Data from: A fungal endophyte alters poplar leaf chemistry, deters insect feeding, and shapes insect community assembly
Data files
Aug 15, 2024 version files 1.95 GB
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README.md
29.87 KB
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Walther_et_al._2024_bipartite_network.csv
293 B
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Walther_et_al._2024_Field_stachydrine.csv
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Walther_et_al._2024_heatmap_neg_annotade.csv
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Walther_et_al._2024_heatmap_neg_anova.csv
4.67 KB
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Walther_et_al._2024_heatmap_neg_intensities.csv
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Walther_et_al._2024_heatmap_pos_annotade.csv
4.81 KB
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Walther_et_al._2024_heatmap_pos_anova.csv
6.35 KB
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Walther_et_al._2024_heatmap_pos_intensities.csv
74.65 KB
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Walther_et_al._2024_MSMS.zip
1.95 GB
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Walther_et_al._2024_performance.csv
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Walther_et_al._2024_raw_data.xlsx
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Walther_et_al._2024_volcano.xlsx
183.91 KB
Sep 26, 2024 version files 1.95 GB
Abstract
The endophytic fungi of certain grasses and other herbaceous plants have long been known to provide plants with anti-herbivore defense compounds, but there is little information about whether the endophytes of trees also engage in such mutualisms. We investigated the influence of the endophytic fungus Cladosporium sp. on the chemical defenses of black poplar (Populus nigra) trees and the consequences for feeding preference and fitness of herbivorous insects and insect community assembly. Endophyte colonization increased both constitutive- and induced poplar defenses. Generalist Lymantria dispar larvae preferred and performed better on uninfected over endophyte-infected poplar leaves, most likely due to higher concentrations of salicinoids in endophytic leaves and the endophyte-produced alkaloid stachydrine. Under field conditions, the endophytic fungus also shapes insect community assembly in young black poplar trees. Our results show that endophytic fungi can play a major role both in defending trees against herbivorous insects and in structuring insect communities of poplar endophytes.
README: Data from: A fungal endophyte alters poplar leaf chemistry, deters insect feeding, and shapes insect community assembly
Corresponding author
Sybille B. Unsicker sunsicker@bot.uni-kiel.de
General description
This README file describes the data package accompanying the above-mentioned publication.
Files used in the analysis are either
- .xlsx and .csv files for R.scripts
- R. scripts
- Excel file with a summary of raw data and data used for statistics in spss
- MSMS data as .mzML files
- Metaboanalyst.zip containing .csv files, R-history and Report.pdf obtained from metaboanalyst
- IBM SPSS-syntax file
Code/ software
- .xlsx and .csv files for R.scripts R 4.3.2
- R. scripts: Files can be opened using R 4.3.2
- Excel file with a summary of raw data and data used for statistics in IBM SPSS statistics 25
- MSMS data as .mzML files: Files can be opened using open software e.g., ProteoWizard or OpenMS.
- Metaboanalyst.zip containing .csv files, R-history, and Report.pdf obtained from metaboanalyst and can be opened with metaboanalyst
- Spss-syntax file can be opened using IBM SPSS statistics 25
File list and description
.xlsx and .csv files for R.scripts
"Walther et al. 2024_volcano.xlsx"
A file containing results of feature intensities done by metaboscape from endophyte-free plants (control) and endophyte-inoculated black poplar trees from the lab experiment
Columns contain the following information:
- Feature: feature name given by metaboscape
- p-Value: p-Value obtained by metaboscape
- p-Value(Rank): rank of p-Value obtained by metaboscape
- Average Ratio "c"/"e": average ratio between control and endophyte
- Fold Change "c"/"e": fold change between control and endophyte
- p-Value(FWER): p-value for family-wise error rate obtained by metaboscape
- p-Value(FDR): p-value for false discovery rate obtained by metaboscape
- Max. Intensity: Maximum intensity obtained by metaboscape
- CV "c": Coefficient of variation for control treatment obtained by metaboscape
- CV "e": Coefficient of variation for endophyte treatment obtained by metaboscape
- Value Count "c": number of replicates for control
- Value Count "e": number of replicates for endophyte
- n/a: not available, under detection limit
"Walther et al. 2024_bipartite network.csv"
A file containing a summary of counted arthropods observed on endophyte-free control plants and endophyte-inoculated plants from the field experiment
Columns contain the following information:
- Treatment: black poplar trees were either inoculated with the endophyte Cladosporium sp. (e) or were treated with a control solution
- Acari: sum of counted individuals observed during the time period of the experiment belonging to this order
- Araneae: sum of counted individuals observed during the time period of the experiment belonging to this order
- Coleoptera: sum of counted individuals observed during the time period of the experiment belonging to this order
- Dermaptera: sum of counted individuals observed during the time period of the experiment belonging to this order
- Diptera: sum of counted individuals observed during the time period of the experiment belonging to this order
- Ephemeroptera: sum of counted individuals observed during the time period of the experiment belonging to this order
- Hemiptera: sum of counted individuals observed during the time period of the experiment belonging to this order
- Hymenoptera: sum of counted individuals observed during the time period of the experiment belonging to this order
- Ixodida: sum of counted individuals observed during the time period of the experiment belonging to this order
- Leaf miner: sum of counted individuals observed during the time period of the experiment belonging to this order
- Lepidoptera: sum of counted individuals observed during the time period of the experiment belonging to this order
- Neuroptera: sum of counted individuals observed during the time period of the experiment belonging to this order
- Orthoptera: sum of counted individuals observed during the time period of the experiment belonging to this order
- Thysanoptera: sum of counted individuals observed during the time period of the experiment belonging to this order
- unknown: sum of counted individuals observed during the time period of the experiment, which could not be classified
"Walther et al. 2024_Field_stachydrine.csv"
File containing stachydrine concentration from black poplar trees standing in the field
Columns contain the following information:
- sample.ID: replicate
- compound: name of the measured compound
- concentration: amount of the measured compound stachydrine in nmol/g
- endophyte: describes the treatment, c (control, tree with no endophyte inoculation), e (endophyte, tree with endophyte inoculation)
- bereich: area of the tree which was observed
- tree: unique number of tree
- herbivory: leaf with damage by herbivory
- damage.perc: leaf area loss in percentages
- damage: leaf area loss in cm²
"Walther et al. 2024_heatmap_neg_annotade.csv"
A file containing significant features (measured in negative mode) annotated by Michael Reichelt. Significant features were obtained by a two-way-ANOVA done in MetaboAnalyst (but see Metaboanalyst.zip)
Columns contain the following information:
- c1..c4: control, uninfected black poplar trees (4 replicates), containing information about the feature intensity
- ch1...ch4: control + herbivory, uninfected black poplar trees which experienced herbivory by L. dispar larvae (4 replicates), containing information about the feature intensity
- e1...e4: endophyte, with Cladosporium sp. inoculated black poplar trees (4 replicates), containing information about the feature intensity
- eh1...eh4: endophyte + herbivory, with Cladosporium sp. inoculated black poplar trees which experienced herbivory by L. dispar larvae (4 replicates), containing information about the feature intensity
- Name: feature name and annotation given by Michael Reichelt
- Formular: sum formula of chemical structure
- bucket: feature name given by metaboscape
- RT..min: Retention time in min
- m.z..Da.: mass to ratio in Dalton
- putative.identification: annotation by Michael Reichelt
- NA in column Formular: chemical formula could not be generated
- NA in column putative.identification: feature could not be annotated
"Walther et al. 2024_heatmap_neg_anova.csv"
The file contains results of a two-way ANOVA done by metaboanalyst features obtained by an LCMS measured in negative polarity from endophyte-free plants (control) and endophyte-inoculated black poplar trees from the lab experiment. The corresponding R.history, Report.pdf file was obtained from MetaboAnalyst and CSV. data used for the analysis can be found in the folder Metaboanalyst.zip.
Columns contain the following information:
- X.1: continuous number of individual feature
- X: Features
- endophyte.F.val:F-value for endophyte (two-way ANOVA)
- endophyte.raw.p.: raw p-value for endophyte
- endophyte.adj.p.: adjusted p-value for endophyte
- herbivory.F.val.: F-value for herbivory (two-way ANOVA)
- herbivory.raw.p.: raw p-value for herbivory
- herbivory.adj.p.: adjusted p-value for herbivory
- interaction.F.val.: F-value for interaction(two-way ANOVA)
- interaction.raw.p.: raw p-value for interaction
- interaction.adj.p.: adjusted p-value for interaction
Related files from the folder Metaboanalyst.zip:
- Walther_et_al._2024_heatmap_metaboanalyst_metadata.csv
- Walther_et_al._2024_heatmap_metaboanalyst_neg.mode_feat1-200.csv
- Walther_et_al._2024_heatmap_metaboanalyst_neg.mode_feat201-400.csv
- Walther_et_al._2024_heatmap_metaboanalyst_neg.mode_feat401-492.csv
- Walther_et_al._2024_heatmap_metaboanalyst_neg.mode_feat1-200_Rhistory.R
- Walther_et_al._2024_heatmap_metaboanalyst_neg.mode_feat201-400_Rhistory.R
- Walther_et_al._2024_heatmap_metaboanalyst_neg.mode_feat401-492_Rhistory.R
- Walther_et_al._2024_heatmap_metaboanalyst_neg.mode_feat1-200_Report.pdf
- Walther_et_al._2024_heatmap_metaboanalyst_neg.mode_feat201-400_Report.pdf
- Walther_et_al._2024_heatmap_metaboanalyst_neg.mode_feat401-492_Report.pdf
"Walther et al. 2024_heatmap_neg_intensities.csv"
The file containing feature obtained by an LCMS measured in negative polarity from endophyte-free plants (control) and endophyte-inoculated black poplar trees from the lab experiment
Columns contain the following information:
- sample: feature name
- c..c4: control, uninfected black poplar trees (4 replicates), containing information about the feature intensity
- ch...ch4: control + herbivory, uninfected black poplar trees which experienced herbivory by L. dispar larvae (4 replicates), containing information about the feature intensity
- e...e4: endophyte, with Cladosporium sp. inoculated black poplar trees (4 replicates), containing information about the feature intensity
- eh...eh4: endophyte + herbivory, with Cladosporium sp. inoculated black poplar trees that experienced herbivory by L. dispar larvae (4 replicates), containing information about the feature intensity
"Walther et al. 2024_heatmap_pos_annotade.csv"
A file containing significant features (measured in positive mode) annotated by Michael Reichelt. Significant features were obtained by a two-way-ANOVA done in MetaboAnalyst (but see Metaboanalyst.zip)
Columns contain the following information:
- c1..c4: control, uninfected black poplar trees (4 replicates), containing information about the feature intensity
- ch1...ch4: control + herbivory, uninfected black poplar trees which experienced herbivory by L. dispar larvae (4 replicates), containing information about the feature intensity
- e1...e4: endophyte, with Cladosporium sp. inoculated black poplar trees (4 replicates), containing information about the feature intensity
- eh1...eh4: endophyte + herbivory, with Cladosporium sp. inoculated black poplar trees that experienced herbivory by L. dispar larvae (4 replicates), containing information about the feature intensity
- Name: feature name and annotation given by Michael Reichelt
- Formular: sum formula of chemical structure
- bucket: feature name given by metabscape
- RT..min: Retention time in min
- m.z..Da.: mass to ratio in Dalton
- putative.identification: annotation by Michael Reichelt
- NA in column Formular: chemical formula could not be generated
- NA in column putative.identification: feature could not be annotated
"Walther et al. 2024_heatmap_pos_anova.csv"
The file contains results of a two-way ANOVA done by metaboanalyst features obtained by an LCMS measured in positive polarity from endophyte-free plants (control) and endophyte-inoculated black poplar trees from the lab experiment. The corresponding R.history, Report.pdf file was obtained from MetaboAnalyst and CSV. data used for the analysis in MetaboAnalyst can be found in the folder Metaboanalyst.zip.
Columns contain the following information:
- X.1: continuous number of individual feature
- X: Features
- endophyte.F.val:F-value for endophyte (two-way ANOVA)
- endophyte.raw.p.: raw p-value for endophyte
- endophyte.adj.p.: adjusted p-value for endophyte
- herbivory.F.val.: F-value for herbivory (two-way ANOVA)
- herbivory.raw.p.: raw p-value for herbivory
- herbivory.adj.p.: adjusted p-value for herbivory
- interaction.F.val.: F-value for interaction(two-way ANOVA)
- interaction.raw.p.: raw p-value for interaction
- interaction.adj.p.: adjusted p-value for interaction
Related files from the folder Metaboanalyst.zip:
- Walther_et_al._2024_heatmap_metaboanalyst_metadata.csv
- Walther_et_al._2024_heatmap_metaboanalyst_pos.mode_feat1-200.csv
- Walther_et_al._2024_heatmap_metaboanalyst_pos.mode_feat201-400.csv
- Walther_et_al._2024_heatmap_metaboanalyst_pos.mode_feat401-600.csv
- Walther_et_al._2024_heatmap_metaboanalyst_pos.mode_feat601-698.csv
- Walther_et_al._2024_heatmap_metaboanalyst_pos.mode_feat1-200_Rhistory.R
- Walther_et_al._2024_heatmap_metaboanalyst_pos.mode_feat201-400_Rhistory.R
- Walther_et_al._2024_heatmap_metaboanalyst_pos.mode_feat401-600_Rhistory.R
- Walther_et_al._2024_heatmap_metaboanalyst_pos.mode_feat601-698_Rhistory.R
- Walther_et_al._2024_heatmap_metaboanalyst_pos.mode_feat1-200_Report.pdf
- Walther_et_al._2024_heatmap_metaboanalyst_pos.mode_feat201-400_Report.pdf
- Walther_et_al._2024_heatmap_metaboanalyst_pos.mode_feat401-600_Report.pdf
- Walther_et_al._2024_heatmap_metaboanalyst_pos.mode_feat601-698_Report.pdf
"Walther et al. 2024_heatmap_pos_intensities.csv"
File containing features obtained by an LCMS measured in negative polarity from endophyte-free plants (control) and endophyte-inoculated black poplar trees from the lab experiment
Columns contain the following information:
- sample: feature name
- c..c4: control, uninfected black poplar trees (4 replicates), containing information about the feature intensity
- ch...ch4: control + herbivory, uninfected black poplar trees which experienced herbivory by L. dispar larvae (4 replicates), containing information about the feature intensity
- e...e4: endophyte, with Cladosporium sp. inoculated black poplar trees (4 replicates), containing information about the feature intensity
- eh...eh4: endophyte + herbivory, with Cladosporium sp. inoculated black poplar trees that experienced herbivory by L. dispar larvae (4 replicates), containing information about the feature intensity
"Walther et al. 2024_performance.csv"
A file containing results of a performance experiment. Larvae of L. dispar (above) and C. tremulae (below) fed either on endophyte-inoculated leaves or control leaves.
Columns contain the following information:
- unique.no.Of.insect: biological replicate (insect species feeding on black poplar leaves)
- insect.species: L. dispar larvae (moth) or C. tremulae (beetle) feeding on black poplar tree
- treatment: black poplar trees were either inoculated with the endophyte Cladosporium sp. (e) or were treated with a control solution (c)
- T0...T10: weight (mg) of insect species on that time point
- W1...W10: weight gain (mg) calculated by T(x)-T(x-1)
- delta1....delta10: weight gain (mg) calculated by T(x)-T(0)
- NA: data not available, as replicate 3 (moth) died or experiment finished (insect.species: C. tremulae (beetle))
R code:
"Walther et al. 2024_heatmap.R"
Metabolomic investigations of black poplar (P. nigra) leaves after fungal endophyte inoculation and herbivory by L. dispar larvae.
R code used to create a heatmap of the significant features obtained by a two-way ANOVA.
"Walther et al. 2024_bipartite network.R"
R code used to visualize plant-arthropod interactions comparing black poplar trees infected with a fungal endophyte to control uninfected trees placed in the field.
"Walther et al. 2024_performance.R"
R code used to estimate the effect of time, endophyte, and the interaction on insect performance.
"Walther et al. 2024_volcano.R"
Detection and quantification of the alkaloid stachydrine
R code used to create a for volcano plot which illustrates metabolite features from leaf tissue inoculated with the endophyte and those of control plants. Features were obtained from an untargeted LC-MS analysis with a QTOF mass spectrometer in positive ionization mode.
"Walther et al. 2024_stachydrine field.R"
R code to test differences in stachydrine concentration of black poplar trees in the field experiment.
Excel file with a summary of raw data
"Walther et al. 2024 raw data 240909.xlsx"
Summary of all data used in the study and used for statistical analysis run in IBM SPSS statistics 25
Sheet: Figure 1 raw data
File containing an overview of raw data about feature intensities obtained from LCMS. Data used for PCA and heatmap
Columns contain the following information:
- feature (metaboscape): feature name given by Metaboscape
- mode: positive or negative ionization mode run on an LCMS
- c1-c4: control, uninfected black poplar trees
- ch1-ch4: control + herbivory, uninfected black poplar trees which experienced herbivory by L. dispar larvae
- e1-e4: endophyte, with Cladosporium sp. inoculated black poplar trees
- eh1-eh4: endophyte + herbivory, with Cladosporium sp. inoculated black poplar trees that experienced herbivory by L. dispar larvae
- chemical formular: chemical formula obtained from metaboscape
- mass to charge ratio: mass to charge ratio of the specific feature
- retention time: retention time in minutes
- n/a: no data available, no chemical formula could be generated
Sheet: Figure 1 PCA
A file containing raw data about PCA loadings
Columns contain the following information:
- mode: positive or negative ionization mode run on an LCMS
- feature (metaboscape): feature name given by Metaboscape
- PC1-16: PCA axis
Sheet: Figure 1 heatmap.1
A file containing results of the 2way ANOVA of significant features obtained from metaboanalyst used for heatmap
Columns contain the following information:
- feature (metaboscape): feature name given by Metaboscape
- mode: positive or negative ionization mode run on an LCMS
- endophyte: with Cladosporium sp. inoculated black poplar trees
- herbivory: black poplar trees which experienced herbivory by L. dispar larvae
- interaction: interaction of endophyte infection and herbivory on black poplar trees
- endophyte(F.val): F-value for endophyte (two-way ANOVA)
- endophyte(raw.p): raw p-value for endophyte
- endophyte(adj.p): adjusted p-value for endophyte
- herbivory(F.val): F-value for herbivory (two-way ANOVA)
- herbivory(raw.p): raw p-value for herbivory
- herbivory(adj.p): adjusted p-value for herbivory
- Interaction(F.val): F-value for interaction(two-way ANOVA)
- Interaction(raw.p): raw p-value for interaction
- Interaction(adj.p): adjusted p-value for interaction
Sheet: Figure 1 heatmap.2
A file containing significant features used for the heatmap.
Columns contain the following information:
- c: control, uninfected black poplar trees
- ch: control + herbivory, uninfected black poplar trees that experienced herbivory by L. dispar larvae
- e: endophyte, with Cladosporium sp. inoculated black poplar trees
- eh: endophyte + herbivory, with Cladosporium sp. inoculated black poplar trees that experienced herbivory by L. dispar larvae
- RT (min): retention time in minutes
- m/z: mass to ratio in Dalton
- mode: positive or negative ionization mode run on an LCMS
- formular: chemical subformula
- feature (metaboscape): feature name given by Metaboscape
- feature (final): feature name after adjustment
- n/a: no data available, no chemical formula could be generated
Sheet: Figure 2
File containing results of the effect of endophyte inoculation and herbivory on salicinoid concentrations in leaves of black
Columns contain the following information:
- c: control, uninfected black poplar trees
- ch: control + herbivory, uninfected black poplar trees that experienced herbivory by L. dispar larvae
- e: endophyte, with Cladosporium sp. inoculated black poplar trees
- eh: endophyte + herbivory, with Cladosporium sp. inoculated black poplar trees that experienced herbivory by L. dispar larvae
- treatment: treatment of black poplar trees in the assays
- endophyte: with Cladosporium sp. inoculated black poplar trees
- herbivory: black poplar trees that experienced herbivory by L. dispar larvae
- concentration: content of the metabolite
- unit: unit of metabolite
- compound: measured metabolite
Sheet: Figure 3
File containing results of the effect of fungal endophyte inoculation on the levels of non-salicinoid phenolic defense
Columns contain the following information:
- c: control, uninfected black poplar trees
- ch: control + herbivory, uninfected black poplar trees which experienced herbivory by L. dispar larvae
- e: endophyte, with Cladosporium sp. inoculated black poplar trees
- eh: endophyte + herbivory, with Cladosporium sp. inoculated black poplar trees which experienced herbivory by L. dispar larvae
- treatment: treatment of black poplar trees in the assays
- endophyte: with Cladosporium sp. inoculated black poplar trees
- herbivory: black poplar trees that experienced herbivory by L. dispar larvae
- concentration: content of the metabolite
- unit: unit of metabolite
- compound: measured metabolite
Sheet: Figure 4b
A file containing results of the effect of fungal endophyte inoculation on the preference of insect herbivores.
Columns contain the following information:
- c: control, uninfected black poplar trees
- e: endophyte, with Cladosporium sp. inoculated black poplar trees
- tree: individual tree number
- caterpillar: individual caterpillar (L. dispar) feeding on black poplar leafs
- damage (cm²): consumed leaf area by L. dispar larvae
- leaf area loss %: consumed leaf area in percentages by L. dispar larvae
Sheet: Figure 4c
A file containing results of the effect of fungal endophyte inoculation on the performance of insect herbivores.
Columns contain the following information:
- c: control, uninfected black poplar trees
- e: endophyte, with Cladosporium sp. inoculated black poplar trees
- moth: L. dispar larvae feeding on black poplar tree
- beetle: C. tremulae larvae feeding on black poplar tree
- sample ID: biological replicate (insect species feeding on black poplar leaves)
- insect species: L. dispar larvae (moth) or C. tremulae (beetle) feeding on black poplar tree
- treatment: treatment of black poplar used in the assays
- time (d): time in days after insects were placed on the black poplar trees
- weight gain (mg): weight gain in mg of observed insect
Sheet: Figure 5a
The volcano plot illustrates metabolite features from leaf tissue inoculated with the endophyte and those of control plants.
Columns contain the following information:
- c: control, uninfected black poplar trees
- e: endophyte, with Cladosporium sp. inoculated black poplar trees
- Feature: feature name given by metaboscape
- p-Value: p-Value obtained by metaboscape
- p-Value(Rank): rank of p-Value obtained by metaboscape
- Average Ratio "c"/"e": average ratio between control and endophyte
- Fold Change "c"/"e": fold change between control and endophyte
- p-Value(FWER): p-value family-wise error rate obtained by metaboscape
- p-Value(FDR): p-value false discovered rate obtained by metaboscape
- Max. Intensity: Maximum intensity obtained by metaboscape
- CV "c": Coefficient of variation for control treatment obtained by metaboscape
- CV "e": Coefficient of variation for endophyte treatment obtained by metaboscape
- Value Count "c": number of replicates for control
- Value Count "e": number of replicates for endophyte
- n/a: no data available, under the detection limit
Sheet: Figure 5b
File containing data on stachydrine concentration from Cladosporium sp. and black poplar leaves from the lab experiment
Columns contain the following information:
- sample ID: replicate
- tissue: tissue used for chemical analysis
- endophyte: with Cladosporium sp. inoculated black poplar trees
- herbivory: black poplar trees that experienced herbivory by L. dispar larvae
- treatment: treatment of black poplar used in the assays
- concentration: content of the metabolite
- unit: unit of metabolite
- compound: measured metabolite
Abbreviation:
- c: control, uninfected black poplar trees
- ch: control + herbivory, uninfected black poplar trees which experienced herbivory by L. dispar larvae
- e: endophyte, with Cladosporium sp. inoculated black poplar trees
- eh: endophyte + herbivory, with Cladosporium sp. inoculated black poplar trees which experienced herbivory by L. dispar larvae
- n/a: not available, collected mycelium, no treatment was applied
Sheet: Figure 5d
A file containing data on leaf area loss from the stachydrine choice experiment
Columns contain the following information:
- replicate: biological replicate
- insect: insect species used for the assay
- damage stachydrine (cm²): leaf area consumed by an insect, leaf discs treated with a solution containing stachydrine
- damage control cm2: leaf area consumed by an insect, leaf discs treated with a control solution
Sheet: Figure 6
A file containing raw data of plant-arthropod interactions comparing black poplar trees infected with a fungal endophyte to control uninfected trees placed in the field.
Columns contain the following information:
- date: observation date
- time: time of observation
- datum: real date
- treatment: treatment of black poplar trees ( c: control, uninfected black poplar trees, e: endophyte, with Cladosporium sp. inoculated black poplar trees)
- tree: individual tree
- Acari ... Thysanoptera: observed Arthropod on a specific observation point
- unknown: not identified arthropod
Sheet: Table S1A
A file containing data on endophyte abundance from different experiments
Columns contain the following information:
- c: control, uninfected black poplar trees
- ch: control + herbivory, uninfected black poplar trees which experienced herbivory by L. dispar larvae
- e: endophyte, with Cladosporium sp. inoculated black poplar trees
- eh: endophyte + herbivory, with Cladosporium sp. inoculated black poplar trees which experienced herbivory by L. dispar larvae
- d: damage
- experiment: type of experiment
- treatment: treatment of black poplar trees
- treat: number abbreviation of treatment of black poplar trees
- target: target sequence to quantify the abundance of the endophyte
- Sample: biological replicate
- expression: Relative endophyte abundance quantified with qPCR (relative expression ∆∆ Ct)
Sheet: Table S1B
A file containing data on stachydrine concentrations from different experiments
Columns contain the following information:
- c: control, uninfected black poplar trees
- ch: control + herbivory, uninfected black poplar trees which experienced herbivory by L. dispar larvae
- e: endophyte, with Cladosporium sp. inoculated black poplar trees
- eh: endophyte + herbivory, with Cladosporium sp. inoculated black poplar trees which experienced herbivory by L. dispar larvae
- experiment: type of experiment
- treatment: treatment of black poplar trees in the assays
- endophyte: with Cladosporium sp. inoculated black poplar trees
- herbivory: black poplar trees that experienced herbivory by L. dispar larvae
- concentration: content of the metabolite
- unit: unit of metabolite
- compound: measured metabolite
- tree: unique number of individual tree
Sheet: Table S1D
A file containing data on stachydrine concentrations from stachydrine preference assay
Columns contain the following information:
- c: control, uninfected black poplar trees
- stach: leaves coated with stachydrine solution
- experiment: type of experiment
- treatment: treatment of black poplar trees in the assays
- concentration: content of the metabolite
- unit: unit of metabolite
- compound: measured metabolite
Sheet: Table S2
A file containing data on leaf chemical analysis from the laboratory experiment
Columns contain the following information:
- c: control, uninfected black poplar trees
- ch: control + herbivory, uninfected black poplar trees which experienced herbivory by L. dispar larvae
- e: endophyte, with Cladosporium sp. inoculated black poplar trees
- eh: endophyte + herbivory, with Cladosporium sp. inoculated black poplar trees which experienced herbivory by L. dispar larvae
- experiment: type of experiment
- treatment: treatment of black poplar trees in the assays
- treat: number abbreviation of treatment of black poplar trees
- endophyte: with Cladosporium sp. inoculated black poplar trees
- herbivory: black poplar trees that experienced herbivory by L. dispar larvae
- concentration: content of the metabolite
- unit: unit of metabolite
- compound: measured metabolite
Sheet: Table S4
A file containing data on arthropods attracted during the field experiment
Columns contain the following information:
- c: control, uninfected black poplar trees
- e: endophyte, with Cladosporium sp. inoculated black poplar trees
- date: observation date
- time: time of observation
- treatment: treatment of black poplar trees
- tree: individual tree
- count: number of observed insects counted on that day during that time on the tree
- class: insect was identified to class level
- order: insect was identified to order level
- suborder: insect was identified to suborder level
- family: insect was identified at the family level
Sheet: Table S5
A file containing data on leaf chemical analysis from the field experiment
Columns contain the following information:
- c: control, uninfected black poplar trees
- e: endophyte, with Cladosporium sp. inoculated black poplar trees
- treatment: treatment of black poplar trees in the assays
- concentration: content of the metabolite
- unit: unit of metabolite
- compound: measured metabolite
Sheet: Table S9
A file containing data on the germination tests of Cladosporium sp. spores for the lab experiment, the preference assay, and the field experiment.
Columns contain the following information:
- experiment: type of experiment
- replicate: 100µl of diluted spore solution were pipetted on a single petri dish (one petri dish = one replicate)
- germinated spores: number of germinated spores
Sheet: Figure S5
File containing data of herbivore damage to endophytic fungus-inoculated (fungus) and uninoculated control (control) trees from the experiment conducted in the lab
Columns contain the following information:
- treatment: treatment of black poplar trees in the assays
- treat: treatment of black poplar trees in the assays
- tree: unique number of individual tree
- sum of damage: sum of damage of the whole tree
- leaf area loss %: leaf area loss in percentage
Abbreviations:
- c: control, uninfected black poplar trees
- e: endophyte, with Cladosporium sp. inoculated black poplar trees
- 1: c
- 2: e
Sheet: Figure S6
File containing data on the effect of fungal endophyte inoculation on concentrations of phytohormones of black poplar
Columns contain the following information:
- treatment: treatment of black poplar trees in the assays
- treat: number abbreviation of treatment of black poplar trees
- endophyte: with Cladosporium sp. inoculated black poplar trees
- herbivory: black poplar trees that experienced herbivory by L. dispar larvae
- concentration: content of the metabolite
- unit: unit of metabolite
- compound: measured metabolite
Abbreviations:
- c: control, uninfected black poplar trees
- ch: control + herbivory, uninfected black poplar trees which experienced herbivory by L. dispar larvae
- e: endophyte, with Cladosporium sp. inoculated black poplar trees
- eh: endophyte + herbivory, with Cladosporium sp. inoculated black poplar trees which experienced herbivory by L. dispar larvae
Sheet: Figure S7b
File containing data on herbivore damage from control and inoculated plants from the field experiment
Columns contain the following information:
- tree: unique number of individual tree
- treatment: treatment of black poplar trees in the assays
- treat: number abbreviation of treatment of black poplar trees
- sum leaf area (cm²): reconstructed area of a whole plant
- damage (cm²): leaf area loss in cm²
- damage %: leaf area loss in %
Abbreviation:
- 1: control
- 2: endophyte
Sheet: Figure S8
A file containing data on stachydrine concentration in aphid honeydew.
Columns contain the following information:
- treatment: treatment of black poplar trees in the assays
- treat: number abbreviation of treatment of black poplar trees
- tree: unique number of individual tree
- concentration: content of the metabolite
- unit: unit of metabolite
- compound: measured metabolite
Abbreviation:
- 1: control
- 2: endophyte
MSMS data as .mzML files
"Walther et al. 2024_MSMS.zip"
Zip-folder containing data of mass spectra from nontarget analysis. Files can be opened using open software e.g., ProteoWizard or OpenMS.
Files .mzML are named after sample name: continues number - treatment - replicate - ionization mode
- c: control, uninfected black poplar trees
- ch: control + herbivory, uninfected black poplar trees which experienced herbivory by L. dispar larvae
- e: endophyte, with Cladosporium sp. inoculated black poplar trees
- eh: endophyte + herbivory, with Cladosporium sp. inoculated black poplar trees which experienced herbivory by L. dispar larvae
Metaboanalyst.zip containing .csv files, R-history and Report.pdf
"metaboanalyst.zip"
Zip-folder containing peak intensities of features obtained from untarget LCMS analysis and proceed in metaboanlayst to create a PCA and to obtain significant features as a result of a 2wayAnova run in MetaboAnalyst to create a heatmap
The folder contains .csv files, which were uploaded to metaboanalyst (including the metadata file), and R-history and a Report.pdf file obtained from metaboanalyst after running the statistics.
File name describes: author_the purpose for the analysis_software_ionization mode_feature range
Rhistory.R and Report.pdf files are named accordingly.
.csv files used to create PCA and files obtained from Metaboanalyst:
- Walther_et_al._2024_PCA_metaboanalyst_neg.mode.csv
- Walther_et_al._2024_PCA_metaboanalyst_neg.mode_Rhistory.R
- Walther_et_al._2024_PCA_metaboanalyst_neg.mode_Report.pdf
- Walther_et_al._2024_PCA_metaboanalyst_pos.mode.csv
- Walther_et_al._2024_PCA_metaboanalyst_pos.mode_Rhistory.R
- Walther_et_al._2024_PCA_metaboanalyst_pos.mode_Report.pdf
Due to computational limitations in metaboanalyst, only the top 200 features (based on variance) are tested. Therefore .csv files with features were split into several .csv files for 2wayanova in order to analyse all the data.
.csv files used for a two-way-ANOVA and files obtained from Metaboanalyst:
- Walther_et_al._2024_heatmap_metaboanalyst_metadata.csv
- Walther_et_al._2024_heatmap_metaboanalyst_neg.mode_feat1-200.csv
- Walther_et_al._2024_heatmap_metaboanalyst_neg.mode_feat201-400.csv
- Walther_et_al._2024_heatmap_metaboanalyst_neg.mode_feat401-492.csv
- Walther_et_al._2024_heatmap_metaboanalyst_neg.mode_feat1-200_Rhistory.R
- Walther_et_al._2024_heatmap_metaboanalyst_neg.mode_feat201-400_Rhistory.R
- Walther_et_al._2024_heatmap_metaboanalyst_neg.mode_feat401-492_Rhistory.R
- Walther_et_al._2024_heatmap_metaboanalyst_neg.mode_feat1-200_Report.pdf
- Walther_et_al._2024_heatmap_metaboanalyst_neg.mode_feat201-400_Report.pdf
Walther_et_al._2024_heatmap_metaboanalyst_neg.mode_feat401-492_Report.pdf
Walther_et_al._2024_heatmap_metaboanalyst_metadata.csv
Walther_et_al._2024_heatmap_metaboanalyst_pos.mode_feat1-200.csv
Walther_et_al._2024_heatmap_metaboanalyst_pos.mode_feat201-400.csv
Walther_et_al._2024_heatmap_metaboanalyst_pos.mode_feat401-600.csv
Walther_et_al._2024_heatmap_metaboanalyst_pos.mode_feat601-698.csv
Walther_et_al._2024_heatmap_metaboanalyst_pos.mode_feat1-200_Rhistory.R
Walther_et_al._2024_heatmap_metaboanalyst_pos.mode_feat201-400_Rhistory.R
Walther_et_al._2024_heatmap_metaboanalyst_pos.mode_feat401-600_Rhistory.R
Walther_et_al._2024_heatmap_metaboanalyst_pos.mode_feat601-698_Rhistory.R
Walther_et_al._2024_heatmap_metaboanalyst_pos.mode_feat1-200_Report.pdf
Walther_et_al._2024_heatmap_metaboanalyst_pos.mode_feat201-400_Report.pdf
Walther_et_al._2024_heatmap_metaboanalyst_pos.mode_feat401-600_Report.pdf
Walther_et_al._2024_heatmap_metaboanalyst_pos.mode_feat601-698_Report.pdf
Abbreviation used:
- feat: features
- c: control, uninfected black poplar trees
- ch: control + herbivory, uninfected black poplar trees which experienced herbivory by L. dispar larvae
- e: endophyte, with Cladosporium sp. inoculated black poplar trees
- eh: endophyte + herbivory, with Cladosporium sp. inoculated black poplar trees which experienced herbivory by L. dispar larvae
IBM SPSS-syntax file
"Walther_et_al._2024_spss_syntax.sps"
The file contains the Syntax of Statistical analysis run by IBM SPSS 25.
Corresponding Excel file:
- Walther_et_al._2024_raw_data_240909.xlsx (description see above).
Version changes
26-sept-2024
1. R-scripts:
- the used package version is now included in each R-script
- corrected the name of all .csv-files in the script for proper data loading
2. Walther_et_al._2024_raw_data_240909:
- Sheets have been updated (table structure changed) for proper data loading in SPSS using the SPSS syntax file Walther_et_al._2024_spss_syntax.sps:
- “Figure 5d”: split the column “damage (cm²)” by column “treatment” to obtain two columns “damage stachydrine cm2” and “damage control cm2”, which fit the table design for paired t-test in SPSS
- “Figure 6”: changed table structure to now have arthropod orders as columns, which matches the table design for statistical analysis in SPSS
- “Figure S5”: summed up the leaf damage and calculated the leaf area loss (%) for all leaves per tree to analyze herbivore damage on whole poplar trees, which was used to compare damage between control and endophyte-infected trees from the lab experiment, non-herbivory treatments were dropped
- “Figure S7b”: summed up the leaf damage and calculated the leaf area loss (%) for all leaves per tree to analyze herbivore damage on whole poplar trees, which was used to compare damage between control and endophyte-infected trees from the field experiment
3. Walther_et_al._2024_spss_syntax.sps:
- uploaded the Syntax of the statistical analysis done in SPSS
4. metaboanalyst.zip: uploaded statistical analysis done in MetaboAnalyst
- File contains R-history and Report.pdf obtained from MetaboAnalyst and corresponding .csv files used to analyze peak intensities of features obtained from untargeted LCMS analysis to create a PCA and to obtain significant features as a result of a 2wayAnova run in MetaboAnalyst to create a heatmap.