Telomere-to-telomere genome assembly of bitter melon (Momordica charantia L. var. abbreviata Ser.) reveals fruit development, composition and ripening genetic characteristics

Abstract

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.

Acknowledgements

This work was supported by the Collaborative innovation center of Beijing Academy of Agricultural and Forestry Sciences (201915), the Special innovation ability construction fund of Beijing Academy of Agricultural and Forestry Sciences (20210437), the Collaborative Innovation Center of Cucurbit Crops, the China Agriculture Research System Project (CARS-23).

Author contributions

J.Z. and Y.Z. planned and designed the research; A.F. wrote the manuscript and analyzed the data; H.M., J.G. and D.G. directed the research and revised manuscript; Q.W., X.Z. and C.W. provided experiment materials and funding support; Y.L. and J.L. supervised the research; X.Z. and Y.Y. provided reagents and analysis tools. All authors contributed to manuscript revision, read, and approved the submitted version.

Data availability

The M. charantia L. var. abbreviata Ser. (Mca) raw genome sequencing, assembly data and TE annotations are available from the NCBI under project ID PRJNA873243.

Conflict of interest

The authors declare that they have no conflict of interest.

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