Data from: Mycobiome simplification in wheat is associated with the pathogen Parastagonospora nodorum
Data files
Jul 09, 2026 version files 1.19 MB
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Allen_SNB_AlphaDiversity.pdf
235.83 KB
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Allen_SNB_AlphaDiversity.Rmd
4.66 KB
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Allen_SNB_BetaDiversity.pdf
236.94 KB
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Allen_SNB_BetaDiversity.Rmd
5.70 KB
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Allen_SNB_Networks.pdf
230.85 KB
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Allen_SNB_Networks.Rmd
16.90 KB
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Allen_SNB_TaxonShifts.pdf
251.35 KB
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Allen_SNB_TaxonShifts.Rmd
11 KB
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M21_SNB_Counts.csv
123.41 KB
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M21_SNB_Sample_Data.csv
6.97 KB
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M21_SNB_Taxonomy.csv
62.07 KB
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README.md
5.30 KB
Abstract
Four wheat (Triticum aestivum L.) cultivars were inoculated with wheat straw harboring the fungal pathogen Parastagonospora nodorum in a randomized complete block design at two North Carolina field sites. Flag leaves of inoculated and uninoculated plants were collected and flash frozen at harvest for amplicon sequencing. We used ITS amplicon metagenomics to characterize wheat mycobiome richness and composition, and analyzed mycobiome structure using network analysis. Counts of ASVs, mycobiome composition, and network analysis data are included.
Allen X. J., Cowger C., Brown-Guedira G., Hawkes C. V. Mycobiome simplification in wheat after inoculation with the pathogen Parastagonospora nodorum.
Supplementary Data and Analysis
Data, R scripts, and analyses of mycobiome responses to inoculation with the wheat pathogen Parastagonospora nodorum in a field experiment in North Carolina, USA.
Experiment description
Wheat (Triticum aestivum) cultivars Catawba, Hilliard, Shirley, and USG3640 were grown in plots with and without inoculation of P. nodorum at two sites in North Carolina in 2020-2021. The sites were located in Wake and Washington counties. Inoculation was done by applying wheat straw infected with naturally occurring P. nodorum prior to stem elongation, with uninoculated plots receiving no straw. Each plot was sampled during anthesis by clipping flag leaves with no signs of disease. The mycobiome of each plot was characterized by Illumina ITS sequencing.
File list
- M21_SNB_Counts.csv
- M21_SNB_Sample_Data.csv
- M21_SNB_Taxonomy.csv
- Allen_SNB_AlphaDiversity.Rmd
- Allen_SNB_AlphaDiversity.pdf
- Allen_SNB_BetaDiversity.Rmd
- Allen_SNB_BetaDiversity.pdf
- Allen_SNB_Networks.Rmd
- Allen_SNB_Networks.pdf
- Allen_SNB_TaxonShifts.Rmd
- Allen_SNB_TaxonShifts.pdf
File descriptions
M21_SNB_Counts.csv: count data of samples (columns) by ASVs (rows). Raw counts are to be scaled using count values of three internal spike-in sequences to calculate estimated absolute abundances.
M21_SNB_Sample_Data.csv: Plant data used for ANOVAs in R. Includes the following variables:
| Variable | Description | Units |
|---|---|---|
| SampleID | Unique sample identifier with site, project, and experiment info | NA |
| Source | Type of sample. Used to remove data for replicates, negative controls, and P. nodorum hyphal ladder | NA |
| Plot | Plot number | NA |
| Block | Block number. All blocks are complete except in the case of missing samples | NA |
| Entry | Combination of cultivar and treatment | NA |
| Cultivar | Cultivated variety of wheat used in experiment | NA |
| Treatment | Whether plot was uninoculated or inoculated with P. nodorum infected straw | NA |
| SiteID | Name of site associated with sample (Wake=Wak_SNB, Washington=Was_SNB) | NA |
| Site | Name of site associated with sample (Wake=WAKSN, Washington=WASSN) | NA |
| Pnodo_Abundance | Estimated absolute abundance of P. nodorum | ITS rRNA copies/g DNA |
M21_SNB_Taxonomy.csv: Taxonomic assignments at the Phylum, Class, Order, Family, Genus, and Species level based on ITS1 rRNA sequences.
Allen_SNB_AlphaDiversity.Rmd and Allen_SNB_AlphaDiversity.pdf: R Markdown script and knitted file for ANOVA of mycobiome alpha diversity as a function of treatment, cultivar, site, and block.
Allen_SNB_BetaDiversity.Rmd and Allen_SNB_BetaDiversity.pdf: R Markdown script and knitted file for PERMANOVA of mycobiome beta diversity as a function of treatment, cultivar, site, and block.
Allen_SNB_Networks.Rmd and Allen_SNB_Networks.pdf: R Markdown script and knitted file for generation of SPRING association values of fungal ASVs for uninoculated and inoculated plots at each site and for each cultivar. Visualization of networks was done using Cytoscape.
Allen_SNB_TaxonShifts.Rmd and Allen_SNB_TaxonShifts.pdf: R Markdown script and knitted file for Beta regression of proportion of estimated absolute fungal abundance from plant pathogens as a function of P. nodorum estimated absolute abundance and analysis of differential abundance of fungal ASVs between uninoculated and inoculated plots of each cultivar and Wake and Washington.
Note
Data files must be placed in your working directory or their paths specified for the analyses to work.
Publication information
A manuscript based on these data is currently in preparation. This section will be updated as appropriate.
Funding information
This work was supported by the Novo Nordisk Foundation (grant NNF19SA0059348) and by the Research Capacity Fund (HATCH; project award no. 7005451) from the U.S. Department of Agricultures National Institute of Food and Agriculture.
Additional data raw sequences
Sequence data are available at the NCBI Sequence Read Archive (PRJNA1255089), including Biosample Accessions SAMN48148523-SAMN48148618.
Four winter wheat cultivars with and without pathogen inoculation were grown in plots at two sites in North Carolina in a randomized complete block design with five replicate blocks. Each block included plots with every combination of cultivar and inoculation treatment (4 cultivars × 2 inoculation treatments × 5 blocks × 2 sites = 80 total plots). Four of the eight plots in each block were inoculated with P. nodorum by application of wheat straw infected with naturally occurring P. nodorum. Flag leaves of four randomly selected plants in each plot were clipped and immediately flash-frozen in liquid nitrogen before transport to the lab.
We generated association networks using the Semi-Parametric Rank-based approach for Inference in Graphical model (SPRING) using NetCoMi v1.1. in R. Sequence data are available on the NCBI Sequence Read Archive under BioProject PRJNA1255089, including Biosample Accessions SAMN48148523-SAMN48148618.