A genome-guided phylogenetic framework predicts the phytochemical similarity and quality consistency of Lonicera japonica

Ensuring quality consistency in botanical drugs remains a global challenge. Through whole-genome analysis of 130 honeysuckle (Lonicera japonica Thunb. ) germplasms, we established a phylogenetic framework revealing eleven evolutionary lineages. Parallel quantification of 16 phytochemical components demonstrated 73.08% congruence between phytochemical profiles and genetic clustering, supporting our “Phylogenetic Proximity-Phytochemical Similarity (PPPS)” hypothesis, and multi-component analysis outperformed single-class metabolite comparisons in predicting quality relationships. RSD profiling shows that phytochemical variability increases with greater genetic divergence, but stabilizes when genetic variation approaches saturation, thereby supporting the PPPS principle. Independent validation using five newly collected germplasms further confirmed PPPS, with phylogenetically proximate accessions showing significantly higher phytochemical similarity than distant relatives. These findings suggest that genomic approaches could offer a promising strategy for enhancing quality assessment of botanicals and potentially help address key challenges in herbal medicine standardization.