A chromosome-level genome assembly of Lycoris radiata unveils evolutionary origin of Amaryllidaceae alkaloids and elucidates the complete pathway of galanthamine biosynthesis

Amaryllidaceae alkaloids (AmAs) are a structurally diverse class of specialized metabolites with substantial pharmacological importance, produced exclusively within the Amaryllidoideae subfamily. However, the limited availability of high-quality genomes from Amaryllidoideae plants has constrained systematic investigations of genes underlying AmAs biosynthesis. Here, we report a high-quality genome assembly of Lycoris radiata, which enabled the discovery of key downstream enzymes in the galanthamine biosynthetic pathway and uncovered reversible reactions between two critical metabolite pairs, providing new mechanistic insight into pathway architecture, and enabling reconstruction of the galanthamine biosynthetic pathway in Yarrowia lipolytica. The core genes for AmAs biosynthesis originated in ancestral angiosperms, and the complete pathway was assembled in the Amaryllidoideae subfamily through gene duplication and neofunctionalization. Furthermore, the tissue-specific accumulation of AmAs and the expression patterns of biosynthetic genes indicate that root tissues could play a role in AmA metabolism in Lycoris.