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Article|11 Jul 2023|OPEN
Genome assembly of Polygala tenuifolia provides insights into its karyotype evolution and triterpenoid saponin biosynthesis
Fanbo Meng1,2 , Tianzhe Chu2 , Pengmian Feng1 , Nan Li3 , Chi Song2,4 , Chunjin Li3 and Liang Leng2,4 , , Xiaoming Song3 , , Wei Chen,1,2,3 ,
1State Key Laboratory of Southwestern Chinese Medicine Resources, School of Basic Medicine, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
2State Key Laboratory of Southwestern Chinese Medicine Resources, Innovative Institute of Chengdu University of Traditional Chinese Medicine, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
3School of Life Sciences, North China University of Science and Technology, Tangshan 063210, China
4Institute of Herbgenomics, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
*Corresponding author. E-mail: lling@cdutcm.edu.cn,songxm@ncst.edu.cn,greatchen@ncst.edu.cn

Horticulture Research 10,
Article number: uhad139 (2023)
doi: https://doi.org/10.1093/hr/uhad139
Views: 81

Received: 05 Feb 2023
Accepted: 05 Jul 2023
Published online: 11 Jul 2023

Abstract

Polygala tenuifolia is a perennial medicinal plant that has been widely used in traditional Chinese medicine for treating mental diseases. However, the lack of genomic resources limits the insight into its evolutionary and biological characterization. In the present work, we reported the P. tenuifolia genome, the first genome assembly of the Polygalaceae family. We sequenced and assembled this genome by a combination of Illumnina, PacBio HiFi, and Hi-C mapping. The assembly includes 19 pseudochromosomes covering ~92.68% of the assembled genome (~769.62 Mb). There are 36 463 protein-coding genes annotated in this genome. Detailed comparative genome analysis revealed that P. tenuifolia experienced two rounds of whole genome duplication that occurred ~39–44 and ~18–20 million years ago, respectively. Accordingly, we systematically reconstructed ancestral chromosomes of P. tenuifolia and inferred its chromosome evolution trajectories from the common ancestor of core eudicots to the present species. Based on the transcriptomics data, enzyme genes and transcription factors involved in the synthesis of triterpenoid saponin in P. tenuifolia were identified. Further analysis demonstrated that whole-genome duplications and tandem duplications play critical roles in the expansion of P450 and UGT gene families, which contributed to the synthesis of triterpenoid saponins. The genome and transcriptome data will not only provide valuable resources for comparative and functional genomic researches on Polygalaceae, but also shed light on the synthesis of triterpenoid saponin.