Haploid‐Phased Chromosomal Telomere‐to‐Telomere Genome Assembly of Medicinal Plant Uncaria rhynchophylla Dissects Genetic Controls on the Biosynthesis of Bioactive Alkaloids.

ABSTRACT Natural indole alkaloids provide important medicinal resources and defences to environmental stresses. The <italic>Uncaria</italic> genus is a recorded traditional medicinal woody plant with high alkaloids. Genomic insights into alkaloid variation remain elusive. Here, we have dissected the haploid‐resolved chromosomal T2T genome assembly of <italic>Uncaria rhynchophylla</italic> with a size of ~634 Mb and contig N50 of 27 Mb using PacBio HiFi long‐reads plus Hi‐C reads and anchored the contigs on 22 pairs of confirmed chromosomes. This genome contains 56% repeat sequences and ~29 000 protein‐encoding genes. <italic>U. rhynchophylla</italic> diverged from a common ancestor shared with <italic>Coffea</italic> around 20 million years ago and contains expanded and contracted gene families associated with secondary metabolites and defences/resistance to stresses. We constructed the pathway and mined genes for rhynchophylline alkaloid biosynthesis. Fifty‐three alkaloids in this pathway and eight differentially expressed genes are the keys to alkaloid accumulation. Elevated alkaloid levels are driven by high copy numbers of critical genes <italic>STR</italic>s and <italic>SGR</italic>s involved in strictosidine synthesis and hydrolysis as evidenced by phylogenetic, expression and RNA interference analyses. These results advance our genetic understanding and guide further breeding improvements, stress adaptation studies and pharmaceutical development. [ABSTRACT FROM AUTHOR]