Proteins released into the plant apoplast by the obligate parasitic protist Albugo selectively repress phyllosphere-associated bacteria
Creators: name: Gómez-Pérez, Daniel
name: Schmid, Monja
name: Chaudhry, Vasvi
name: Hu, Yiheng
name: Velic, Ana
name: Maček, Boris
name: Ruhe, Jonas
name: Kemen, Ariane
name: Kemen, Eric
Publisher: name: Zenodo
Year: 2023
Subjects: albugo
antimicrobial
arabidopsis thaliana

description: This repository includes the data and code for the publication "Proteins released into the plant apoplast by the obligate parasitic protist <em>Albugo</em> selectively repress phyllosphere-associated bacteria" (http://doi.org/10.1111/nph.18995). They are divided into four .zip files, corresponding to the different analyses reported in the article. All code is Python 3 unless specified. To reproduce, the conda environment description is found in requirements.yaml. network_analysis The amplicon sequencing data, consisting of taxonomy, OTU table and representative sequences is found in the folders PrV9Output, outputBv5, and FungiOutput for 18S, 16S and ITS, respectively. full.tsv contains the metadata for the network correlation analysis before filtering. otu_table.tsv and metadata.tsv contain the input data for the network correlation analysis. full_005_noheader.edgelist contains the edgelists of the correlation network. The following jupyter notebooks are in this folder: flash_weave.ipynb (written in Julia), code for performing network correlation inference. figure1.ipynb, code for Figure 1. draw_positive_network.ipynb, code for Figure S1. edge_figure.ipynb, code for Figure S2. degree_plot_python.ipynb contains the code for Figure 1b. proteomics_analysis The folder database contains the fasta and functional annotation file for proteomics search of <em>Albugo</em> <em>candida</em> proteins. The folder disorder contains the intrinsically disorder analysis of the genome of <em>Albugo</em>. The folder go_analysis contains the data for the GO analysis. The folder peptides_candidates contains the peptides as identified in the proteomics analysis for the candidates. The folder signalp contains the signalp 6 slow model on <em>Albugo candida </em>proteins. The folder plant_proteases contains the analysis for the enrichment of the proteases from the plant. The folder arabidopsis_albugo_venn contains the analysis of the overlap of peptides between the plant and <em>Albugo</em>. The folder mitochondrial_localization contains the output files for the mitochondrial localization prediction of the predicted proteome of <em>Albugo candida</em>. evidence.txt, parameters.txt, proteinGroups.txt contain the text output files for the raw proteomics as analyzed with MaxQuant, and protein_Groups_cleaned.csv contains the filtered version of proteinGroups.txt. predicted_proteome_predictions.csv contains the antimicrobial predictions for the predicted proteome of <em>Albugo candida.</em> The following jupyter notebooks are in this folder: venn.ipynb, code for Figure 2b and Figure S3. go_analysis/go_graph_nc2_paper.ipynb, code for the analysis of the GO enrichment and Figure 2c. histogram.ipynb, code for the analysis of antimicrobial predictions and Figure 2d. amp_predictors_graph.ipynb, code for Figure S4. peptides_candidates/peptides.ipynb, code for the search of peptides in the proteomics analysis. plant_proteases/plant_proteases.ipynb, code for the plant protease search in the proteomics analysis. proteomics_figure.ipynb, code for Figure 3a. arabidopsis_albugo_venn/venn.ipynb, code for peptide overlap between plant and <em>Albugo </em>and Figure S5. mitochondrial_localization/mit_loc.ipynb contains the analysis of the mitochondrial localization prediction. disorder/fldpnn_nc2_cutoff03.ipynb, code for the analysis of disorder prediction and Figure S22. antimicrobial_analysis The folder fldpnn_candidates contains disorder predictions per amino acid for the candidates. The folder fragments contains the antimicrobial tests for the protein fragments. The folder mic contains the data for the concentration dependent antimicrobial tests. The file antimicrobial_tests.csv contains the data for the antimicrobial tests on the full proteins. The folder ph contains the data for the antimicrobial tests at varying pH. The folder strains contains fasta files for tables S2 and S3. The folder syncom contains the antimicrobial tests on the SynCom members. The folder clavibacter contains the antimicrobial tests on <em>Clavibacter </em>and<em> Rhodococcus </em>strains. The folder cd_spectroscopy contains the data for the CD spectroscopy analyses. The folder compositional_bias contains the analysis for the compositional bias of the protein candidates. The following jupyter notebook are in this folder: figure_matplotlib.ipynb, code for Figures 3b, S8 and S9. figure4.ipynb, code for Figure 4. ph/ph_curve_analysis.ipynb code, for analysis of the varying pH curves and Figure S10. cd_spectroscopy/parse_all_spectra.ipynb, code for the analysis of all CD spectroscopy data and for Figure S11. fragments/domain_analysis.ipynb, code for the analysis of inhibition by the protein fragments and Figure S12. mic/mic_analysis.ipynb, code for the analysis of concentration dependent antimicrobial tests and Figure S13. clavibacter/clavi_fig.ipynb, code for the analysis of the antimicrobial effect of the candidate proteins on the <em>Clavibacter </em>and <em>Rhodococcus </em>strains, and Figure S15. syncom/syncom.ipynb, code for the analysis of the antimicrobial effect of the candidate proteins on the SynCom strains and Figure S16. compositional_bias/parse_flps2.ipynb, code for the analysis of the compositional bias of the protein candidates. syncom_analysis The folder nanopore contains all files related to the NanoPore analyses performed in this study. It includes the compressed fastq files matched to the corresponding barcodes, as well as the processed data (quality_filter subdirectory). The Bash script nanoprep.sh includes the processing of these files. The folder qpcr contains the data related to the qPCR analyses performed in this study. The folder syncom_plant contains the sequencing data analysis from the plant SynCom experiments. It includes the compressed fastq files matched to the corresponding barcodes (raw_fastq subdirectory) and rarefied data (rarefied_13732_sd subdirectory) The folder syncom_culture contains the data related to the SynCom analysis <em>in vitro</em>. The following jupyter notebooks are in this folder: syncom_culture/plot_syncom_replicates.ipynb, code for Figure S17. nanopore/quality_filter/analysis_nanopore.ipynb, code for the analysis of the NanoPore sequencing, and Figures 5c and S18b. fig5.ipynb, code for Figures 5 and S19. syncom_plant/pcoa.ipynb, code for the PCoA of the <em>in planta </em>SynCom experiments and Figure 5d. syncom_plant/relative_abundances_pst.ipynb, code for the calculation of the relative abundances in the <em>in planta </em>SynCom experiments. qpcr/qpcr.ipynb, code for analysis of qPCR experiments and Figures 5b and S18a. <br> <br>