Dataset DOI: 10.5061/dryad.n5tb2rc7r

Description of the data and file structure

We obtained transcriptomic and metabolomic data of the wild-type Fusarium graminearum strain PH-1 under treatment with different concentrations of quinofumelin. The impact of various exogenous substrates on the inhibitory effect of quinofumelin was evaluated using a hyphal growth rate assay. Molecular docking was performed using AutoDockTools-1.5.7 software. Surface plasmon resonance (SPR) analysis of the binding affinity between quinofumelin and FgDHODHII was conducted using a Biacore T200 instrument (GE Healthcare). Microscale thermophoresis (MST) analysis was performed with a Monolith NT.115 instrument (NanoTemper) to further assess the interaction between quinofumelin and FgDHODHII.

Files and variables

File: Figure_1.zip

Description: Analysis of transcriptome sequencing data in F. graminearum PH-1 treated with quinofumelin. This file contains the transcriptome sequencing data analysis of Fusarium graminearum PH-1 following quinofumelin treatment. The F. graminearum strain PH-1 was treated with quinofumelin at EC₅₀ and EC₉₀ concentrations, respectively. Upregulated and downregulated differentially expressed genes were analyzed based on the KO and GO databases. All files are provided in directly accessible formats.

Description of the Result File Structure

The tree diagram below represents the structure of the result files, and the text following each item describes the corresponding file type or content.

================================================================
1. DETAILED DIRECTORY DESCRIPTION
================================================================

├── 1.ReadsStat Raw data filtering result directory
│ ├── all.filter_stat.xls Summary table of filtering statistics for all samples
│ ├── all.reads_info.xls Reads information table for all samples
│ ├── *.old.png Statistical plots for each sample before filtering
│ ├── *.new.png Statistical plots for each sample after filtering
│ └── *.pie.pdf(png) Sequencing quality pie chart for each sample
│
├── 2.AlignmentStat Alignment result directory
│ ├── all.rRNA.stat.xls Statistical results of rRNA alignment
│ ├── all.align_stat.xls Summary table of reference alignment statistics
│ └── all.region_stat.xls(png, pdf) Statistical table of alignment to reference regions
│ (stacked plot)
│
├── 3.newGeneAnnotation Novel gene result directory
│ └── new.Annot.xls Novel gene annotation table
│
├── 4.GeneAssessment Gene assessment result directory
│ ├── *.coverage.xls(png,pdf) Gene coverage result table for each sample
│ │ (pie chart)
│ ├── *.geneBodyCoverage.xls(png,pdf) Statistical table of gene body coverage
│ │ distribution for each sample (line chart)
│ └── *.saturation.png Gene saturation plot for each sample
│
├── 5.ExpressionStat Gene expression result directory
│ ├── all.genes.expression.annot.xls Summary table of gene expression levels for all samples
│ ├── all.genes.fpkm_distribution.png(pdf) Distribution plot of gene expression abundance
│ └── all.genes.violin.png(png) Violin plot of gene expression levels
│
├── 6.SampleRelation Sample relationship analysis directory
│ ├── all.samples.PCA.png(pdf) PCA analysis plot
│ └── all.samples.pearson.png(pdf) Sample correlation heatmap
│
├── 7.GroupDiffExpression Differential expression analysis result directory
│ ├── A-vs-B.all.annot.xls Complete differential expression result table
│ │ for A-vs-B
│ ├── A-vs-B.filter.annot.xls Significant differential expression table
│ │ for A-vs-B
│ ├── diff.stat.xls(png, pdf) Statistical table (and plot) of differential
│ │ expression results
│ ├── A-vs-B.DE.volcano.png(pdf) Volcano plot for A-vs-B
│ ├── A-vs-B.heatmap.png(pdf) Heatmap for A-vs-B
│ └── enrich Enrichment result directory
│
├── 8.String Interaction network analysis result directory
│ ├── *.cytoscape.html Cytoscape file
│ ├── *.string.txt Interaction relationship file
│ ├── *.node.txt Gene information file
│ └── cytoscape.js JavaScript file for cytoscape.html
│
├── 9.GSEA GSEA analysis result directory
│ ├── *Gsea.xls GSEA result table for each comparison group
│ └── -vs-.GSEA Result directory for each comparison group
│
├── 10.SingleNucleotidePolymorphism SNP result directory
│ ├── snp.annot.xls SNP/InDel information table
│ ├── snp.annot.stat.xls SNP/InDel statistical summary table
│ ├── function_stat SNP functional annotation statistics directory
│ │ └── *.function_stat.xls(png,pdf) Functional annotation statistics table (and plot)
│ │ for each sample
│ ├── location_stat SNP location statistics directory
│ │ └── *.location_stat.xls(png,pdf) SNP location statistics table (and plot)
│ │ for each sample
│ ├── trans_stat SNP mutation type statistics directory
│ │ └── *.trans_stat.xls(png,pdf) SNP mutation type statistics table (and plot)
│ │ for each sample
│ └── editing RNA editing result directory
│ ├── editing.xls RNA editing annotation table
│ ├── editing.type.png Statistical plot of RNA editing types
│ └── editing.frequency.png Frequency distribution plot of RNA editing
│
├── 11.GeneStructureOptimization Gene structure optimization directory
│ ├── merge.xls Summary table of gene structure optimization
│ ├── merge.png Overall plot of gene structure optimization
│ ├── SampleA.xls Gene structure optimization table for Sample A
│ └── SampleA.pdf Gene structure optimization plot for Sample A
│
├── 12.Alternative Splicing Alternative splicing analysis result directory
│ └── -vs- Result directory for each comparison group
│ ├── *.summary.xls Summary table of differential AS categories
│ │ and counts
│ ├── *.xls Differential AS result table
│ └── *.png(pdf) Statistical plot of differential AS categories

Variables

• RNA-SEQ: RNA sequencing, a high-throughput technique used to analyze gene expression profiles at the transcriptome level.
• EC₅₀: Half maximal effective concentration, the concentration of a compound required to achieve 50% of its maximal inhibitory or effective response.
• EC₉₀: 90% effective concentration, the concentration of a compound required to achieve 90% of its maximal inhibitory or effective response.
• CK: Control check (untreated control), the sample or treatment group without quinofumelin exposure, used as the experimental control.
• PCA: Principal component analysis, a statistical method used to reduce data dimensionality and visualize sample clustering or variation.
• GO: Gene Ontology, a functional classification system used to annotate genes based on biological process, molecular function, and cellular component.
• KO: KEGG Orthology, a database classification used to assign genes to functional ortholog groups and metabolic or signaling pathways.
• SNP: Single-nucleotide polymorphism, a variation at a single nucleotide position in the genome.

File: Figure_2-figure_supplement_4.zip

Description: This file contains the qPCR data for DHODH II gene expression in F. graminearum after treatment with quinofumelin at EC₅₀ and EC₉₀ concentrations.GAPDH was used as the reference gene for normalization.

Variables

• qPCR: Quantitative polymerase chain reaction, a technique used to quantify gene expression levels.
• EC₅₀: Half maximal effective concentration, the concentration of a compound required to achieve 50% of its maximal inhibitory or effective response.
• EC₉₀: 90% effective concentration, the concentration of a compound required to achieve 90% of its maximal inhibitory or effective response.

File: Figure_3.zip

Description: Phylogenetic tree of DHODHII proteins. The sequences of DHODHII proteins in this file were retrieved from the NCBI database, the domains were obtained from the Conserved Domain Database (CDD), the motifs were identified using the MEME Suite 12, and the phylogenetic tree was constructed with the free software TBtools.

Variables

• Motif: A short, conserved sequence pattern in a protein or nucleic acid that is often associated with a specific structural or functional role.
• domain: A distinct conserved region of a protein that can fold independently and usually corresponds to a particular biological function or structural feature.

File: Figure_6-figure_supplement_6.zip

Description: This file contains the original gel images and the edited gel images of the SDS–PAGE electrophoresis of the fusion protein.

Variables

• SDS-PAGE: Sodium dodecyl sulfate–polyacrylamide gel electrophoresis, a technique used to separate proteins based on their molecular weight.

File: Figure_4-figure_supplement_5.zip

Description: This file contains the mycelial diameter and inhibition rate of mycelial growth for different F. asiaticum fungal strains exposed to various fungicide treatments and exogenous compounds in the recovery assay of quinofumelin-suppressed mycelial growth.

File: Figure_2.zip

Description: Difference analysis and enrichment analysis of metabolome data in F. graminearum PH-1 treated with quinofumelin. This file contains the metabolome sequencing data analysis of Fusarium graminearum PH-1 following quinofumelin treatment. The F. graminearum strain PH-1 was treated with quinofumelin at EC₅₀ and EC₉₀ concentrations, respectively. All files are provided in directly accessible formats.

Description of the Result File Structure

The tree diagram at the beginning represents the structure of the result files, and the text following “--” describes the corresponding file type.

1. TOP-LEVEL DIRECTORY CATEGORIES

================================================================

MW-* Project ID

├── MW-*/1.Data_assess Data assessment directory

│ (mainly contains quality assessment results for all samples,

│ including QC samples (such as PCA information)

├── MW-*/2.Basic_analysis Basic data analysis directory

│ (mainly contains differential screening and enrichment results

│ for each group comparison, as well as the Venn diagram results

│ among different comparison groups)

================================================================

2. DETAILED DIRECTORY DESCRIPTION

================================================================

Note:

- pos = positive ion mode

- neg = negative ion mode

├── 1.Data_assess Data assessment directory

│

│ ├── pos(neg) Data assessment under positive ion mode

│ │ (or negative ion mode)

│ │

│ │ ├── all_group Information for all samples

│ │ │ ├── *ALL_sample_data.xlsx Metabolite information table for all samples

│ │ │ under positive or negative ion mode

│ │ ├── *ALL_sample_correlation.xlsx Pearson correlation coefficient table for all

│ │ │ samples under positive or negative ion mode

│ │ ├── *hmdb_anno.xlsx HMDB annotation table for metabolites under

│ │ │ positive or negative ion mode

│ │ │ (available only when the species is human: hsa)

│ │ └── readme.txt Documentation file

│ │

│ │ ├── pca Principal component analysis of all samples

│ │ │ ├── _all_PCA. Overall sample PCA 2D plot

│ │ │ (including QC samples)

│ │ │ ├── _all_PCA_ellipse. Overall sample PCA 2D plot

│ │ │ (including QC samples; confidence ellipse is shown

│ │ │ when each group has more than 3 samples)

│ │ │ ├── _all_PCA3D. Overall sample PCA 3D plot

│ │ │ (including QC samples)

│ │ │ ├── _all_PCA_variance. Explained variance of the top 5 principal components

│ │ │ components for the overall sample PCA

│ │ │ (including QC samples)

│ │ │ ├── *_all_PCA_components.xlsx Data for all principal components of the overall

│ │ │ sample PCA (including QC samples)

│ │ │ ├── *_all_PCA_variance_proportion.xlsx Explained variance proportion of principal

│ │ │ components for the overall sample PCA

│ │ │ (including QC samples)

│ │ │ ├── _all_no-QC_PCA. Overall sample PCA 2D plot

│ │ │ (excluding QC samples)

│ │ │ ├── _all_no-QC_PCA_ellipse. Overall sample PCA 2D plot

│ │ │ (excluding QC samples; confidence ellipse is shown

│ │ │ when each group has more than 3 samples)

│ │ │ ├── _all_no-QC_PCA3D. Overall sample PCA 3D plot

│ │ │ (excluding QC samples)

│ │ │ ├── _all_no-QC_PCA_variance. Explained variance of the top 5 principal components

│ │ │ components for the overall sample PCA

│ │ │ (excluding QC samples)

│ │ │ ├── *_all_no-QC_PCA_components.xlsx Data for all principal components of the overall

│ │ │ sample PCA (excluding QC samples)

│ │ │ ├── *_all_no-QC_PCA_variance_proportion.xlsx

│ │ │ Explained variance proportion of principal

│ │ │ components for the overall sample PCA

│ │ │ (excluding QC samples)

│ │ │ ├── _all_PC1_QCC. PC1 control chart for all samples

│ │ │ └── readme.txt Documentation file

│ │

│ │ ├── heatmap Heatmaps of all metabolites

│ │ │ ├── all_heatmap_col-row_cluster.* Clustered heatmap of metabolite abundance

│ │ │ (both metabolites and samples clustered)

│ │ │ ├── all_heatmap_col-row_cluster.xlsx Corresponding data for the clustered heatmap

│ │ │ (z-score transformed)

│ │ │ ├── all_heatmap_class.* Heatmap of metabolite abundance

│ │ │ (showing metabolite classes)

│ │ │ ├── all_heatmap_class.xlsx Corresponding data for the class heatmap

│ │ │ (z-score transformed)

│ │ │ └── readme.txt Documentation file

│ │

│ │ ├── Class_Count Metabolite class composition

│ │ │ ├── _Class_Count_Ring. Ring chart of metabolite class composition

│ │ │ (pdf or png)

│ │ │ └── readme.txt Documentation file

│ │

│ │ ├── QC Sample experimental quality control directory

│ │ │ (exists only when QC samples are present)

│ │ │ ├── QC_TIC. TIC overlay plot of QC samples detected by

│ │ │ mass spectrometry

│ │ │ ├── BLANK_EIC. EIC plot of the internal standard in blank

│ │ │ samples

│ │ │ ├── QC_correlation. Correlation plot of QC samples (pdf and png)

│ │ │ ├── CV_ECDF. CV distribution plot of samples in each group

│ │ │ (pdf and png)

│ │ │ ├── *internal_standard.xlsx Stability of internal standards in QC samples

│ │ │ └── readme.txt Documentation file

│

│ ├── metabolitesCount.xlsx Summary table of identified metabolite counts

│ ├── sample_info.xlsx Sample information table

│ └── protein_concentration.xlsx Protein quantification results for each sample

│ (available only for cell samples)

├── 2.Basic_analysis Basic data analysis directory

│

│ ├── Difference_analysis Differential analysis result directory

│ │

│ ├── group-ID_vs_group-ID Basic analysis directory for the corresponding

│ │ group comparison

│ │ ├── pos(neg) Group analysis under positive ion mode

│ │ │ (or negative ion mode)

│ │ │ ├── group-ID_vs_group-ID*_filter.xlsx

│ │ │ Differential metabolite-related information for

│ │ │ the corresponding group comparison

│ │ │ ├── group-ID_vs_group-ID*_info.xlsx Information for all metabolites in the

│ │ │ corresponding group comparison

│ │ │ ├── *sigMetabolitesCount.xlsx Statistical table of known significantly

│ │ │ differential metabolites for each comparison

│ │ │ ├── *sigMetabolitesSummary.xlsx Summary table of differential metabolites

│ │ │

│ │ │ ├── enrichment Differential enrichment analysis directory

│ │ │ │ ├── Graph Directory of differential enrichment pathway plots

│ │ │ │ ├── KEGG_heatmap Clustered heatmap of differential metabolites

│ │ │ │ in KEGG pathways

│ │ │ │ ├── group-ID_vs_group-ID*_filter_anno.xlsx

│ │ │ │ KEGG annotation table of significantly

│ │ │ │ differential metabolites

│ │ │ │ ├── group-ID_vs_group-ID_KEGG_barplot.

│ │ │ │ KEGG differential enrichment classification plot

│ │ │ │ ├── group-ID_vs_group-ID_KEGG_Enrichment.

│ │ │ │ KEGG differential enrichment bubble plot

│ │ │ │ ├── group-ID_vs_group-ID_KEGG_DA_score.

│ │ │ │ KEGG differential abundance score plot

│ │ │ │ ├── group-ID_vs_group-ID*_KEGG.xlsx

│ │ │ │ KEGG differential enrichment statistics

│ │ │ │ ├── group-ID_vs_group-ID*_KEGG_DA_score.xlsx

│ │ │ │ KEGG differential abundance statistics table

│ │ │ │ ├── group-ID_vs_group-ID*_KEGG_stat.xlsx

│ │ │ │ KEGG differential enrichment classification

│ │ │ │ statistics

│ │ │ │ ├── group-ID_vs_group-ID*_filter_hmdb.xlsx

│ │ │ │ HMDB annotation table of significantly

│ │ │ │ differential metabolites

│ │ │ │ (available only when the species is human: hsa)

│ │ │ │ ├── group-ID_vs_group-ID*_SMPDB_primary.xlsx

│ │ │ │ HMDB differential enrichment statistics table

│ │ │ │ (available only when the species is human: hsa)

│ │ │ │ ├── group-ID_vs_group-ID_SMPDB_primary_Enrichment.

│ │ │ │ HMDB differential enrichment plot of

│ │ │ │ differential metabolites

│ │ │ │ (available only when the species is human: hsa)

│ │ │ │ ├── SMP_primary_pathway Directory of enriched HMDB pathway plots

│ │ │ │ (available only when the species is human: hsa)

│ │ │ │ ├── group-ID_vs_group-ID_msea.

│ │ │ │ MSEA enrichment analysis plot

│ │ │ │ (available only when the species is human: hsa;

│ │ │ │ files containing kegg_pathway indicate KEGG

│ │ │ │ pathway metabolite sets; blood indicates blood

│ │ │ │ disease metabolite sets; urine indicates urine

│ │ │ │ disease metabolite sets; CSF indicates

│ │ │ │ cerebrospinal fluid metabolite sets)

│ │ │ │ ├── group-ID_vs_group-ID*_msea.xlsx

│ │ │ │ MSEA enrichment analysis table

│ │ │ │ (available only when the species is human: hsa;

│ │ │ │ files containing kegg_pathway indicate KEGG

│ │ │ │ pathway metabolite sets; blood indicates blood

│ │ │ │ disease metabolite sets; urine indicates urine

│ │ │ │ disease metabolite sets; CSF indicates

│ │ │ │ cerebrospinal fluid metabolite sets)

│ │ │ │ ├── group-ID_vs_group-ID*_sigDiseasesTable.xlsx

│ │ │ │ Disease association table of differential

│ │ │ │ metabolites

│ │ │ │ (available only when the species is human: hsa)

│ │ │ │ └── readme.txt Documentation file

│ │ │

│ │ │ ├── dendrogram Hierarchical clustering tree of samples in the

│ │ │ │ corresponding group comparison

│ │ │ │ ├── _group-ID_vs_group-ID_dendrogram.*

│ │ │ │ Hierarchical clustering tree (pdf or png)

│ │ │ │ └── readme.txt Documentation file

│ │ │

│ │ │ ├── heatmap Heatmap of differential metabolites in the

│ │ │ │ corresponding group comparison

│ │ │ │ ├── _group-ID_vs_group-ID_heatmap_class.*

│ │ │ │ Heatmap of metabolite abundance classified by

│ │ │ │ metabolite type (pdf or png)

│ │ │ │ ├── _group-ID_vs_group-ID_heatmap_class.xlsx

│ │ │ │ Corresponding data for the class heatmap

│ │ │ │ (z-score transformed)

│ │ │ │ ├── _group-ID_vs_group-ID_heatmap_col-row_cluster.*

│ │ │ │ Clustered heatmap of metabolite abundance

│ │ │ │ (both metabolites and samples clustered;

│ │ │ │ pdf or png)

│ │ │ │ ├── _group-ID_vs_group-ID_heatmap_col-row_cluster.xlsx

│ │ │ │ Corresponding data for the clustered heatmap

│ │ │ │ (z-score transformed)

│ │ │ │ ├── _group-ID_vs_group-ID_heatmap_row_cluster.*

│ │ │ │ Clustered heatmap of differential metabolites

│ │ │ │ abundance (metabolites clustered only;

│ │ │ │ pdf or png)

│ │ │ │ ├── _group-ID_vs_group-ID_heatmap_row_cluster.xlsx

│ │ │ │ Corresponding data for the row-clustered heatmap

│ │ │ │ (z-score transformed)

│ │

│ │ │ ├── opls Orthogonal partial least squares discriminant

│ │ │ │ analysis for the corresponding group comparison

│ │ │ │ ├── _group-ID_vs_group-ID_OPLS-DA_permutation.

│ │ │ │ OPLS-DA permutation validation plot

│ │ │ │ ├── _group-ID_vs_group-ID_OPLS-DA_model.

│ │ │ │ OPLS-DA model summary plot

│ │ │ │ ├── _group-ID_vs_group-ID_OPLS-DA_SPlot.

│ │ │ │ OPLS-DA S-plot

│ │ │ │ ├── _group-ID_vs_group-ID_OPLS-DA_scorePlot.

│ │ │ │ OPLS-DA score plot

│ │ │ │ ├── _group-ID_vs_group-ID*_OPLS-DA_summary.xlsx

│ │ │ │ OPLS-DA model summary table

│ │ │ │ └── readme.txt Documentation file

│ │

│ │ │ ├── pls Partial least squares discriminant analysis

│ │ │ │ ├── group-ID_vs_group-ID_PLS-DA_model.*

│ │ │ │ PLS-DA model summary plot

│ │ │ │ ├── group-ID_vs_group-ID_PLS-DA_permutation.*

│ │ │ │ PLS-DA model validation plot

│ │ │ │ ├── group-ID_vs_group-ID_PLS-DA_scorePlot.*

│ │ │ │ PLS-DA score plot

│ │ │ │ └── readme.txt Documentation file

│ │

│ │ │ ├── PCA Principal component analysis for the

│ │ │ │ corresponding group comparison

│ │ │ │ ├── _group-ID_vs_group-ID_PCA3D.

│ │ │ │ PCA 3D plot of metabolites

│ │ │ │ ├── _group-ID_vs_group-ID_PCA.

│ │ │ │ PCA plot of metabolites

│ │ │ │ ├── _group-ID_vs_group-ID_PCA_variance.

│ │ │ │ Explained variance plot of the top 5 principal components

│ │ │ │ components

│ │ │ │ ├── _group-ID_vs_group-ID*_components.xlsx

│ │ │ │ Data for all principal components

│ │ │ │ ├── _group-ID_vs_group-ID*_variance_proportion.xlsx

│ │ │ │ Explained variance proportion of principal

│ │ │ │ components

│ │ │ │ └── readme.txt Documentation file

│ │

│ │ │ ├── cpdCorr Correlation heatmap of differential metabolites

│ │ │ │ ├── group-ID_vs_group-IDraw_cpdCorr.*

│ │ │ │ Correlation heatmap of all differential

│ │ │ │ metabolites

│ │ │ │ ├── group-ID_vs_group-IDtop50_cpdCorr.*

│ │ │ │ Correlation heatmap of the top 50 VIP

│ │ │ │ differential metabolites

│ │ │ │ ├── group-ID_vs_group-IDraw_cpdCorr.xlsx

│ │ │ │ Correlation coefficient table of all

│ │ │ │ differential metabolites

│ │ │ │ ├── group-ID_vs_group-IDtop50_cpdCorr.xlsx

│ │ │ │ Correlation coefficient table of the top 50 VIP

│ │ │ │ differential metabolites

│ │ │ │ ├── group-ID_vs_group-IDcpdCorrCir.*

│ │ │ │ Chord diagram of all differential metabolites

│ │ │ │ ├── group-ID_vs_group-IDcpdCorr_Pvalue.xlsx

│ │ │ │ Correlation coefficient table of all

│ │ │ │ differential metabolites

│ │ │ │ Note:

│ │ │ │ - row/column: metabolite names

│ │ │ │ (including Index and Compounds)

│ │ │ │ - Correlation: Pearson correlation coefficient

│ │ │ │ - P-value: corresponding P value

│ │ │ │ ├── group-ID_vs_group-IDcpdCorrNet.*

│ │ │ │ Correlation network plot of all differential

│ │ │ │ metabolites

│ │ │ │ └── readme.txt Documentation file

│ │

│ │ │ ├── TopFcMetabolites Plots of abundance differences for the top N

│ │ │ │ metabolites ranked by fold change

│ │ │ │ ├── group-ID_vs_group-IDTopFcDistribution.*

│ │ │ │ Dynamic distribution plot of abundance

│ │ │ │ differences for the top 20 metabolites ranked

│ │ │ │ by fold change

│ │ │ │ ├── group-ID_vs_group-IDTopFcBarChart.*

│ │ │ │ Bar chart of the top 20 differential

│ │ │ │ metabolites ranked by fold change

│ │ │ │ ├── group-ID_vs_group-IDTopFcRadarChart.*

│ │ │ │ Radar chart of the top 10 differential

│ │ │ │ metabolites ranked by fold change

│ │ │ │ └── readme.txt Documentation file

│ │

│ │ │ ├── vipscore VIP value plots of differential metabolites

│ │ │ │ ├── group-ID_vs_group-ID_vipScore.*

│ │ │ │ VIP value plot of differential metabolites

│ │ │ │ └── readme.txt Documentation file

│ │

│ │ │ ├── vol Volcano plots for the corresponding group

│ │ │ │ comparison

│ │ │ │ ├── group-ID_vs_group-ID_vol.

│ │ │ │ Volcano plot

│ │ │ │ └── readme.txt Documentation file

│ │

│ │ │ ├── fullViolin Violin plots for the corresponding group

│ │ │ │ comparison

│ │ │ │ ├── group-ID_vs_group-ID_fullViolin.*

│ │ │ │ Violin plot of the top 50 VIP differential

│ │ │ │ metabolites

│ │ │ │ ├── singleViolin Folder containing individual violin plots of

│ │ │ │The top 50 VIP differential metabolites

│ │ │ │ └── readme.txt Documentation file

│ │

│ │ │ ├── zScore Z-score plots of differential metabolites

│ │ │ │ ├── group-ID_vs_group-ID_zScore.*

│ │ │ │ Z-score plot of differential metabolites

│ │ │ │ └── readme.txt Documentation file

│ │

│ │ │ ├── ROC ROC analysis of differential metabolites

│ │ │ │ ├── *ROC. ROC curve of differential metabolites

│ │ │ │ ├── group-ID_vs_group-ID*.auc.xls

│ │ │ │ AUC statistics table of differential metabolites

│ │ │ │ └── readme.txt Documentation file

│

│ ├── kmeans K-means clustering analysis of differential

│ │ metabolites

│ │ ├── pos(neg) K-means clustering plots among differential

│ │ │ comparison groups under positive or negative

│ │ │ ion mode

│ │ │ ├── *kmeans_group.xlsx K-means clustering information table of

│ │ │ differential metabolites

│ │ │ ├── kmeans_cluster. Trend plot of K-means clustering for

│ │ │ differential metabolites

│ │ └── readme Documentation file

│

│ ├── Venn diagrams among differential comparison

│ │ groups

│ │ ├── pos(neg) Venn diagrams among differential comparison

│ │ │ groups under positive or negative ion mode

│ │ │ ├── *_venn. Venn diagram files

│ │ │ ├── **_venn_result.xlsx Distribution table of differential metabolites

│ │ │ in each group of the Venn diagram

│ │ │ └── readme.txt Documentation file

Variables

• EC₅₀: Half maximal effective concentration, the concentration of a compound required to achieve 50% of its maximal inhibitory or effective response.
• EC₉₀: 90% effective concentration, the concentration of a compound required to achieve 90% of its maximal inhibitory or effective response.
• CK: Untreated control, the sample or treatment group without fungicide exposure, used as the experimental control.
• PCA: Principal component analysis, a statistical method used to reduce data dimensionality and visualize sample clustering or variation.
• NEG: Negative ion mode, a mass spectrometry acquisition mode used for detecting negatively charged ions.
• POS: Positive ion mode, a mass spectrometry acquisition mode used for detecting positively charged ions.
• QC: Quality control, samples, or procedures used to assess the reliability, reproducibility, and stability of experimental data.
• SNP: Single-nucleotide polymorphism, a variation at a single nucleotide position in the genome.

File: Figure_4.zip

Description: This file contains the mycelial diameter and inhibition rate of mycelial growth for different F. graminearum fungal strains exposed to various fungicide treatments and exogenous compounds in the recovery assay of quinofumelin-suppressed mycelial growth.

File: Figure_6.zip

Description:  This file contains the raw data generated from the MST and SPR assays used to determine the binding affinity between quinofumelin and the DHOHII protein. For the SPR assay, the affinity constant (Kd) was determined by kinetic analysis or the steady-state affinity method. For the MST assay, Monolith NT.115 software was used to evaluate the binding affinity between the target protein and quinofumelin based on the Kd values and the signal-to-noise ratio, and the results were further combined and analyzed using MO. Affinity Analysis v2.3 software.

Variables

• Kd: Equilibrium dissociation constant, representing the binding affinity between the ligand and the target protein. A lower Kd value indicates a stronger binding affinity.

File: Figure_5.zip

Description:  This file contains the mycelial diameter and inhibition rate of mycelial growth for FgDHODHII deletion mutants exposed to various fungicide treatments and exogenous compounds in the recovery assay of quinofumelin-suppressed mycelial growth.

Code/software

1. Based on the transcriptomic data, principal component analysis was performed using R (http://www.r-project.org/), and hierarchical clustering heatmaps were generated with the "pheatmap" package. Differential gene expression between treatment groups was analyzed using the DESeq2 package.
2. The identified metabolites were analyzed using MBRole 2.0 (https://csbg.cnb.csic.es/mbrole2/index.php) and the KEGG database (http://www.kegg.jp). Partial least squares discriminant analysis (PLS-DA) was applied to identify differentially accumulated metabolites (DAMs).
3. The SPR assays were conducted using the Biacore T200 instrument.
4. The MST assays were performed using the Monolith NT.115 instrument (NanoTemper Technologies).