Salmonella enterica pangenome

The repository with working scripts, figures, data, and supplementary materials for pangenome analysis of 1598 Salmonella enterica genomes.

Contents

This repository contains scripts used for statistical analysis of pangenome, phylogeny, and phenotypical associations. Please consult the methods section in the paper for extra details:

Merkushova, A.V.; Shikov, A.E.; Nizhnikov, A.A.; Antonets, K.S. For Someone, You Are the Whole World: Host-Specificity of Salmonella enterica. Int. J. Mol. Sci. 2023, 24, 13670. https://doi.org/10.3390/ijms241813670

Figures

Figures are available in the pics/ directory. For the description, please consult the results section of the article.

Supplementary

All supplementary material is located in the supplementary/ directory. Supplementary_figures.docx is a Microsoft Word document with a description of all supplementary figures. Supplementary_tables.xlsx is an Excel table with all supplementary tables and descriptions.

Data

Analyzed data are included in the data/ directory.

• data/pangenome/ folder contains the gene presence/absence table obtained using Panaroo.
• data/trees/ folder contains phylogenetic inferences in Newick format based on core gene alignments (aligned with MAFFT).
• data/pyseer/ folder includes Pyseer results attributed to particular hosts.

Scripts

The scripts/analysis directory includes all code used for pangenome analysis:

• IO_lib.py is an ancillary script with functions for processing CSV files;
• metadata_downloader.py was applied to download metadata of studied assemblies;
• split_fasta_to_chunks.py - script for re-naming Panaroo-attributed gene codes to real protein accession numbers;
• make_table_for_pysser.py - script for generating a table with phenotypic traits used for Pyseer analysis;
• create_matrix_for_enrichments.py - script generates two distance matrices based on sequence alignments: one using the Jaccard metric and the other using the Shimkevich-Simpson metric
• filter_virDB_hits.py - script for filtering hits matching the VFDB database using identity and coverage;
• topGO_enrichment.R - script for GO enrichment analysis using topGO;

The scripts/figures directory includes all code used for building images:

• Salmonella_trees_plots.R - R script for generating phylogenetics tree figure;
• Salmonella_statistics_plot.py - script to build the picture that illustrates GC content, genome length and number of hypothetical proteins;
• Salmonella_pangenome_plot.py - script to plot the main characteristics of the reconstructed pangenome;
• Salmonella_enrichment_plot.py - was used to build results of testing GO terms using topGO.