Telomere-to-telomere reference genome for Panax ginseng highlights the evolution of saponin biosynthesis

Abstract

Ginseng (Panax ginseng) is a representative of Chinese traditional medicine, also used worldwide, while the triterpene saponin ginsenoside is the most important effective compound within it. Ginseng is an allotetraploid, with complex genetic background, making the study of its metabolic evolution challenging. In this study, we assembled a telomere-to-telomere ginseng reference genome, constructed of 3.45 Gb with 24 chromosomes and 77 266 protein-coding genes. Additionally, the reference genome was divided into two subgenomes, designated as subgenome A and B. Subgenome A contains a larger number of genes, whereas subgenome B has a general expression advantage, suggesting that ginseng subgenomes experienced asymmetric gene loss with biased gene expression. The two subgenomes separated approximately 6.07 million years ago, and subgenome B shows the closest relation to Panax vietnamensis var. fuscidiscus. Comparative genomics revealed an expansion of gene families associated with ginsenoside biosynthesis in both ginseng subgenomes. Furthermore, both tandem duplications and proximal duplications play crucial roles in ginsenoside biosynthesis. We also screened functional genes identified in previous research and found that some of these genes located in colinear regions between subgenomes have divergence functions, revealing an unbalanced evolution in both subgenomes and the saponin biosynthesis pathway in ginseng. Our work provides important resources for future genetic studies and breeding programs of ginseng, as well as the biosynthesis of ginsenosides.

Acknowledgements

We thank Dr Jianbin Yan for comments and advice; Dr Guiqi Bi and Huan Wang for guiding bioinformatics analysis. This work is supported by the National Key R&D Program of China (grant nos 2020YFA0907900 and 2022YFD1700200), Agricultural Genomics Institute at Shenzhen (AGIS-ZLXM202204), Science and Technology Development Project of Jilin Province (20210509022RQ).

Author contributions

W.L. conceived and designed the study with B.L., Y.W., L.L., H.Z., and Y.L. Y.Z. prepared the materials. Y.S. performed the bioinformatic analyses. X.Y. and X.W. assisted in bioinformatics analyses. Y.S. and W.L. wrote the manuscript. All authors read and approved the final manuscript.

Data availability

RNA-seq data and ONT data were obtained from the NCBI BioProjects database under accession numbers PRJNA752920 and PRJNA302556. HiFi data, Hi-C data, Illumina data, genome assembly data have been deposited in the China National Center for Bioinformation (https://www.cncb.ac.cn/) under BioProject number PRJCA022032. Genome annotation files are stored at https://doi.org/10.6084/m9.figshare.25477741.v1.

Conflict of interest statement

The authors declare that they have no conflicts of interest.

Supplementary data

Supplementary data is available at Horticulture Research online.

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