Pan-genome assembly of vine tea (Nekemias grossedentata) reveals structural variation in its dihydromyricetin biosynthesis diversity

Abstract

Vine tea (Nekemias grossedentata) is a dual-purpose medicinal and edible liana with a documented history of consumption in China spanning millennia. It has been extensively utilized among ethnic minority groups, including the Tujia, Yao, and Dong communities, for at least 700-1000 years, where it is traditionally revered as the ‘Immortal Herb’ or ‘Longevity Tea’. This study reports the haplotype-resolved chromosome-scale genomes of two major cultivated diploid vine tea accessions (N. grossedentata, 2n = 40). Phylogenetic analysis revealed that N. grossedentata diverged from Cissus rotundifolia ~26.27 million years ago (MYA) and from Vitis vinifera around 17.30 MYA. Comparative genomic analysis within the genus uncovered species-specific evolutionary patterns. Furthermore, we constructed a pan-genome encompassing 39 vine tea cultivars and characterized structural variations among cultivated varieties. Correlation analysis between dihydromyricetin (DMY) content and leaf transcriptomes across these cultivars identified ~1 kb presence/absence variations (PAVs) associated with the expression of F3′5′H, a gene critical for DMY biosynthesis in vine tea. Collectively, this genomic resource provides a valuable foundation for advancing herbal crop breeding and development, while offering insights into the biosynthetic pathways underlying specialized metabolism in Vitaceae.

Acknowledgements

This work was supported by Guangdong Science and Technology Program key projects (2022B0202110003, 2024B1212060007), National Natural Science Foundation of China (32200436, 32270292), Guangdong Modern Agro-industry Technology Research System (2023KJ114), and the Program for Changjiang Scholars.

Authors contributions

D.H., S.N., Z.H., F.L., and C.Z. performed the data analysis. D.H., Q.M., J.C., Y.L., Y.Z., and S.X. performed the experiments. D.H., J.L., X.Z., and C.Y. prepared the manuscript. All authors read and approved the final manuscript.

Data availability

The raw genome sequence and raw transcriptome sequencing data are available in China National center for Bioinformation under Bioproject ID: PRJCA045905. Genome assembly and annotation are available in Figshare link: 10.6084/m9.figshare.30136549.v3. The RNA-seq data from PRJNA549404 were also incorporated to support transcriptome analyses.

Conflicts of interest statement

The authors declare that they have no conflicts of interest.

Supplementary material

Supplementary material is available at Horticulture Research online.

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