We report the development of a procedure for ultrasound-assisted microscale extraction of metabolites from the flowers of Saint John’s wort (Hypericum perforatum L.), designed for comparative metabolite analysis of plants from genetic resource collections and natural and segregating populations. The procedure involves high-throughput methanol extraction of metabolites from ground-frozen flowers at a selected stage of flower development, which is carried out in a standard 2 mL Eppendorf tube. A total of 18 compounds, including chlorogenic acid, catechins, glycosylated flavonoids, hypericins, and hyperforin, were identified based on LC/DAD/QTOF analysis, of which 16 could be detected in the UV-Vis spectrum. Two alternative versions of the procedure were evaluated: the “single-flower” procedure, including repeated collection and analysis of single flowers from the tested plant, and the “bulk-flower” procedure, employing the collection of a bulk flower sample from the tested plant and analysis of a portion of the ground sample. The results showed excellent technical reproducibility of the “single-flower” procedure when used with the suggested combination of the peak areas for the proto- and stable forms of pseudohypericin and hypericin. Application of the developed “single-flower” procedure for comparison of the plants derived from seed progeny of the apomictic line Hp93 revealed significantly lower metabolite variation among the apomictic progeny plants compared to the variation observed among plants belonging to different genotypes.

Temporary immersion systems (TISs) are an advanced biotechnological platform for the large-scale cultivation of medicinal plants and the consistent production of high-value secondary metabolites. In this study, we evaluated three immersion regimes with stand-by periods of 4, 8, or 12 h, each paired with a 15-minute immersion period, to optimise shoot growth and colchicine accumulation in Colchicum autumnale L. and Colchicum bivonae Guss. The 4 h stand-by/15 min immersion regime yielded the highest growth index (C. autumnale: 0.75 ± 0.08; C. bivonae: 1.25 ± 0.03) and maximum colchicine content (C. autumnale: 0.19 ± 0.01 mg/g dry biomass; C. bivonae: 0.25 ± 0.02 mg/g dry biomass). Using gas chromatography-mass spectrometry (GC-MS), detailed metabolic profiling of cultures grown under this optimised regime was performed, resulting in the identification of 46 metabolites, including amino acids, organic acids, sugars, sugar alcohols, phenolic, and fatty acids. Volcano plot analysis revealed 11 upregulated and 5 downregulated metabolites in C. autumnale relative to C. bivonae. Significance analysis of metabolomics (SAM) identified 34 metabolites with statistically significant differences between two species. Hierarchical clustering and partial least squares discriminant analysis (PLS-DA) confirmed clear species separation, with Component 1 explaining 68.8% of the total metabolic variance. Glucose-6-phosphate (VIP = 2.01), citric acid (VIP = 1.85), asparagine (VIP = 1.67), and γ-aminobutyric acid (GABA; VIP = 1.52) were the primary biomarkers differentiating the species. These findings confirm that TISs provide an optimised environment for biomass accumulation and stable alkaloid biosynthesis in the Colchicum genus, with C. bivonae emerging as a promising candidate for biotechnological exploitation.