristics of four stages: within 24 h, 1–5 days, 10–30 days, and long term. The metabolic regulation in response to wound stress mainly involved the TCA cycle, glycolysis, starch and sucrose metabolism, phenylalanine biosynthesis, and flavonoid biosynthesis, along with some signal transduction pathways, which were all well connected. Flavonoid biosynthesis and modification were the main reactions against wound stress, mainly comprising 109 flavonoid metabolites and 93 wound-induced genes. A group of 21 genes encoding CHS, CHI, DFR, PPO, OMT, LAR, GST, and MYBs were closely related to loureirin B and loureirin C. Wound-induced responses at the metabolome and transcriptome level exhibited phase characteristics. Complex responses containing primary metabolism and flavonoid biosynthesis are involved in the defense mechanism against wound stress in natural conditions, and flavonoid biosynthesis and modification are the main strategies of D. cochinchinensis in the long-term responses to wound stress.

Peucedanum praeruptorum is increasingly cultivated as wild resources are depleted. However, cultivated plants often contain lower levels of coumarins than wild individuals and may not meet the standards of the Chinese Pharmacopoeia. To clarify whether growth year could influence coumarin accumulation, we analyzed P. praeruptorum populations cultivated for 1–3 years using a newly developed 17-coumarin quantification method and conducted transcriptomics to characterize gene expression across growth years. The results suggest that total coumarins and major pyranocoumarins (notably praeruptorin B) increased steadily with growth years, while furanocoumarins and simple coumarins increased initially then declined. Notably, despite substantial intra-population variation in coumarin content, cultivated plants could be classified into two distinct chemotypes: chemotype A (higher praeruptorin A and praeruptorin E, lower praeruptorin B) and chemotype B (lower praeruptorin A and praeruptorin E, higher praeruptorin B, pteryxin, and qianhucoumarin D than chemotype A). Both chemotypes coexisted across all examined populations, with the proportion of chemotype B increasing with growth years. Transcriptomic profiling revealed that 3-year-old plants showed higher expression of pyranocoumarin biosynthetic genes and lower expression of genes associated with simple coumarin and furanocoumarin biosynthesis compared with 1-year-old plants. Differential expression analysis further identified key candidate genes associated with growth years and chemotypes. Together, these results demonstrate that growth year and chemotype synergistically regulate coumarin accumulation in cultivated P. praeruptorum, providing a two-dimensional framework for improving the quality of cultivated medicinal materials.

Perilla frutescens(L.) Britt. (P. frutescens) is an important medicinal and aromatic plant, whose leaf color and chemotype strongly influence its medicinal quality and economic value. All the previously discovered perillene (PL)-type P. frutescens are double-sided green, and whether the PL-type trait is tightly linked with the green-leaf trait in genetics remains to be clarified. This study aimed to address this question and attempt to create purple-leaf PL-type germplasm through perillaldehyde (PA) × PL hybridization. Three parallel experiments were conducted using purple-leaf PA-type P. frutescens as male parents and green-leaf PL-type P. frutescens as female parents. Chemotypes were identified by gas chromatography (GC). Association analyses between leaf color and chemotype were performed in segregating F₂ populations. Genes involved in leaf color formation and PL biosynthesis were mapped onto the published Hoko-3 reference genome to provide genomic evidence for the genetic relationship between the two traits. All F₁ individuals were uniformly PA-type. The three F₂ populations exhibited distinct leaf color–chemotype association patterns: Z01 (n = 118) showed a strong association (Fisher’s exact p = 9.13 × 10⁻¹⁰; φ = 0.564), Z02 (n = 117) showed no detectable association (p = 0.9; φ = 0.012), and Z03 (n = 88) showed a moderate association (p = 0.00669; φ = 0.289). Importantly, purple-leaf PL-type recombinants were obtained in F₂ populations and stably maintained through subsequent generations (F₃–F₅), demonstrating that the PL-type trait is not tightly linked with the green-leaf trait in P. frutescens. Genomic mapping genes related to leaf color and PL biosynthesis are distributed across multiple chromosomes and usually present as multiple loci, which is consistent with the pattern of incomplete linkage. The PL-type trait is recessive and not genetically tightly linked to the green-leaf traits in P. frutescens. The successful creation of a purple-leaf PL-type germplasm breaks the historical phenotypic constraint and provides a novel material for further dissection of the molecular mechanisms regulating secondary metabolism and organ coloration in P. frutescens.

Perilla frutescens is an important medicinal and edible plant in Asia and was introduced in Europe and North America mainly as a spice plant. The commonly cultivated species is an allotetraploid (AABB). While the identity of its AA diploid donor has been preliminarily clarified, the other donor, BB, has not been discovered yet, and the taxonomic status and characteristics of the BB donor remain unresolved. Based on the published genomes of Perilla spp., we employed a collinearity analysis, gene structure similarity assessment, and multi-level functional annotation to infer the genomic and phenotypic features of the B subgenome. Results suggest that the protein sequences of the B and A subgenomes exhibit the highest similarity, while the protein sequences of Lavandula angustifolia or Ocimum basilicum are less similar to the B subgenome, and two subgenomes also possess the largest number of homologous genes and have similar gene structures. A total of 90 BB progenitor-specific genes were significantly enriched in pathways related to secondary metabolite biosynthesis and environmental stress response. Among these genes, the terpene synthase genes constitute the main genetic basis for the diversity of bioactive components in perilla. The discovery of a homologous gene containing the NB-ARC domain, associated with resistance to late blight, suggests that BB may contribute to key disease-resistant traits. Further gene family analysis revealed that compared with the A subgenome, the B subgenome exhibited fewer genes and lower diversity in the TPS and NB-ARC families. These findings indicate that BB may have originated from an unfound or extinct species within the Perilla spp. The BB donor might be less diversified than AA, possibly adapting to a narrow geographic and climatic range.