Genome assembly of Polygala tenuifolia 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 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.

Acknowledgements

This work was supported by the Natural Science Foundation of Sichuan (No. 2023NSFSC0683), Innovation Team and Talents Cultivation Program of the National Administration of Traditional Chinese Medicine (No: ZYYCXTD-D-202209), and the ‘Xinglin Scholar’ Discipline Talent Research Promotion Program of Chengdu University of TCM (No. MPRC2021036). The genome sequencing, Hi-C sequencing and primary assembly were performed with the help of Novogene.

Author contributions

W.C., L.L., and X.S. conceived the project and were responsible for the project initiation. W.C., L.L., and X.S. supervised and managed the project and research. Experiments and analyses were designed by W.C., L.L., and X.S. Data generation and bioinformatic analyses were performed by F.M., T.C., P. F., N.L., C.S., and C.L. The manuscript was organized, written and revised by F.M., X.S., L.L., and W.C. All authors read and revised the manuscript.

Data availability

The genome sequence and RNA-seq data of P. tenuifolia were deposited in the Genome Sequence Archive in BIG Data Center at Beijing Institute of Genomics (BIG, Chinese Academy of Sciences), under the accession numbers CRA009096 and CRA009246, which are publicly accessible at http://bigd.big.ac.cn/gsa. The annotations of the P. tenuifolia genome can be downloaded from the TCM Plant Genome Database (TCMPG: http://cbcb.cdutcm.edu.cn/TCMPG/resource/genomes/details/?id=TCMPG20196).

Conflict of interest statement

None declared.

Supplementary data

Supplementary data is available at Horticulture Research online.

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