Hemsleya plants have long been used in traditional Chinese medicine, particularly for their tuberous roots. However, rising demand, declining wild resources, slow growth, and strict ecological requirements have made stable production increasingly difficult. H. ellipsoidea is especially valuable because selected cultivars can accumulate more than 2.5% cucurbitacin IIa (CuIIa), yet harvesting typically requires three to five years. Although cucurbitacin biosynthesis has been studied in fruit-bearing cucurbits such as cucumber and melon, little was known about medicinal cucurbits that accumulate these compounds mainly in roots. Due to these challenges, there is an urgent need to investigate the biosynthetic pathway and regulatory mechanisms of cucurbitacins in depth.
Researchers from the Institute of Resource Biology and Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, together with Yunnan Shanyuan Biotechnology Co., Ltd., published (DOI: 10.1093/hr/uhaf363) the study in Horticulture Research on January 13, 2026. The article reports the first chromosome-scale genome assembly for a medicinal Cucurbitaceae species and uses multiomics analysis to connect genome evolution with specialized CuIIa biosynthesis in H. ellipsoidea.
Using Oxford Nanopore, Illumina, and high-throughput chromosome conformation capture (Hi-C) sequencing, the researchers assembled a 535.68-megabase genome anchored to 14 pseudochromosomes and predicted 25,230 protein-coding genes. Comparative genomic analysis showed that H. ellipsoidea diverged from other cucurbits about 84.7 million years ago and followed an independent evolutionary path without recent whole-genome duplication (WGD). Although it retained ancestral chromosomal segments, lineage-specific rearrangements may have contributed to its metabolic specialization.
To uncover the genetic basis of CuIIa biosynthesis, the team identified genes in the mevalonate (MVA) and methylerythritol phosphate (MEP) pathways, as well as genes involved in triterpenoid skeleton formation and downstream modification. Two biosynthetic gene clusters (BGCs), cluster No. 27 and cluster No. 50, were especially notable. Cluster No. 27 contained key candidates including HeOSC, HeACT, and several cytochrome P450 monooxygenase (CYP450) genes, while cluster No. 50 included enzymes and transport-related genes that may help modify or move cucurbitacin-like compounds. Transcriptomic analysis further suggested tissue-specific regulation, with precursor-related activity in leaves and downstream pathway activity in stems and root tubers. Weighted gene co-expression network analysis (WGCNA) highlighted CYP450 genes, alcohol dehydrogenase genes, a multidrug and toxic compound extrusion (MATE) transporter, and transcription factor families including bHLH, MYB, BZIP, and WRKY as possible regulators.
The authors said the genome turns H. ellipsoidea from a traditionally valued medicinal plant into a tractable system for studying how plants build complex natural products. They said CuIIa production appears to depend not on a single genetic switch, but on an organized network shaped by chromosome evolution, gene clustering, tissue-specific expression, and coordinated regulation. This integrated view helps explain why Xuedan is chemically distinctive among cucurbits and provides a clearer map for testing candidate genes in future functional studies.
The findings have practical implications for medicinal plant conservation and sustainable production. Because wild Hemsleya resources face increasing pressure, a genome-guided understanding of CuIIa biosynthesis could help reduce dependence on slow-growing or wild-harvested plants. Candidate genes and regulatory modules identified in this work may support marker-assisted breeding, development of high-yield cultivars, and metabolic engineering platforms for cucurbitacin-related compounds. More broadly, the genome offers a reference for exploring other medicinal Cucurbitaceae species and for discovering how plant lineages evolve specialized chemical defenses that can become valuable pharmaceutical resources.
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Referenes
DOI
10.1093/hr/uhaf363
Original Source URL
https://doi.org/10.1093/hr/uhaf363
Funding information
This work was supported by the Yunnan Province Expert Workstation (grant 202505AF350038).
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.