Fig 1.
Phylogenetic tree of rpoB gene from Corynebacterium species.
The phylogeny was inferred using the Maximum Likelihood method and the Tamura-Nei (TN93 + G) model implemented in the Mega v10.1.6. The Corynebacterium ulcerans strains PO100/5, 04–13, W25 and 05–13 cluster with the Corynebacterium silvaticum KL0182T (yellow). C. ulcerans strains form lineage 1 (red, collapsed) and lineage 2 (orange).
Fig 2.
Phylogenetic tree of the tox gene from Corynebacterium species.
The phylogeny was inferred using the Maximum Likelihood method and the Tamura-Nei (T92 + G) model implemented in Mega v10.1.6. The strains PO100/5, 04–13, W25 and 05–13 cluster with Corynebacterium silvaticum. Clade colors represent rpoB clades of C. silvaticum (yellow) and C. ulcerans (red and orange).
Fig 3.
goeBURST diagram for the MLST data set of 38 Corynebacterium silvaticum and 76 C. ulcerans strains generated using PHILOViZ 2.0.
Blue–C. ulcerans lineage 1. Green—C. ulcerans lineage 2. Orange–C. silvaticum. The numbers on the links indicate the number of divergent alleles between STs.
Table 1.
Presence of 16 known niche and virulence factors of Corynebacterium in C. silvaticum.
Fig 4.
Circular map of Corynebacterium silvaticum genomes generated using BRIG v0.95.
From inner to outer circle: strain PO100/5 (reference); CG content; CG Skew; strains KL0182T, KL0183, KL0259, KL0260, KL0374, KL0382, KL0386, KL0394, KL0395, KL0396, KL0400, KL0401, KL0581, KL0598, KL0615, KL0707, KL0709, KL0773, KL0774, KL0882, KL0883, KL0884, KL0886, KL0887, KL0938, KL0957, KL0968, KL1003, KL1006, KL1007, KL1008, KL1009, KL1010, KL1196, 04–13, 05–13, W25; genomic islands compared to C. pseudotuberculosis ATCC19410T (blue) and C. ulcerans strain NCTC7910T (grey); and prophages (black). Genomic islands (GI) and prophage detection were performed using GIPSy and PHASTER, respectively.
Fig 5.
Alignment of tox+ prophages form Corynebacterium silvaticum PO100/5 and C. ulcerans 0102.
The red lines connect sequences with at least 75% identity. Light blue–Phage integrase; Orange–Phage-related transcriptional regulator; Pink–Phage-related coding sequence (CDS); Yellow–Diphtheria toxin CDS; Dark blue–other CDS; Green–tRNA.
Table 2.
Genomic islands in strain PO100/5 compared to Corynebacterium pseudotuberculosis ATCC19410T and C. ulcerans NCTC7910T.
Fig 6.
Pangenome, core genome and singletons development graphs and formulas for 38 genomes of Corynebacterium silvaticum and 76 C. ulcerans genomes.
Fig 7.
Clusters of orthologous groups (COGs) in the accessory and exclusive core genomes of Corynebacterium silvaticum and C. ulcerans annotated using eggNOG-mapper v2.
COG categories are sorted from most abundant to less abundant in C. silvaticum. In C. silvaticum, 356 out of 793 proteins from the accessory genome and 93 out of 174 proteins of the exclusive core genome had a COG category. In C. ulcerans, 1,065 out of 2,064 proteins from the accessory genome and six out of nine proteins of the exclusive core genome had a COG category.
Table 3.
Number of genes (orthogroups) in subsets across Corynebacterium silvaticum and C. ulcerans genomes.