Supplementary dataset for The sociality of pathogenicity and virulence throughout Human pathogen diversity

This supplementary dataset provides the list of species included in each analysis and corresponding representative strain genomes used. There are two lists of species: one used for the comparative analysis of virulence factors and pathogenicity, and one used for the case fatality rate comparative analysis.

For each set, the resulting annotations are provided in tab-delimited tables format, for both gene-level annotations, and summarised at species-level. These datasets are directly usable to replicate our analysis, using codes provided at https://github.com/CamilleAnna/CooperativePathogenicityVirulence_repo.git.

1.1_pathogen_commensal_genomes_118.txt: list of pathogen and non-pathogen species and corresponding representative strain genome used in comparative analysis of virulence factors and pathogenicity. Fields:

species_id = species/strain id in MIDAS database

genome_name = corresponding genome name in PATRIC database,

genome_id = corresponding genome id in PATRIC database

is_rep_genome = is genome representative strain in MIDAS database

count_genomes = number of genomes for this species in MIDAS database

genus = genus for species

species = species name for plotting

pathogen = binary variable of whether species was classified as pathogen or non-pathogen

gram_profile = gram profile assigned to species (used for specifying gram profile in PSORTb pipeline), with p = gram-positive, n = gram-negative, OM+ = gram-positive with outer membrane.

2.2_assembled_SPECIES_annotation.txt: assembled dataset for species included in comparative analysis of pathogenicity (n = 118 species).

Fields 1 to 3: genome used for analysis, with:

species_id = species/strain id in MIDAS database

genus = genus for species

species = species name for plotting.

Fields 4 to 13: genome annotations, with

gram_profile = species gram staining profile

total_cds = proteome size

is_victor_vf = number of CDS annotated as virulence factors in VICTOR database

pathogen = pathogenic status

other fields indicate the number of genes for this species annotated with each of the six forms of cooperation.

2.3_assembled_GENES_annotation.txt: gene-level annotations that were used to assemble the table “2.2_assembled_SPECIES_annotation.txt”. This dataset was used for the comparative analysis of virulence factors (n = 118 species, nrows = 367162 genes) total. Each CDS if flagged “1” if it was annotated with the 6 forms of cooperation, and whether it was recorded as a virulence factor in VICTOR database. “peg” and “product_patric” CDS name and annotation in PATRIC database.

3.2_cfr_SUPFAM_match: list of pathogen and non-pathogen species and corresponding representative strain genome used in comparative analysis of virulence factors and pathogenicity. Fields:

Legget_species: species name in Legget et al (2017) supplementary data table

matching_supfam_id: corresponding strain code in SCOP database

genome_name: corresponding genome name in PATRIC database

genome_id: corresponding genome id in PATRIC database

file_name_record: internal naming for annotations

gram_profile: gram profile assigned to species (used for specifying gram profile in PSORTb pipeline), with p = gram positive, n = gram-negative, OM+ = gram-positive with outer membrane.

4.1_assembled_CFR_SPECIES_annotation.txt: assembled dataset for species included in comparative analysis of case fatality rate (n = 50 species). Fields 1 to 10 are ecological data about species provided in Leggett et al (2017) supplementary tables.

Fields 11 to 13: genome used for analysis, with:

species_id = internal naming

genome_id = corresponding PATRIC genome id

matching_supfam_id = corresponding strain code in SCOP database

Fields 14 to 22: genome annotations, with:

gram_profile = species gram staining profile

total_cds = proteome size

is_victor_vf = number of CDS annotated as virulence factors in VICTOR database

other fields indicate number of genes for this species annotated with each of the six forms of cooperation.

4.2_assembled_CFR_GENES_annotation.txt: gene-level annotations that was used to assemble the table “4.2_assembled_CFR_SPECIES_annotation.txt”, n = 50 species, nrows = 180754 genes total. Each CDS if flagged “1” if it was annotated with the 6 forms of cooperation, and whether it was recorded as a virulence factor in VICTOR database. “peg” and “product_patric” CDS name and annotation in PATRIC database.

midas_tree_renamed.newick: phylogeny used for comparative analyses of virulence factors and pathogenicity. We used the MIDAS phylogeny of PATRIC genomes, which we trimmed to our focus species (N = 118) and ultrametricised using chronopl function in ape package.

Supfam_cfr_tree.newick: phylogeny used for comparative analyses of virulence factors and pathogenicity. We used the SCOP database generated phylogeny which we ultrametricised using chronopl function in ape package.