The genome of the medicinal plant Uncaria rhynchophylla provides new insights into monoterpenoid indole alkaloid metabolism and its molecular regulatory mechanism

The high-quality chromosomal-level genome assembly (627.72 Mb, contig N50 1.80 Mb) of Uncaria rhynchophylla, a Chinese herb used for hypertension and Alzheimer's disease. Integrated genomic and transcriptomic analyses identified 46,909 genes, including 72 UrWRKY transcription factors. Sixty-four candidate genes for monoterpenoid indole alkaloid (MIA) biosynthesis were screened. Functional validation confirmed UrTDC6 catalyzes tryptamine formation and UrLAMT1/UrLAMT2 catalyze loganin production. Correlation analysis linked MIA content with UrWRKY expression, identifying UrWRKY37 as a key regulator. UrWRKY37 directly activates UrTDC and UrSGD transcription. Overexpression in hairy roots upregulated MIA pathway genes and significantly increased accumulation of isocorynoxeine, corynoxeine, and isorhynchophylline. This work elucidates MIA biosynthesis and its transcriptional regulation in U. rhynchophylla.