Whole-genome sequencing provides insights into the genetic diversity and domestication of bitter gourd (Momordica spp.)

Junjie Cui,Weiming He,Le Wang,Changyuan Zhang,Dai Shan,Fang Hu,Xiaoxia Han,Haishan Zhu ,Nansheng Miao,Ziji Liu,Rukui Huang,Xiujue Zheng ,N.s Dhillon ,Yan Yang,Chengcheng Feng,Yulan Yang,Shunjing Luo ,Dong Zhou ,Qingfang Wen,Yu Niu,Jimin Cheng ,Xia Wan ,Jianwen Su,Kailin Hu

doi:10.1038/s41438-020-0305-5

Abstract

Bitter gourd (Momordica charantia) is a popular cultivated vegetable in Asian and African countries. To reveal the characteristics of the genomic structure, evolutionary trajectory, and genetic basis underlying the domestication of bitter gourd, we performed whole-genome sequencing of the cultivar Dali-11 and the wild small-fruited line TR and resequencing of 187 bitter gourd germplasms from 16 countries. The major gene clusters (Bi clusters) for the biosynthesis of cucurbitane triterpenoids, which confer a bitter taste, are highly conserved in cucumber, melon, and watermelon. Comparative analysis among cucurbit genomes revealed that the Bi cluster involved in cucurbitane triterpenoid biosynthesis is absent in bitter gourd. Phylogenetic analysis revealed that the TR group, including 21 bitter gourd germplasms, may belong to a new species or subspecies independent from M. charantia. Furthermore, we found that the remaining 166 M. charantia germplasms are geographically differentiated, and we identified 710, 412, and 290 candidate domestication genes in the South Asia, Southeast Asia, and China populations, respectively. This study provides new insights into bitter gourd genetic diversity and domestication and will facilitate the future genomics-enabled improvement of bitter gourd.

Highlights

Bitter gourd (Momordica charantia) is an economically important vegetable crop in the family Cucurbitaceae, which includes common vegetables and fruits such as cucumber (Cucumis sativus), watermelon (Citrullus lanatus), and melon (Cucumis melo)
Sequencing and de novo assembly of the bitter gourd genomes We performed whole-genome sequencing of the bitter gourd cultivar Dali-11 (M. charantia) from Guangdong, China, and the wild small-fruited line TR from Singida, Tanzania
Geographic diversity of M. charantia Based on a neighbor-joining tree, we found that all 30 samples of muricata were nested within the cultivated M. charantia clade and that many were basal to a cluster of M. charantia (Fig. 2b), supporting the aforementioned conclusion that muricata is the wild progenitor of M. charantia

Summary

Introduction

Bitter gourd (Momordica charantia) is an economically important vegetable crop in the family Cucurbitaceae, which includes common vegetables and fruits such as cucumber (Cucumis sativus), watermelon (Citrullus lanatus), and melon (Cucumis melo). Bitter gourd is a popular vegetable characterized by its bitter fruits. This bitterness is a result of cucurbitane triterpenoids, including cucurbitacins (sapogenins) and cucurbitane glycosides (saponins)[9,10]. Bitter gourd has been cultivated for centuries, the improvement of its varieties and cultivars has been hindered by the extreme genetic homogeneity of commercial varieties, as well as the low-genetic diversity in natural populations[14]; there is great demand for genetic resources that can improve bitter gourd varieties

Methods

Results

Conclusion