The content of metal ions in fruits is inseparable from plant intake of trace elements and health effects in the human body. To understand metal ion content in the fruit and pericarp of melon (Cucumis melo L.) and the candidate genes responsible for controlling this process, we analyzed the metal ion content in distinct parts of melon fruit and pericarp and performed RNA-seq. The results showed that the content of metal ions in melon fruit tissue was significantly higher than that in the pericarp. Based on transcriptome expression profiling, we found that the fruit and pericarp contained elevated levels of DEGs. GO functional annotations included cell surface receptor signaling, signal transduction, organic substance metabolism, carbohydrate derivative binding, and hormone-mediated signaling pathways. KEGG pathways included pectate lyase, pentose and glucuronate interconversions, H⁺-transporting ATPase, oxidative phosphorylation, plant hormone signal transduction, and MAPK signaling pathways. We also analyzed the expression patterns of genes and transcription factors involved in hormone biosynthesis and signal transduction. Using weighted gene co-expression network analysis (WGCNA), a co-expression network was constructed to identify a specific module that was significantly correlated with the content of metal ions in melon, after which the gene expression in the module was measured. Connectivity and qRT–PCR identified five candidate melon genes, LOC103501427, LOC103501539, LOC103503694, LOC103504124, and LOC107990281, associated with metal ion content. This study provides a theoretical basis for further understanding the molecular mechanism of heavy metal ion content in melon fruit and peel and provides new genetic resources for the study of heavy metal ion content in plant tissues.

Fruit ripening is accompanied by extensive reprogramming of secondary metabolism, which determines the antioxidant value of medicine-food homologous fruits. Ziziphus jujuba Mill. cv. ‘Junzao’ (Junzao) is a high-quality cultivar rich in bioactive compounds, yet its stage-dependent metabolite accumulation and the corresponding antioxidant capacity remain poorly resolved. In this study, widely targeted metabolomics was combined with the quantification of total phenolic (TPC), total flavonoid (TFC), and total triterpenoid (TTC) contents and with 1,1-diphenyl-2-picrylhydrazyl radical (DPPH) and 2,2′-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) radical (ABTS) radical-scavenging assays to profile Junzao fruits at five developmental stages. A total of 2388 secondary metabolites were identified, with flavonoids and terpenoids representing the major classes. TPC and TFC were highest at the immature YG (young-fruit) stage, whereas TTC peaked at the BS (white-ripe) stage; all three decreased during subsequent ripening, consistent with the stronger DPPH and ABTS radical-scavenging activities observed in early-stage fruits. Multivariate analyses revealed distinct metabolic profiles among developmental stages, and 2111 differentially accumulated metabolites (DAMs) were identified. K-means clustering resolved nine temporal accumulation patterns, and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment indicated dynamic regulation of flavonoid biosynthesis, phenylpropanoid metabolism, and triterpenoid-related pathways. Spearman correlation analyses further identified ten metabolites, comprising six flavonoids, three triterpenes, and one phenolic acid, that were strongly associated with antioxidant capacity (|r| ≥ 0.5, p < 0.05), highlighting their potential as biomarkers for quality evaluation. Overall, immature Junzao fruits exhibited superior antioxidant capacity, supporting their promise as functional-food ingredients and providing a basis for stage-specific harvesting and utilization.

Enzyme-assisted ultrasound extraction offers a synergistic dual-disruption strategy, yet its differential effects on the jujube metabolome and antioxidant capacity have not been systematically characterized. This study compared ultrasound-assisted extraction (UAE) alone (N), pectinase-assisted UAE (G), cellulase-assisted UAE (X), and composite enzyme-assisted UAE (GX) for metabolite recovery from Ziziphus jujuba Mill. cv. ‘Junzao’ fruits using untargeted metabolomics and multiple antioxidant assays. The GX group exhibited the highest total phenolic content (33.42 ± 0.73 mg GAE/g DW) and total flavonoid content (7.70 ± 0.18 mg RE/g DW), significantly exceeding those of the control (N). Untargeted metabolomic profiling annotated 839 metabolites classified into 16 chemical superclasses, with lipids and lipid-like molecules, amino acids and derivatives, and organic acids and derivatives being the most abundant categories. Multivariate analysis confirmed clear compositional separation between the enzyme-assisted groups and the control, with 107 differentially extracted metabolites (DEMs) identified across the three pairwise comparisons based on extraction efficiency differences. The GX group consistently showed the strongest antioxidant activity in 2,2′-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) (ABTS), 2,2-diphenyl-1-picrylhydrazyl (DPPH), ferric reducing antioxidant power (FRAP), and hydroxyl radical scavenging assays, and eight metabolites with significantly higher extraction yield showed significant positive correlations with multiple antioxidant indices in Spearman correlation analysis. These findings demonstrate that composite enzyme-assisted UAE achieved superior metabolite coverage and antioxidant potency through synergistic cell-wall deconstruction, providing a metabolomic framework for the green extraction of bioactive compounds from jujube fruits; however, further targeted validation is warranted.