Haploid-phased chromosomal telomere to telomere genome assembly of Uncaria rhynchophylla accelerating gene mining on the biosynthesis of medicinal alkaloids

Recorded traditionary medicinal plants contain important resources, including many natural medicinal alkaloids, for new medicine discovery and development. Uncaria genus is such a woody plant, with a high medicinal value in alkaloids, e.g. (iso)rhynchophylline. Natural alkaloids contents usually vary between germplasms and are affected by the growth environment, which requires a genomics solution to understand the genetic and environmental factors that influence alkaloid production in more detail. Here, we have dissected the haploid-resolved chromosomal T2T genome assembly of Uncaria rhynchophylla with a size of [~]634 Mb and contig N50 of 26 Mb using PacBio HiFi long-reads and Hi-C and anchored the contigs on 22 pairs of confirmed chromosomes. This genome contains 56% repeat sequences and [~]2,9000 protein-encoding genes. U. rhynchophylla diverged from a common ancestor shared with Coffea around 20 million years ago and contains expanded and contracted gene families associated with secondary metabolites and plant-associated defenses. We constructed the pathway for (iso)rhynchophylline biosynthesis with genes mined from the genome and comparative transcriptomes. 53 alkaloids out of 2,578 metabolites were identified in (iso)rhynchophylline biosynthesis, where eight differentially expressed genes were the key for regulating the catalytic steps leading to alkaloid abundance difference between tissues. The chromosome-level genome and pathways of (iso)rhynchophylline constructed in this study provide a genetic basis and guidance for further breeding improvements and the development of pharmaceutical alkaloids.