Metabolite expression was normalized by TPM using Salmon 0.8.2 software, and differentially expressed genes were identified by R package: edgeR (version 3.12.1) software (| log2FC | >= 2 and P-value < 0.05 were considered significant). Functional enrichment analysis of differentially expressed genes was conducted using in-house Scripts 1.3 software.
"],"repository":["MetaboLights"],"study_status":["Public"],"ptm_modification":[""],"instrument_platform":["Liquid Chromatography MS - negative - reverse-phase","Liquid Chromatography MS - positive - reverse-phase"],"chromatography_protocol":["Metabolite profiling and data acquisition were performed using ultra-high-performance liquid chromatography (UHPLC) coupled with high-resolution tandem mass spectrometry (HRTMS). Chromatographic separations were performed using a Thermo Scientific UltiMate 3000 HPLC (High performance liquid chromatography) system with an ACQUITY UPLC BEH (Bridged ethylene hybrid) C18 column (100 mm x 2.1 mm, 1.8 microm; Waters, UK) in reversed-phase mode. The column oven was maintained at 35°C throughout the analysis. The flow rate was set at 0.4 mL/min, and solvents A (water with 0.1% formic acid) and B (acetonitrile with 0.1% formic acid) were used to prepare the mobile phase. Gradient elution was programmed as follows: 0-0.5 min, 5% B; 0.5-7 min, 5%-100% B; 7-8 min, 100% B; 8-8.1 min, 100%-5% B; 8.1-10 min, 5% B, with an injection volume of 4 microL per sample.
"],"publication":["Multi-omics dissection of Trametes versicolor CS05-mediated defense enhancement in Crocus sativus under Fusarium oxysporum corm rot stress."],"submitter_name":["Duo Keai"],"submitter_affiliation":["Peking University"],"organism_part":["Crocus sativus"],"technology_type":["mass spectrometry assay"],"disease":[""],"extraction_protocol":["The extracts were stored at 20 overnight to precipitate proteins. The supernatants were centrifuged at 4000 x g for 20 min and transferred into a 96-well plate. For quality control (QC), 10 microL from each sample was aliquoted and mixed.
"],"organism":["Crocus sativus"],"full_dataset_link":["https://www.ebi.ac.uk/metabolights/MTBLS14647"],"author":["Bo Zhu. Zhejiang Chinese Medical University. zhubo@zcmu.edu.cn.","Yutong Wu. Zhejiang Chinese Medical University. wuyutong000315@163.com."],"data_transformation_protocol":["Untargeted metabolomic sequencing analysis was conducted by Hangzhou Lianchuan Biotechnology Co. Ltd. Multivariate analyses, including principal component analysis (PCA) and partial least squares discriminant analysis (PLS-DA), were performed using SIMCA 14.1 software. Differential metabolites were quantified and screened using MetaX software, with differential ions satisfying both FC >= 2 or <= 1/2, P-value < 0.05, and VIP (Variable importance in projection) >= 1.
"],"study_factor":["Group"],"submitter_email":["keaiduoduo998@126.com"],"sample_collection_protocol":["On day 24, approximately 200 mg of tissue samples were collected from the PDB treatment (injection with aseptic PDB solution), FO treatment (FO, injection with FO spore suspension and aseptic PDB solution), and FO + CS05 treatment (injection with FO and CS05 spore suspension), with six biological replicates per treatment group, as described in Section 2.2. Samples were sectioned into fragments < 0.5 cm under sterile conditions in an ultra-clean bench and transferred into RNase-free 1.5 mL aseptic centrifuge tubes for rapid grinding in liquid nitrogen. Metabolite was extracted by adding 120 microL of 50% methanol to each centrifuge tube, followed by thorough mixing with shaking and incubation at room temperature for 10 min.
"],"omics_type":["Metabolomics"],"study_design":["Thermo Scientific UltiMate 3000 HPLC","Metabolomics","Crocus sativus","Corm rot","Disease resistance enhancement","untargeted analysis","Endophytic fungus","corm","Q-Exactive tandem","Trametes versicolor"],"curator_keywords":["Thermo Scientific UltiMate 3000 HPLC","Metabolomics","Corm rot","Disease resistance enhancement","Crocus sativus","untargeted analysis","Endophytic fungus","corm","Q-Exactive tandem","Trametes versicolor"],"mass_spectrometry_protocol":["Metabolites eluting from the column were analyzed using a high-resolution Q-Exactive tandem mass spectrometer (Thermo Scientific) operated in both positive and negative ion modes. Full-scan precursor spectra (70-1050 m/z) were acquired at 70,000 resolution with an AGC (Automatic gain control) target of 3 x 10^6 and a maximum injection time of 100 ms. DDA (Data-dependent acquisition) was performed using a top-3 method, with fragment spectra collected at 17,500 resolution, 1e5 AGC target, and a maximum injection time of 80 ms. A pooled quality control sample was analyzed after every 10 runs to monitor instrument stability throughout the acquisition.
"],"additional_accession":[]},"is_claimable":false,"name":"Multi-omics dissection of Trametes versicolor CS05-mediated defense enhancement in Crocus sativus under Fusarium oxysporum corm rot stress","description":"Saffron (Crocus sativus) is a high-value crop prized in culinary and pharmaceutical applications for its nutritional and therapeutic properties. However, corm rot caused by Fusarium oxysporum severely compromises yield and quality. Here, we isolated F. oxysporum strain CSP01 from diseased corms and confirmed it as the primary causal agent. Five endophytic fungi-CS05 (Trametes versicolor), CS06 (Bjerkandera adusta), CS07 (Phlebia acerina), CS33 (Penicillium sp.), and CS65 (Trichoderma sp.)-were screened for biocontrol efficacy against CSP01. CS05 showed the strongest suppression, achieving a 75.97% control rate and outperforming the positive controls Mortierella alpina and Trichoderma harzianum. To elucidate CS05-mediated protection, we integrated transcriptomic, proteomic, and metabolomic analyses. Transcriptome profiling revealed robust induction of host defense genes following CS05 treatment, particularly in phenylpropanoid biosynthesis (PAL2, 4CL1, CCR4), jasmonic acid (JA) signaling (COI1), and hydrogen peroxide (H2O2) metabolism (CAT1). Metabolomic analysis identified 461 differentially accumulated metabolites in CS05-treated corms; notably, L-tyrosine, coniferin, and p-coumaraldehyde were enriched within phenylpropanoid pathways and associated with enhanced resistance. qRT-PCR and enzyme activity assays validated the involvement of PAL2, 4CL1, and CCR4 in phenylpropanoid biosynthesis. Phytohormone measurements showed significantly elevated JA in CS05-treated corms (12.774 pmol/L) relative to pathogen-only corms (7.773 pmol/L). Oxidative stress assessments indicated that H2O2 in infected corms peaked at day 30 (41.189 mmolg-1 protein); at day 24, infected corms contained 20.904 mmolg-1 protein versus 16.760 mmolg-1 protein in CS05-treated corms, demonstrating mitigation of excessive reactive oxygen species. Collectively, these results show that T. versicolor CS05 enhances saffron resistance to corm rot by coordinating phenylpropanoid pathway activation, amplifying JA signaling, and improving H2O2 detoxification. This study provides the first evidence that T. versicolor CS05 is an effective, eco-friendly biocontrol agent for saffron corm rot and offers mechanistic insight into endophyte-driven plant defense, supporting its potential for sustainable disease management.
","dates":{"publication":"2026-06-01","submission":"2026-06-01"},"accession":"MTBLS14647","cross_references":{}}