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.

Acknowledgements

This study was supported by the National Natural Science Foundation of China (Nos. 32000256, 31900273, 31770229, and 31270364), a Project funded by the China Postdoctoral Science Foundation (No. 2020M673627XB), and the Key Program of Research and Development of Shaanxi Province (No. 2022ZDLSF06-02).

Author Contributions

Zhao G. F. and Li Z. H. conceived and designed the study. Zhang X., Yang J., Zhang H., and Zhao Y. M. collected the samples. Zhang X. and Zhao Y. H. interpreted the assembly and annotations and contributed to the genome evolution analyses. Zhao Y. H. performed the comparative transcriptome analyses. Zhang X., Kou Y. X. and Zhao Z. conducted the population genomic analyses based on genotyping-by-sequencing data. Chen X. D. analyzed the niche comparisons data. Zhang X. wrote the draft manuscript and Li Z.H. then revised the English content of the manuscript. The final manuscript has been read and approved by all authors.

Data Availability

The whole genome sequence data including NGS short reads, Nanopore long reads, Hi-C interaction reads, transcriptome data, and genome file have been deposited in the NCBI database under BioProject: PRJNA810200.

Conflict of interest

No conflict of interest declared.

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