Genome Assembly of <i>Polygala tenuifolia</i> Provides Insights into Its Karyotype Evolution and Triterpenoid Saponin Biosynthesis

Abstract Polygala tenuifolia is a perennial medicinal plant that has been widely used in traditional Chinese medicine for treating mental disease. However, the lack of genomic resources limits insight into its evolutionary and biological characterization. In present work, we reported P. genome, first genome assembly Polygalaceae family. We sequenced assembled this by combination Illumnina, PacBio HiFi, Hi-C mapping. The includes 19 pseudochromosomes covering ~92.68% (~769.27 Mb). There are 36,463 protein-coding genes annotated genome. Detailed comparative analysis revealed experienced two rounds whole duplication occurred ~39-44 ~18-20 million years ago, respectively. Accordingly, systematically reconstructed ancestral chromosomes inferred chromosome evolution trajectories from common ancestor core eudicots to species. Based on transcriptomics data, enzyme transcription factors involved synthesis triterpenoid saponin were identified. Further demonstrated duplications tandem play critical roles expansion P450 UGT gene families, which contributed saponins. transcriptome data will not only provide valuable functional researches Polygalaceae, but also shed light saponin.