Welcome to CucurbitAgent
A next-generation intelligent platform for Cucurbitaceae research, integrating large language models with multi-omics data.

About CucurbitAgent
Cucurbits—including watermelon, cucumber, melon, pumpkin, bitter gourd, and related crops—are important crops worldwide. Genomic datasets and published research provide valuable information for understanding gene function and improving crop traits. These resources, however, are distributed across databases and formats, and gene identifiers can differ between genome versions. Researchers often need to consult multiple sources to connect a gene with its expression patterns, genetic variants, predicted protein structure, and published findings.
Developed by the Beijing Vegetable Research Center (BVRC), Beijing Academy of Agriculture and Forestry Sciences (BAAFS), CucurbitAgent brings together multi-omics resources from nine cultivated cucurbit species. The platform integrates gene annotations and candidate homologs, cross-version gene ID mappings, natural genetic variants, tissue expression profiles and co-expression relationships, ESMFold-predicted protein structures, GPSite-predicted binding sites, and a curated literature corpus.
Users can explore these resources by asking questions in natural language. A conversational AI agent selects relevant tools, retrieves information from the underlying databases, and integrates the results into answers linked to source records. Researchers can also search the Gene, Expression, Protein, and Literature modules directly and download available genome resources.
By connecting these complementary sources of evidence, CucurbitAgent helps researchers investigate candidate genes, interpret expression patterns, examine variants in their sequence and structural context, and develop hypotheses for functional studies and crop improvement.
Latest Literature
(2026-11-01)Downy mildew, caused by the oomycete Pseudoperonospora cubensis, is a major disease of cucumber, but the developmental and experimental conditions under which resistance can be reliably recognized remain poorly defined. A series of experiments conducted during 2023-2026 examined susceptible cultivar SMR, resistant PI 197088 and PI 330628, their F1 hybrids, and F2 populations. In the 2026 follow-up, individually marked F2 plants were first inoculated at the 1-leaf stage under controlled laboratory conditions and later reinoculated in the field at 6-8 leaves with the same isolate, 273. Disease was then assessed at 7 and 15 days post inoculation (dpi) after this second inoculation, corresponding to approximately 10-12 and 18-20 leaves. One-leaf severity was unrelated to the 7-dpi field observation (r = 0.085 and 0.096 in PI 197088 × SMR and PI 330628 × SMR, respectively) and was only weakly associated with 15-dpi severity (r = 0.180 and 0.206). In contrast, the 7- and 15-dpi observations from the same field inoculation were strongly associated (r = 0.598 and 0.618). F1 plants were intermediate in quantitative disease severity, whereas the stringent full-resistance class (≤5% disease) was rare in the F2. Because developmental stage, inoculation history, and environment were not experimentally separable in 2026, the results are interpreted as evidence that resistance expression is strongly context dependent rather than as a test of plant age alone. For breeding, first-leaf screening should therefore not be used as a definitive predictor of the response expressed after later field challenge.
Cultivated meat (CM) biomanufacturing faces major challenges in cost and in scaling adherent-cell processes from the laboratory toward pilot and industrial production. This study presents a proof-of-concept (POC) in which watermelon rind, an agricultural waste by-product, was valorized into decellularized plant scaffolds (vDPS) and evaluated in a dynamic fixed-bed reactor (FBR). By replacing Triton® X-100 (1% v/v) with Tween-20 (10% v/v), we achieved effective decellularization, reducing residual DNA to below 25 ng/mg while eliminating the use of the toxic Triton X-100, making the scaffolds more suitable for CM applications. The resulting scaffolds exhibited high porosity (85.6%) and a Young's modulus of 36.8 ± 5.9 kPa, confirming their suitability for use as CM scaffolds. For dynamic bioreactor evaluation, the scaffolds were coated with Corning® Synthemax® II SC substrate and cultured with murine myoblast C2C12 cells under the process control capabilities of the Corning Ascent® fixed bed reactor (FBR) system. Over seven days, cells attached, proliferated, and differentiated; relative to static culture, the dynamic condition showed higher metabolic activity and denser cell coverage. Myogenic differentiation was confirmed by Myosin heavy chain and Desmin expression, and cross-sectional imaging showed cell penetration into the scaffold. The prototypes remained structurally stable after cooking. Overall, this work demonstrates the feasibility of integrating waste-valorized scaffolds into a dynamic FBR system, providing a POC foundation for future scale-up studies.
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Cite Us
If you find this platform helpful for your research, please cite:
CucurbitAgent: An AI agent for exploring cucurbit multi-omics resources. Rong Zhang, Jian Zhang, Yuming Zhang, et al. bioRxiv 2026.10.09.758138; doi: https://doi.org/10.64898/2026.10.09.758138