Untargeted LC–MS/MS Metabolite Profiling of Wild, Field-Domesticated and Tissue-Cultured Rhizomes of the Endangered Medicinal Fern Cibotium barometz

Cibotium barometz (Gouji) is a widely prescribed traditional medicine whose supply still depends on wild-harvested rhizomes of this CITES-listed medicinal tree fern. We asked whether field domestication or tissue culture reproduces its chemical profile. Wild-collected (WP), field-domesticated (DM) and tissue-cultured (ZP) rhizomes (n = 3) were profiled by untargeted LC-MS/MS. Of 2828 annotated features, 2787 (98.6%) were detected in all three materials and fewer than ten were group-exclusive, indicating that differences are quantitative rather than qualitative, although this overlap partly reflects gap filling and detection limits. Replicate-level distances to the WP centroid were metric-dependent: correlation- and magnitude-based measures ranked DM closer (1 − Pearson 0.290 vs. 0.371), whereas abundance-weighted Bray–Curtis favoured ZP (0.398 vs. 0.459), consistent with PCA showing both substitutes displaced from WP along independent axes. Within nine literature-prioritized classes, ZP retained 93% of the WP response and an essentially identical organic-acid core (log2FC = −0.01), whereas DM retained 63%, losing organic acids, alkaloids, nucleosides and organosulfur compounds and gaining flavonoids and pterosins. N6-hydroxymethyladenosine, crotonoside and modified nucleosides are proposed as candidate authentication markers requiring validation with authentic standards. Chemical similarity alone does not establish therapeutic equivalence.