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).

本研究生成的附加数据集涵盖克隆树、序列比对、变异位点及基因组图。

基因组学

所有患者代表性样本的样本元数据（samples_qc_filtered_and_annotated_v2.txt）。
所有样本的样本元数据（samples_qc_filtered_annotated_per_patient_v2.txt）。
基于FastTree推断的所有患者代表性分离株与环境分离株的系统发育树（all_pa_patients.nwk）。
匹配所有克隆比对位点与基因组坐标的表格（alignment_position_mapping.tar.gz）。
所有克隆的Gubbins推断重组预测结果表格（recombination_prediction.tar.gz）。
去除重组来源变异后，各单个克隆出现至今的变异位点及详细变异效应表（all_mutations_wo_recomb.txt.gz）。
155个单克隆的拟基因组比对文件（all_clones_aln.fasta.tar.gz）。
经Gubbins/RaxML推断的克隆树（all_clones.nwk.tar.gz）。
所有分离株的成对单核苷酸多态性（Single Nucleotide Polymorphism, SNP）距离矩阵（dist_aggr.txt.gz）。
所有患者代表性样本与环境样本的SNP距离矩阵文件（all_patient_dist_square.txt.gz）。

定年分析

21个经修剪的流行克隆的BEAST输入比对文件（epidemic_clones_alignments_for_beast.fasta.tar.gz）。
21个流行克隆的BEAST输入XML文件（适用于对数正态分布、均匀分布及日期随机化检验场景）（beast_xmls.tar.gz）。
21个流行克隆的BEAST合并树文件（beast_trees.tar.gz）。
3个流行克隆的离散性状系统地理学分析的BEAST输入XML文件（beast_phylogeography.xmls.tar.gz）。
3个流行克隆的BEAST合并系统地理学树文件（phylogeography_trees.tar.gz）。

祖先基因组分析

针对祖先基因组代表性序列完成布局并子集化的Panaroo基因组图Cytoscape会话文件（ancestral_representatives_graph_layout.cys）。
基于所有患者代表性/环境基因组的Panaroo基因组图输出文件（final_graph.gml.gz）。
同源基因簇（Clusters of Orthologous Genes, COG）类别与缩写名称的匹配表格（COG_categories.txt）。
祖先克隆代表性序列的COG注释表格（emapper_clone2function.txt）。

流行克隆特征

各克隆的囊性纤维化（Cystic Fibrosis, CF）占比（CF患者、非CF患者与环境样本）（cf_per_clone_sts21.txt）。
临床分离株的毒力因子表达量表格（measurements_all_vfs.txt）。

表达分析

用于基因表达与CF占比关联分析的基因计数及元数据表格（transcriptomic_data.tar.gz）。

致病适应性演化

本分析所用的来自www.pseudomonas.com的铜绿假单胞菌（Pseudomonas aeruginosa）基因产物注释文件（Pseudomonas_aeruginosa_PAO1_107.tsv.gz）。
用于突变负荷检验分析的、基于Panaroo泛基因组聚类的PAO1参考基因组基因家族频率表格（reference_genes_coverage.txt.gz）。
系统发育树节点的传播类型/感染类型分类表格（node2type.txt.gz）。
所有导致氨基酸改变的单核苷酸变异的汇总表，包含SIFT与FoldX预测结果（all_aa_variants_info.txt.gz）。
路径适应性STRING基因产物网络的Cytoscape会话文件（pathoadaptive_gene_products_string_odds_ratio.cys）。
标注致病适应性基因内系统发育树节点上游获得突变的二值表格（用于UMAP分析）（patho_per_node.txt.gz）。
致病适应性基因中作为致病适应性演化轨迹一部分获得的单个突变的位置表格（gene2position_v2.txt.gz）。