Telomere-to-telomere gap-free genome assembly provides genetic insight into the triterpenoid saponins biosynthesis in Platycodon grandiflorus

Abstract

Platycodon grandiflorus has been widely used in Asia as a medicinal herb and food because of its anti-inflammatory and hepatoprotective properties. P. grandiflorus has important clinical value because of the active triterpenoid saponins in its roots. However, the biosynthetic pathway of triterpenoid saponins in P. grandiflorus remains unclear, and the related genes remain unknown. Therefore, in this study, we assembled a high-quality and integrated telomere-to-telomere P. grandiflorus reference genome and combined time-specific transcriptome and metabolome profiling to identify the cytochrome P450s (CYPs) responsible for the hydroxylation processes involved in triterpenoid saponin biosynthesis. Nine chromosomes were assembled without gaps or mismatches, and nine centromeres and 18 telomere regions were identified. This genome eliminated redundant sequences from previous genome versions and incorporated structural variation information. Comparative analysis of the P. grandiflorus genome revealed that P. grandiflorus underwent a core eudicot γ-WGT event. We screened 211 CYPs and found that tandem and proximal duplications may be crucial for the expansion of CYP families. We outlined the proposed hydroxylation steps, likely catalyzed by the CYP716A/72A/749A families, in platycodin biosynthesis and identified three PgCYP716A, seven PgCYP72A, and seven PgCYP749A genes that showed a positive correlation with platycodin biosynthesis. By establishing a T2T assembly genome, transcriptome, and metabolome resource for P. grandiflorus, we provide a foundation for the complete elucidation of the platycodins biosynthetic pathway, which consequently leads to heterologous bioproduction, and serves as a fundamental genetic resource for molecular-assisted breeding and genetic improvement of P. grandiflorus.

Acknowledgements

We thank Benagen Technology Co., Ltd (China) for the T2T assembly of P. grandiflorus. This work was supported by the National Natural Science Foundation of China (U21A20406), the Excellent Young Scholars Project of Natural Science Foundation of Anhui Province in China (2208085Y30), the Key Project Foundation of Support Program for the Excellent Young Faculties in Universities of Anhui Province in China (gxyqZD2022051), Science Research Project at the Universities of Anhui Province for Distinguished Young Scholars (2023AH020036), Young Elite Scientists Sponsorship Program by CACM (CACM-2023-QNRC2-B23), Traditional Chinese Medicine High-Level Key Discipline Construction Project of National Administration of Traditional Chinese Medicine Science of Chinese Medicinal Material Resources (pharmaceutical botany) (zyyzdxk-2023095), Research Funds of Center for Xin’an Medicine and Modernization of Traditional Chinese Medicine of IHM (2023CXMMTCM008), and China Postdoctoral Science Foundation-Anhui Joint Support Program under grant (2024T030AH).

Author Contributions

S.G., L.Z., and P.S. conceived the project, supervised and managed the project. S.G., L.Z., P.S., H.Y., H.W., and X.L. designed the experiments. H.Y., J.L., and C.J. performed bioinformatic analyses. S.G., L.Z., P.S., H.Y., X.C. and N.Z. organized, wrote and revised the manuscript. All authors have read and approved the final version of the paper.

Data availability

The T2T genome assembly and RNA-seq data of P. grandiflorus were deposited in the National Genome Data Center, under the accession numbers PRJCA031148 and PRJCA026736. The genome data referred in this article: Arabidopsis thaliana (NCBI: GCF_000001735.4), Arctium lappa (NCBI: GCA_023525745.1), Camellia sinensis (NGDC: GWHASIV00000000), Daucus carota (NGDC: GCA_030127425.1), Cannabis sativa (NGDC: GWHABGK00000000), Helianthus annuus (NCBI: GCA_026651805.1), Lactuca sativa (NGDC: GCF_002870075.4), Oryza sativa (NCBI: GCF_001433935.1), Panax ginseng (NGDC: GWHBEIL00000000.1), Solanum lycopersicum (NCBI: GCA_915070445.1), Vitis vinifera (NCBI: GCF_030704535.1), Codonopsis lanceolata (https://figshare.com/articles/dataset/First_Report_of_Chromosome-Level_Genome_Assembly_for_Lance_Asiabell_Codonopsis_lanceolata_A_Medicinal_and_Vegetable_Plant_in_the_Campanulaceae_Family/21507774?file=38116599).

Conflict of interests

The authors declare that they have no conflicts of interest.

Supplementary Data

Supplementary data is available at Horticulture Research online.

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