Whole Genome Assembly and Full-Length Transcriptome Sequencing of the Uncaria rhynchophylla Provides Insights into Genetic Control of Bioactive Alkaloid Biosynthesis

The medicinal plant Uncaria rhynchophylla is valued for producing tetracyclic oxindole alkaloids, including the neuro- and cardioprotective alkaloids rhynchophylline (RIN) and isorhynchophylline (IRN). However, the genomic and genetic basis of alkaloid biosynthesis remains poorly elucidated. Here, we report a chromosome-level genome assembly (653.3 Mb, contig N50 = 24.61 Mb) for U. rhynchophylla, revealing high repetitive content (63.71%) and 30,200 annotated genes. Evolutionary analysis uncovered an ancient whole-genome duplication event and species-specific gene families that could be potentially linked to metabolic diversification. Full-length transcriptome sequencing highlighted tissue-specific expression patterns with hooks showing strong enrichment of alkaloid-biosynthetic genes. A CYP71 family member, UrCYP13, was identified and exhibited high hook-specific expression. Heterologous expression in Nicotiana benthamiana confirmed that UrCYP13 catalyzes the conversion of hirsutine (1) to RIN (2) and IRN (3). The high-quality genome and transcriptome provide a platform for RIN/IRN discovery and establish that UrCYP13 is a key enzyme in the helical oxyindole pathway with hook-specific expression and post-transcriptional regulation underlying metabolite accumulation. These genomic resources will facilitate functional genomics, evolutionary studies, and the sustainable biotechnological production of these valuable alkaloids.