Chrysanthemum x morifolium isolate:Virus-free Fubai | cultivar:Fubaiju Genome sequencing and assembly

Virus-free propagation of the medicinal chrysanthemum cultivar 'Fubaiju' (Chrysanthemum morifolium) induces epigenetic reprogramming that stabilizes phenylpropanoid biosynthesis in leaves, termed the "Metabolic Partitioning Lock". Multi-site field trials (2022-2024) across seven locations in China demonstrate that virus-free leaves accumulate higher levels of chlorogenic acid and 3,5-O-dicaffeoylquinic acid with 3-fold reduced environmental variance compared to virus-infected plants and flowers. Whole-genome bisulfite sequencing (WGBS) reveals promoter hypomethylation at key biosynthetic genes (PAL, 4CL, HCT) correlating with enhanced transcript abundance. Virus-induced gene silencing (VIGS) of the DNA demethylase ROS1 restores promoter methylation and reduces leaf chlorogenic acid content by 42%, establishing causality. These findings enable sustainable utilization of non-traditional vegetative biomass for consistent production of bioactive compounds.