The Haplotype-Resolved Pentaploid Gynostemma pentaphyllum Genome Provides Insights into Chromosomal Evolution and the Convergent Evolution of Protopanaxadiol Synthases

Chuyi Zhang; Lingling Yun; Ziqin Li; Sijie Sun; Yini Niu; Li Qiu; Feng Cao; Xiaofeng Shen; Li Xiang; Ying Li; Baolin Guo; Vincent Courdavault; Chao Sun

doi:10.1016/j.eng.2025.11.022

Engineering ›› :202511022 DOI: 10.1016/j.eng.2025.11.022

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The Haplotype-Resolved Pentaploid Gynostemma pentaphyllum Genome Provides Insights into Chromosomal Evolution and the Convergent Evolution of Protopanaxadiol Synthases

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Abstract

As an important natural source of dammarane-type triterpenoid saponins, Gynostemma pentaphyllum (G. pentaphyllum ) holds significant potential for applications in the healthcare and pharmaceutical industries. In this study, we successfully assembled a high-quality, haplotype-resolved pentaploid genome of G. pentaphyllum, which is rich in protopanaxadiol (PPD)-type saponins. By incorporating genomic data from G. pentaphyllum and other species positioned near the evolutionary base of Cucurbitaceae, we reconstructed and updated the ancestral karyotype of Cucurbitaceae to include 14 chromosomes. Comparative genomic analyses among G. pentaphyllum accessions of different ploidy levels revealed extensive chromosomal inversions and notable sequence variation in centromeric regions. Transposable elements (TEs) are hypothesized to have played a key role in shaping chromosomal structure and centromere evolution, potentially contributing to ploidy diversification in G. pentaphyllum. Notably, two PPD synthases (PPDSs) from the CYP88 family of cytochrome P450s (CYPs) were characterized in G. pentaphyllum. Molecular docking analysis revealed that, compared with the PPDS of Panax ginseng (P. ginseng ), the isozyme in G. pentaphyllum orients its substrate in the opposite direction during catalysis because of distinct amino acid interactions. Phylogenetic analysis further indicated that the PPDSs in G. pentaphyllum and P. ginseng independently recruited different key residues, highlighting a case of convergent evolution. Overall, the high-quality genome assembled in this study provides new insights into chromosome evolution and the mechanisms underlying ploidy diversification while also establishing a foundation for advancing our understanding of triterpene saponin biosynthesis in this species.

Keywords

Gynostemma pentaphyllum / Dammarane-type saponins / Convergent evolution / Centromeres / Ancestral karyotype

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Chuyi Zhang, Lingling Yun, Ziqin Li, Sijie Sun, Yini Niu, Li Qiu, Feng Cao, Xiaofeng Shen, Li Xiang, Ying Li, Baolin Guo, Vincent Courdavault, Chao Sun. The Haplotype-Resolved Pentaploid Gynostemma pentaphyllum Genome Provides Insights into Chromosomal Evolution and the Convergent Evolution of Protopanaxadiol Synthases. Engineering 202511022 DOI:10.1016/j.eng.2025.11.022

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