Data from: Early maturation of host antimicrobial peptide defenses is associated with host-pathogen coexistence
Data files
Apr 09, 2026 version files 8.64 MB
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DRYAD_upload.zip
8.63 MB
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README.md
6.25 KB
Abstract
Epizootic outbreaks of invasive pathogens, such as the fungal pathogen Batrachochytrium dendrobatidis (Bd), are increasingly recognised as a global threat to biodiversity. However, not all susceptible host populations are equally impacted by these disease outbreaks. While some populations persist despite intense infections and high mortality rates, others can transition to enzootic coexistence with the pathogen. Here, we use comparative peptidomics to identify differences in antimicrobial peptide (AMP) maturation in the Bd-susceptible Common midwife toads (Alytes obstetricans) through metamorphosis. Here, we show that animals that metamorphose prior to AMP immune maturation display a low-AMP-diversity phenotype, which is deficient in anti-Bd AMPs. Where a high incidence of post-metamorphic animals occurs with immature AMPs, populations are associated with epizootic disease dynamics. Conversely, populations associated with mature AMPs remain stable following pathogen invasion. Our results show that even intrinsically susceptible amphibian species can possess the tools that allow populations to recover following a severe Bd epizootic.
Dataset DOI: 10.5061/dryad.k0p2ngfn6
Description of the data and file structure
Supporting data and R scripts for peptidomic data generated as part of a study on the role of antimicrobial peptide defences in the recovery of wild populations of Alytes obstetricans from an epizootic outbreak of amphibian chytridiomycosis.
Files and variables
File: DRYAD_upload.zip
Folder_1: Peptide structures
Subfolders contain supporting files from the PEP-3 peptide conformation server, which were used to generate the predicted conformation of Alyteserin AMPs (Alyteserin1a, Alyteserin1b, Alyteserin1c, Alyteserin1d, Alyteserin2a, Alyteserin2Mb) as well as the supplementary figure from the publication.
Folder_2: Pyrenees_RNAseq_reference
FASTA file of translated (EMBOSS-sixpack) and clustered (CD-HIT) protein sequences predicted from the combined skin transcriptomes of both larval and post-metamorphic Alytes obstetricans
Folder_3: Statistical analysis
Subfolder: Field_analysis
Pyrenees_peptidome_2.R - R script for statistical analysis of field peptidomic data (see manuscript for experimental details)
Allpeptides.fasta - A fasta file containing all the peptides in this study with PTMs removed
Alytes_data2.csv - field metadata for the samples collected during the study, including Bd-qPCR results
- Sample- sample name
- Site- site name
- Species- species name
- Life stage- "Tadpole" or "Metamorph."
- Comment- any other comments recorded from the sample
- Year- year
- Infection.status- Bd infection status of the animal as determined by BdqPCR "positive" or "negative."
- GE- infection intensity of animal determined by Bd qPCR, in units of "genomic equivalents" of Bd, where 1GE is the amount of genetic material contained in 1 zoospore
- Recovery_state- indicates enzootic (Recovering) or epizootic (Non-recovering) disease dynamics
lfq.peptides.csv - PEAKsStudio12 output from mass spec files.
- Contains peak areas of each peptide (row) by sample (columns)
Pyrenees2_file_labels.csv - conversion table for sample numbers (from lfq.peptides) to sample codes (Alytes_data2.csv)
- File - Name of mass spec file associated with the field sample
- Sample_name- sample number assigned during PEAKs pipeline
Standards.csv - contains the peak areas for Alyteserin standards. This is used for relative quantification in the R script
- Peptide- name of peptide being quantified (Alyteserin 1a, 1b, or 2Mb)
- Concentration- Concentration of standard (Micromolar)
- uMol- quantity of peptide injected onto the column in micromoles
- Peak area- peak area from the mass spec
- m/z- mass: charge ratio of the peptide
Subfolder: Inhibition_assays
Inhibition_assays.R - statistical analysis and model fitting of Bd in-vitro inhibition assays for each Alyteserin AMP (see manuscript for experimental details)
Inhibition_assays.csv - by-well OD results of Bd inhibition assays taken at the end point of each experiment
- Peptide name- Alyteserin AMP used in assay
- Label- name of column on plate (X1-X6)
- Row- row number on plate (1-6)
- OD- optical density reading
- Percentage inhibition- Percentage AMP inhibition calculated relative to the positive control
AMP summary table.pptx - summary table of the OD Bd inhibition assay results described above
Subfolder: Map Figure
Map_Figure.R - statistical analysis of Bd-qPCR and mortality data from the Pyrenees field sampling
map.png - map of the field sites used in this study
Mortality_data.csv - Data showing the number of mortalities at each site during the survey period
- Site- name of site
- Mortalities- number of metamorphs found dead during surveys
- Living_metas- number of metamorphs found alive during surveys
- Ymin- lower Clopper-Pearson confidence interval (%)
- Ymax- upper clopper pearson confidence interval (%)
- Mortality_rate- percentage of mortalities from total metamorphs encountered on surveys (%)
- Recovery.status- indicates enzootic (Recovering) or epizootic (Non-recovering) disease dynamics
Mortality_data_long.csv - Same as above, but each sample has its own line
Alytes_data2.csv- Same as the folders above
- Sample- sample name
- Site- site name
- Species- species name
- Life stage- "Tadpole" or "Metamorph."
- Comment- any other comments recorded from the sample
- Year- year
- Infection.status- Bd infection status of the animal as determined by BdqPCR "positive" or "negative."
- GE- infection intensity of animal determined by Bd qPCR, in units of "genomic equivalents" of Bd, where 1GE is the amount of genetic material contained in 1 zoospore
- Recovery_state- indicates enzootic (Recovering) or epizootic (Non-recovering) disease dynamics.
Subfolder: Peptide_diverisity
PeptideTree.R - Statistical analysis and construction of Figure 2 in the main manuscript
MACREL_output- subfolder containing raw AMP prediction data from the MACREL web server
Full_MACREL_output.csv - table containing the combined outputs from the MACREL AMP prediction web server
- Access- peptide name
- Sequence- peptide amino acid sequence
- AMP_family- name of AMP family (see MACREL webserver for details of codes)
- is_AMP- TRUE or FALSE, threshold for AMP assignment is 0.5 AMP probability
- AMP_probability- probability sequence is an AMP, used to assign predicted AMP status in the previous column
- Hemolytic- Hemo or NonHemo, threshold for hemolytic activity assignment is 0.5
- Hemolytic_probability- probability sequence is hemolytic, used to assign predicted hemolytic status in the previous column
Allpeptides.fasta - A fasta file containing all the peptides in this study with PTMs removed
All_peps.aln-fasta - alignment file of peptide fasta above
Tree_annotations.csv - file containing annotation data for the tree in the R script above
- Peptide names- peptide names
- Peptide- amino acid sequence of peptide
- Accession- alignments with known peptides in the APD3 database
- Alyteserin_accession- TRUE or FALSE, does the peptide align with known Alyteserin in the PEAKs pipeline
Code/software
RStudio, Microsoft Excel
