Browse Articles

Article|19 Oct 2022|OPEN
Diploid chromosome-level reference genome and population genomic analyses provide insights into Gypenoside biosynthesis and demographic evolution of Gynostemma pentaphyllum (Cucurbitaceae)
Xiao Zhang1 , Yuhe Zhao1 , Yixuan Kou2 , Xiaodan Chen1,3 , Jia Yang1 , Hao Zhang1,4 , Zhe Zhao1 and Yuemei Zhao5 , Guifang Zhao1 , , Zhonghu Li,1 ,
1Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, Xi’an, Shaanxi, 710069, China
2Laboratory of Subtropical Biodiversity, Jiangxi Agricultural University, Nanchang, 330045, China
3College of Life Sciences, Shanxi Normal University, Taiyuan, Shanxi, 030012, China
4College of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, 510275, China
5School of Biological Sciences, Guizhou Education University, Guiyang, Guizhou, 550018, China
*Corresponding author. E-mail: gfzhao@nwu.edu.cn,lizhonghu@nwu.edu.cn

Horticulture Research 10,
Article number: uhac231 (2023)
doi: https://doi.org/10.1093/hr/uhac231
Views: 395

Received: 27 May 2022
Accepted: 01 Oct 2022
Published online: 19 Oct 2022

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.