Diploid chromosome-level reference genome and population genomic analyses provide insights into Gypenoside biosynthesis and demographic evolution of Gynostemma pentaphyllum (Cucurbitaceae)

Abstract

Gynostemma pentaphyllum (Thunb.) Makino is a perennial creeping herbaceous plant in the family Cucurbitaceae, which has great medicinal value and commercial potential, but urgent conservation efforts are needed due to the gradual decreases and fragmented distribution of its wild populations. Here, we report the high-quality diploid chromosome-level genome of G. pentaphyllum obtained using a combination of next-generation sequencing short reads, Nanopore long reads, and Hi-C sequencing technologies. The genome is anchored to 11 pseudo-chromosomes with a total size of 608.95 Mb and 26,588 predicted genes. Comparative genomic analyses indicate that G. pentaphyllum is estimated to have diverged from Momordica charantia 60.7 million years ago, with no recent whole-genome duplication event. Genomic population analyses based on genotyping-by-sequencing and ecological niche analyses indicated low genetic diversity but a strong population structure within the species, which could classify 32 G. pentaphyllum populations into three geographical groups shaped jointly by geographic and climate factors. Furthermore, comparative transcriptome analyses showed that the genes encoding enzyme involved in gypenoside biosynthesis had higher expression levels in the leaves and tendrils. Overall, the findings obtained in this study provide an effective molecular basis for further studies of demographic genetics, ecological adaption, and systematic evolution in Cucurbitaceae species, as well as contributing to molecular breeding, and the biosynthesis and biotransformation of gypenoside.

From Sequencing to Genome Editing in Cucurbitaceae: Application of Modern Genomic Techniques to Enhance Plant Traits

“…Moreover, Herpetospermum pedunculosum [66], horned cucumber (Cucumis metuliferus) [67] and jiaogulan (Gynostemma pentaphyllum, n = 2) [68,69] are subsequent species within the Cucurbitaceae family whose genomes have been reported in the last three years.…”

Single-cell transcriptome profiling reveals the spatiotemporal distribution of triterpenoid saponin biosynthesis and transposable element activity in Gynostemma pentaphyllum shoot apexes and leaves

“…Gynostemma pentaphyllum (Thunb.) Makino is a perennial vine native to East Asia within the Cucurbitaceae family ( Zhang et al., 2023 ). For centuries, this plant has been extensively used as a dietary herbal medicine due to its diverse pharmacological benefits, including antitumor, antiaging, immunomodulatory, and neuroprotective activities ( Wang et al., 2020 ).…”

“…More than 200 gypenosides have been identified in G. pentaphyllum ( Nguyen et al., 2021 ). Notably, some gypenosides share identical structures with ginsenosides from Panax ginseng , making G. pentaphyllum the first ginsenoside-producing plant outside of the Araliaceae family ( Zhang et al., 2023 ). Consequently, G. pentaphyllum may serve as an alternative resource for ginsenosides.…”