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).