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Article|11 Oct 2022|OPEN
Telomere-to-telomere genome assembly of bitter melon (Momordica charantia L. var. abbreviata Ser.) reveals fruit development, composition and ripening genetic characteristics
Anzhen Fu1,2 ,† , Yanyan Zheng1 ,† , Jing Guo3,4 , Xiaoyan Zhao1 , Changlong Wen5 , Ye Liu2 , Jian Li2 , Xuewen Zhang6 , Ying Yu6 and Hong Ma7 , , Qing Wang1 , , Jinhua Zuo,1 ,
1Institute of Agri-food Processing and Nutrition, Beijing Academy of Agricultural and Forestry Sciences, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Key Laboratory of Vegetable Postharvest Processing of Ministry of Agriculture and Rural Areas, Beijing 100097, China
2Beijing Engineering and Technology Research Center of Food Additives, Beijing Advanced Innovation Center for Food Nutrition and Human Health, School of Food and Health, Beijing Technology and Business University (BTBU), Beijing, 100048, China
3Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering and State Key Laboratory of Genetic Engineering, Institute of Biodiversity Sciences and Institute of Plant Biology, School of Life Sciences, Fudan University, 2005 Songhu Road, Shanghai 200438, China
4School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire, LE12 5RD, United Kingdom
5Beijing Vegetable Research Center (BVRC), Beijing Academy of Agricultural and Forestry Sciences, National Engineering Research Center for Vegetables, Beijing Key Laboratory of Vegetable Germplasms Improvement, Beijing 100097, China
6Biomarker Technologies Corporation, Beijing 101300, China
7Department of Biology, the Huck Institutes of Life Sciences, the Pennsylvania State University, University Park, PA 16802, USA
*Corresponding author. E-mail:,,zuojinhua@126
Both authors contributed equally to the study.

Horticulture Research 10,
Article number: uhac228 (2023)
Views: 279

Received: 04 Jul 2022
Accepted: 26 Sep 2022
Published online: 11 Oct 2022


Momordica charantia L. var. abbreviata Ser. (Mca), known as bitter gourd or bitter melon, is a Momordica variety with medicinal value and belongs to the Cucurbitaceae family. In view of the lack of genomic information on bitter gourd and other Momordica species and to promote Mca genomic research, we assembled a 295.6-Mb telomere-to-telomere (T2T) high-quality Mca genome with six gap-free chromosomes after Hi-C correction. This genome is anchored to 11 chromosomes, which is consistent with the karyotype information, and comprises 98 contigs (N50 of 25.4 Mb) and 95 scaffolds (N50 of 25.4 Mb). The Mca genome harbors 19 895 protein-coding genes, of which 45.59% constitute predicted repeat sequences. Synteny analysis revealed variations involved in fruit quality during the divergence of bitter gourd. In addition, assay for transposase-accessible chromatin by high-throughput sequencing and metabolic analysis showed that momordicosides and other substances are characteristic of Mca fruit pulp. A combined transcriptomic and metabolomic analysis revealed the mechanisms of pigment accumulation and cucurbitacin biosynthesis in Mca fruit peels, providing fundamental molecular information for further research on Mca fruit ripening. This report provides a new genetic resource for Momordica genomic studies and contributes additional insights into Cucurbitaceae phylogeny.