Telomere-to-telomere genome assembly of yellow-fruited allotetraploid American ginseng (Panax quinquefolius L.) provides insights into flavonoid biosynthesis

Abstract

Panax quinquefolius L., commonly known as American ginseng, is a valuable beneficial medicinal herb renowned for its health-promoting properties and rich phytochemical profile. Despite significant progress in understanding ginsenoside biosynthesis, the genetic basis for flavonoid diversity in American ginseng remains unclear. This study reports the first telomere-to-telomere (T2T) genome assembly for yellow-fruited American ginseng cultivar ‘Zhongnongyangshen No. 2’. The genome assembly, achieved using PacBio HiFi and Oxford Nanopore Technology ultra-long read technologies, offers a high-quality reference for genomic research, addressing previous gaps in structural accuracy. Combining transcriptomic and metabolomic analyses, we investigated flavonoid biosynthesis and the regulatory mechanisms underlying fruit color variation during different developmental stages of American ginseng. Our findings highlight the phylogenetic evolution of the American ginseng genome and offer new insights into the biosynthetic pathways of anthocyanins and flavonols. This comprehensive genomic resource facilitates deeper exploration of flavonoid diversity, supports genetic improvement efforts, and enhances the potential for future applications in medicinal plant research.

Acknowledgements

This research was funded by the Science and Technology Development Program of Jilin Province (20230402038GH); the National Key Research and Development Program of China (2021YFD1600901); the Natural Science Foundation of China (U21A20405); Long-term and Medium-term Conservation Center for Ginseng Germplasm Resources; Jilin Provincial Department of Human Resources and Social Security (201020012); The 111 Project, Northeast Advantageous Characteristic Resources and Health Food Discipline Innovation Introduction Base (D23007); Jilin Agricultural University high-level researcher grant (JLAUHLRG20102006); and the Postdoctoral Fellowship Program of CPSF (GZC20240596).

Author contributions

X.J.L., Y.P.W., and J.Z. conceptualized and drafted the manuscript. J.B.R., M.Y.Z., and W.H.J. review and revise. J.Z., X.C., H.H., Y.J.J., J.W., L.W.F., and Y.F.W. read and advise. M.K.D. modification revised the manuscript. P.D., J.Z., and A.S.X. supervised reading, and revised the manuscript. Y.P.W., J.Z. conceptualized, financially supported, supervised reading, and revised the manuscript. All authors read and approved the manuscript.

Data availability

The raw transcriptome sequence data for P. quinquefolius have been deposited in the National Center for Biotechnology Information (NCBI), assigned with the BioProject number PRJNA1226493. Additionally, the genome assembly data for P. quinquefolius have been archived in the China National Center for Bioinformation, under the project number PRJCA036445. All pertinent data related to this study are included in the supplementary materials that accompany this paper.

Conflict of interest statement

The authors report no conflict of interest.

Supplementary data

Supplementary data is available at Horticulture Research online.

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