DOI: 10.5281/zenodo.10035485
title: Supplementary data for Competition and Virulence in Pseudomonas syringae

description: Supplementary data 2.1.1
CSV file describing 2,161 PSSC genomes used in the evaluation of PCR primers in chapter 2.1 and used as reference genomes for classification of isolates at syringae.org in chapter 2.2. file contains RefSeq accession numbers for each genome, T3E family repertoires, and phylogroup and ANI clusters assigned to each genome (metadata.csv) 
 
Supplementary data 2.1.2
Table describing columns contained in Supplementary data 2.1.1
 
Supplementary data 2.2
Excel file with in-silico amplification rates for all 16 primer sets evaluated in chapter 2.1, both overall and by phylogroup.
 
Supplementary data 2.3
Newick tree file containing the phylogenetic tree of 2,161 PSSC genomes used throughout chapters 2 and 3, with bootstrap values.
 
Supplementary data 2.4
HMM file containing hidden Markov models for all VFOCs identified in chapter 2.1 and 2.2.
 
Supplementary data 2.5.1
JSON file describing all canonical T3SS, T3E, and WHOP genes in the 2,161 genomes used in chapter 2.1 and 2.2, as detected by HMMER, with genome accessions as top-level keys. Additional keys found in each file are described in Table 2.2.3.
 
Supplementary data 2.5.2
Table containing description of JSON structure for Supplementary data 2.5.1
 
Supplementary data 2.6.1
JSON file describing all canonical T3SS, T3E, and WHOP genes in the 2,161 genomes used in chapter 2.1 and 2.2, as detected by HMMER, with protein accessions as top-level keys. Additional keys found in each file are described in Table 2.2.3.
 
Supplementary data 2.6.2
Table containing description of JSON structure for Supplementary data 2.6.1
 
Supplementary data 2.7
TSV file containing LIN numbers associated with each reference genome, used as input for training classifiers. 
 
Supplementary data 2.8
FASTA file containing in-silico amplicons generated from primer set CTS_Hwang, used as input for training a Naïve Bayes classifier.
 
Supplementary data 2.9
FASTA file containing in-silico amplicons generated from primer set gapA_Hwang, used as input for training a Naïve Bayes classifier. 
 
Supplementary data 2.10
FASTA file containing in-silico amplicons generated from primer set gyrB_Hwang, used as input for training a Naïve Bayes classifier. 
 
Supplementary data 2.11
FASTA file containing in-silico amplicons generated from primer set pgi_Yan, used as input for training a Naïve Bayes classifier. 
 
Supplementary data 2.12
FASTA file containing in-silico amplicons generated from primer set rpoD_Hwang, used as input for training a Naïve Bayes classifier. 
 
Supplementary data 2.13
Naïve Bayes classifier for primer set CTS_Hwang
 
Supplementary data 2.14
Naïve Bayes classifier for primer set gapA_Hwang
 
Supplementary data 2.15
Naïve Bayes classifier for primer set gyrB_Hwang
 
Supplementary data 2.16
Naïve Bayes classifier for primer set pgi_Yan
 
Supplementary data 2.17
Naïve Bayes classifier for primer set rpoD_Hwang
 
Supplementary data 3.1
HMM1, representing tailocin tail fibers associated with killing class 1
 
Supplementary data 3.2
HMM2, representing tailocin tail fibers associated with killing class 2
 
Supplementary data 3.3
HMM3, representing tailocin tail fibers from PSSC strain UB246
 
Supplementary data 3.4
Amino acid sequence for WP_044313553.1, representative of type 1a tailocin-associated tail fiber used for protein structure prediction in Supplementary data 3.5
 
Supplementary data 3.5
PDB file containing predicted structure of WP_044313553.1, representative of type 1a tailocin-associated tail fiber 
 
Supplementary data 3.6
Amino acid sequence for WP_122688044.1, representative of type 1b tailocin-associated tail fiber used for protein structure prediction in Supplementary data 3.7
 
Supplementary data 3.7
PDB file containing predicted structure of WP_122688044.1, representative of type 1b tailocin-associated tail fiber
 
Supplementary data 3.8
Amino acid sequence for WP_005768002.1, representative of type 2 tailocin-associated tail fiber used for protein structure prediction in Supplementary data 3.9
 
Supplementary data 3.9
PDB file containing predicted structure of WP_005768002.1, representative of type 2 tailocin-associated tail fiber
 
Supplementary data 3.10
Amino acid sequence for WP_024674765.1, representative of type 3 tailocin-associated tail fiber used for protein structure prediction in Supplementary data 311
 
Supplementary data 3.11
PDB file containing predicted structure of WP_024674765.1, representative of type 3 tailocin-associated tail fiber
 
Supplementary data 3.12
Amino acid sequence for WP_198721597.1, representative of RSA1-like prophage-associated tail fiber used for protein structure prediction in Supplementary data 3.13
 
Supplementary data 3.13
PDB file containing predicted structure of WP_198721597.1, representative of RSA1-like prophage-associated tail fiber
 
Supplementary data 3.14
CSV file containing HMM1 and HMM2 genomic screen results, with accession numbers and identities of tail fibers detected in each genome.
 
Supplementary data 3.15
CSV file containing HMM3 genomic screen results, with copy number of tail fibers detected in each genome and the phylogroup the genome belongs to