A research team has assembled the first haplotype-resolved, telomere-to-telomere genome of monk fruit, creating a complete genetic map of a crop valued for mogroside V, a natural sweetener about 300 times sweeter than sucrose. By combining genome assembly, population resequencing and developmental transcriptomics, the researchers traced the crop’s origin, showed that its low genetic diversity reflects ancient climate-driven population decline more than severe domestication, and identified stage-specific gene activity linked to mogroside production. The work provides a clearer view of how monk fruit became cultivated and offers a powerful foundation for breeding sweeter, more resilient varieties and designing biological systems that can produce mogrosides efficiently.
Monk fruit, or Siraitia grosvenorii , has long been used as both a medicinal plant and a source of zero-calorie sweetness. Yet modern production relies heavily on only a few cultivars grown in a narrow region, raising concerns about genetic vulnerability. Earlier genome assemblies were fragmented and differed sharply in estimated size, making it difficult to resolve chromosome structure, distinguish the two haplotypes or identify genomic changes associated with domestication. Researchers also lacked enough whole-genome data from wild populations to determine whether low diversity arose mainly from farming or from older demographic events. Because of these challenges, deeper investigation is needed into monk fruit’s complete genome, population history and the developmental control of mogroside biosynthesis.
Researchers from Guangxi Normal University reported (DOI: 10.1093/hr/uhag103) the study on 18 March 2026 in Horticulture Research . They generated a gapless, haplotype-resolved telomere-to-telomere (T2T) genome for the widely cultivated ‘Qingpiguo’ monk fruit and analyzed 173 resequenced genomes, including cultivated plants, wild Siraitia grosvenorii populations and Siraitia siamensis as an outgroup. The team also compared gene expression across seven stages of fruit development. Together, these analyses clarified the crop’s domestication history, revealed the forces shaping its genetic diversity and identified candidate genes associated with the timed production of mogrosides.
The team combined Pacific Biosciences high-fidelity (HiFi) reads, Oxford Nanopore Technologies (ONT) ultra-long reads and high-throughput chromosome conformation capture (Hi-C) data to assemble two complete haplotypes, each spanning about 316 megabases across 14 chromosomes. The assembly exposed extensive structural variation, including inversions, translocations, duplications and deletions, as well as contrasting distributions of transposable elements between the two haplotypes. Population analysis of more than 10 million single-nucleotide polymorphisms (SNPs) showed that cultivated monk fruit was mainly domesticated in place from wild populations in northern Guangxi. Its diversity was only slightly lower than that of wild groups, supporting a mild domestication bottleneck. Demographic modeling instead linked much of the diversity loss to population contractions associated with historical glacial cycles. The researchers also detected selective sweeps across all chromosomes, including regions containing UPF3 , AGL12 , KIN17 and CPL4 . Transcriptome analysis then separated mogroside formation into three developmental phases: mogroside IIE before about 30 days after pollination, mogroside IV-A and siamenoside from about 30 to 75 days, and mogroside V from about 60 days until ripening. Distinct UDP-glucosyltransferase (UGT) gene subfamilies were active in each phase, while candidate genes such as chr04.g256 , chr02.g284 , chr02.g690 and chr08.g532 emerged as possible pathway regulators.
The authors said the study shows that monk fruit’s genetic story cannot be explained by domestication alone. The cultivated crop appears to have passed through relatively gentle selection, while much older climate-driven population declines left a stronger imprint on its present-day diversity. They said the complete genome now makes it possible to connect chromosome-scale variation with traits important to growers and consumers. The stage-specific expression map also sharpens the search for genes that control when individual mogrosides accumulate, providing a more precise route toward functional validation rather than relying on broad pathway predictions.
The findings could support molecular breeding programs aimed at widening the crop’s genetic base, improving disease and stress resistance, and increasing desirable mogroside profiles without sacrificing yield. The complete genome can guide marker development, genome-wide association studies and targeted gene editing, while the newly identified candidate genes offer starting points for functional assays and synthetic biology. The developmental timing results may also inform harvest decisions: fruit collected around 75 days after pollination could maximize siamenoside content without reducing fruit size, whereas later harvest favors mogroside V accumulation. More broadly, the resource may help researchers develop microbial or plant-based production platforms for high-value mogrosides and reduce dependence on a geographically restricted crop.
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References
DOI
Original Source URL
https://doi.org/10.1093/hr/uhag103
Funding information
This work was supported by the National Natural Science Foundation of China (32560054, 32460058), the Natural Science Foundation of Guangxi of China (2023JJA130029), and Training Program for Major Talents of Guangxi of China (Y.K.).
About Horticulture Research
Horticulture Research is an open access journal of Nanjing Agricultural University and ranked number one in the Horticulture category of the Journal Citation Reports ™ from Clarivate, 2023. The journal is committed to publishing original research articles, reviews, perspectives, comments, correspondence articles and letters to the editor related to all major horticultural plants and disciplines, including biotechnology, breeding, cellular and molecular biology, evolution, genetics, inter-species interactions, physiology, and the origination and domestication of crops.
Horticulture Research
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Haplotype-resolved T2T genome and population resequencing provide insights into the domestication and mogroside biosynthesis of Siraitia grosvenorii (Cucurbitaceae)
18-Mar-2026
The authors declare that they have no competing interests.