Data for Weimann et al - Evolution and host-specific pathoadaptation of Pseudomonas aeruginosa

Additional data that were generated as part of this work, including clone trees, alignments, variants and genome graph. 

Genomics

• Sample meta data for all patient representative samples (samples_qc_filtered_and_annotated_v2.txt).
• Sample meta data for all samples (samples_qc_filtered_annotated_per_patient_v2.txt).
• FastTree inferred phylogenetic tree of all patient representative and environmental isolates (all_pa_patients.nwk).
• Tables matching alignmnent position with genomic coordinates for all clones (alignment_position_mapping.tar.gz).
• Tables with recombination predictions as inferred by Gubbins for all clones (recombination_prediction.tar.gz).
• Variants that have occurred since the emergence of individual clone with detailed variant effects with variants due to recombination removed (all_mutations_wo_recomb.txt.gz).
• Pseudo-genome alignments for 155 individual clones (all_clones_aln.fasta.tar.gz).
• Clone trees inferred with Gubbins/RaxML (all_clones.nwk.tar.gz).
• Pairwise SNP distances between all isolates (dist_aggr.txt.gz).
• SNP distances between all patient representative and environmental samples in matrix format (all_patient_dist_square.txt.gz).

Dating

• BEAST input alignments for 21 epidemic clones (after pruning) (epidemic_clones_alignments_for_beast.fasta.tar.gz).
• BEAST input XMLs  for 21 epidemic clones (lognormal/uniform/date randomisation test where applicable) (beast_xmls.tar.gz).
• BEAST combined trees for 21 epidemic clones (beast_trees.tar.gz).
• BEAST input XMLs  for discrete trait phylogeographic analysis for 3 epidemic clones (beast_phylogeography.xmls.tar.gz).
• BEAST combined phylogeographic trees for 3 epidemic clones (phylogeography_trees.tar.gz).

Ancestral genome analysis

• Cytoscape session file for Panaroo genome graph laid out and subset to ancestral genome representatives (ancestral_representatives_graph_layout.cys).
• Panaroo genome graph output based on all patient representative/environmental genomes (final_graph.gml.gz).
• Table matching COG categories with abbreviated category names (COG_categories.txt).
• Table with ancestral clone representative COG annotations (emapper_clone2function.txt).

Epidemic clone characteristics

• Clone CF proportions (CF vs non-CF patients + environmental samples) (cf_per_clone_sts21.txt).
• Table with virulence factor expression across clinical isolates (measurements_all_vfs.txt).

Expression analysis

• Table with gene counts and meta data for the gene expression CF proportion association analysis (transcriptomic_data.tar.gz).

Pathoadaptation

• Pseudomonas aeruginosa gene product annotation from www.pseudomonas.com used in the analysis (Pseudomonas_aeruginosa_PAO1_107.tsv.gz). 
• Gene family frequencies for the PAO1 reference genome based on Panaroo pan-genome clustering used in mutational burden test analysis (reference_genes_coverage.txt.gz).
• Table with phylogenetic tree node transmission type/infection type classification (node2type.txt.gz).
• A summary of all single nucleotide variants that lead to amino acid changes with SIFT and FoldX predictions (all_aa_variants_info.txt.gz)
• Cytoscape session file for pathoadaptive STRING pathoadaptive gene-product network (pathoadaptive_gene_products_string_odds_ratio.cys)
• Table with binary values indicating mutations acquired upstream of phylogenetic tree nodes in pathoadaptive genes (used for UMAP) (patho_per_node.txt.gz).
• Table with position of individual mutations as acquired as part of a pathoadaptive trajectory in the pathoadaptive genes (gene2position_v2.txt.gz).