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

The medicinal plant <i>Uncaria rhynchophylla</i> 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 <i>U. rhynchophylla</i>, 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 <i>Nicotiana benthamiana</i> confirmed that UrCYP13 catalyzes the conversion of hirsutine (<b>1</b>) to RIN (<b>2</b>) and IRN (<b>3</b>). 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.