The Nothapodytes nimmoniana genome provides insights into the independent evolution of camptothecin biosynthesis in asterids

Abstract Nothapodytes nimmoniana is known to produce the highest content of the anticancer compound camptothecin (CPT) in the plant kingdom. We present the chromosome-level allotetraploid genome of N. nimmoniana, marking the first genome sequence from the order Icacinales. This 5-Gb genome encodes 92,630 genes, with subgenome B exhibiting dominant gene expression. Through genome mining, we identified and characterized four key enzymes involved in CPT biosynthesis, revealing that N. nimmoniana shares a similar prestrictosidine pathway with most monoterpene indole alkaloid-producing plants. Notably, homoeologous pairs of all characterized enzymes maintained their functions across both subgenomes, suggesting that gene duplication from allotetraploidization likely enhances CPT production in this species. Phylogenetic and syntenic analyses revealed that strictosidine synthase and strictosamide epoxidase were independently recruited in N. nimmoniana, Camptotheca acuminata, and Ophiorrhiza pumila, supporting the hypothesis that CPT biosynthesis evolved independently at least three times within the asterid clade.