Scripts and data associated with T7SS adaptation paper

Preprint: Mortimer TD, Weber AM, Pepperell CS. 2016. Evolutionary thrift: mycobacteria repurpose plasmid diversity during adaptation of type VII secretion systems. bioRxiv:67207. http://biorxiv.org/content/early/2016/08/01/067207

.faa files containing amino acids sequences for chromosomes and plasmids (output of prokka)

Alignments used for phylogenetic analysis

Concatenated alignment of amino acid sequences of all core genes of Actinobacteria used in this project

Alignment of eccA from plasmids

Alignment of eccB from plasmids

Alignment of espI from plasmids

Concatenated alignment of amino acid sequences of ESX-4 genes from ESX-4 and ESX-4 bis loci in Actinobacteria

Concatenated alignment of amino acid sequences of ESX genes for all ESX loci

Concatenated alignment of nucleotide sequences of ESX genes for all ESX loci

Concatenated alignment of nucleotide sequences of ESX genes for plasmid-borne ESX loci

Alignment of tcpC from plasmids

Concatenated alignment of amino acid sequences of genes common to all M. ulcerans plasmids.

Alignment of virB from plasmids

Contains input and output of HyPhy analysis of alignment trimmed with GBlocks

Contains input and output of HyPhy analysis of alignment trimmed with Guidance

Contains input and output of HyPhy analysis of untrimmed alignment

.ffn files containing nucleotide sequences for chromosomes and plasmids (output of prokka)

All orthologous groups output by OrthoMCL

Orthologous groups corresponding to the core genome

Orthologous groups containing ESX genes

Orthologous groups in plasmids

Checks that all ESX genes identified on a plasmid are on the same component in the plasmidSPAdes assembly

Usage: checkPlasmidESX.py [-h] group plasmid

Concatenates fasta format sequences of eccCa1 and eccCb1

Usage: concatenateEccC1.py [-h] eccCa1 eccCb1

Creates fasta files of nucleotide and amino acid sequences for alignment of ESX genes. Requires input file formatted as follows:

species1_locus1 eccA_gene_name  eccB_gene_name  eccC_gene_name  eccD_gene_name  eccE_gene_name  mycP_gene_name
species2_locus1 eccA_gene_name  eccB_gene_name  eccC_gene_name  eccD_gene_name  eccE_gene_name  mycP_gene_name
species2_locus2 eccA_gene_name  eccB_gene_name  eccC_gene_name  eccD_gene_name  eccE_gene_name  mycP_gene_name

Usage: esxFASTAs_oneLocus.py [-h] esx nucleotide protein

Creates fasta files of nucleotide and amino acid sequences for alignmnent. Creates separate files for each ESX locus. Each ESX locus requires an input file as described for esxFASTAs_oneLocus.py.

Usage: esxFASTAs.py [-h] esx1 esx2 esx3 esx4 esx5 nucleotide protein

Performs treescape analysis on MrBayes output

Downloads genomes from NCBI and names them genus_species_strain.fasta

Usage: getNCBIGenome.py [-h] accession email

Creates Actinobacteria core phylogeny with ESX presence/absence matrix.

Creates ESX-4 tree with bootstrap values colored according to support.

Runs prokka v 1.11 and compresses the output directory

Usage: run_prokka.sh genus species strain genus_species_strain.fasta

Uses orthomcl output to separate genes on the same component as ESX locus from other components and outputs new fasta files

Usage: separateComponents.py [-h] group plasmid

Calculates the number of shared genes between all pairs of plasmids in OrthoMCL output.

Usage: sharedGeneContent.py [-h] group categories

Submit files and DAGs to run scripts on HTCondor

List of gene names of ESX genes in M. tuberculosis

Table containing strain/locus names and locus tags for paralogs/orthologs of eccA, eccB, eccC, eccD, eccE, and mycP

Same as above, but only plasmid-borne loci

Presence/absence matrix of ESX loci in genomes in the core genome phylogeny

Accession numbers of finished plasmids

Table to match short names by OrthoMCL to full names

OrthoMCL group names and the M. tb ESX genes they contain

ESX genes in M.tb with their Rv numbers and ESX locus

SRR/ERR accessions, genus, species, and strain information for assembled plasmids

Comparison of number of shared genes between ESX containing plasmids and whetheror not they are in the same group (e.g. ESX-1P, ESX-2P, etc.)

List of all genomes in analysis

Table with genomes and accessions used in analysis

Contains trees from MrBayes phylogenetic analysis of eccA, eccB, virB, tcpC, and espI in plasmids

Core genome phylogeny

ESX-4 phylogeny

ESX phylogeny from finished genomes trimmed with Guidance

ESX phylogeney from finished genomes trimmed with Gblocks

Phylogeny of M. ulcerans plasmids