Table 1.
Corynebacterium bovis isolates evaluated in this study.
Table 2.
Genomic features of 21 C. bovis isolates.
Fig 1.
A neighbor-joining phylogenetic tree of 16S rRNA gene sequences from species Type strains within the Corynebacterium genus.
Rhodococcus equi is the rooted outlier. Bootstraps (n = 1,000) are expressed as percentages at each node. The type strain for C. bovis has its branch highlighted in blue for emphasis. The scale bar represents substitutions per site of the 1,618 total sites including gaps.
Fig 2.
Genomes clustered according to pairwise average nucleotide identity (ANI) distances.
Each pairwise ANI result is represented in a greyscale square, with none occurring between 95–97%. Corynebacterium falsenii is shown as a neighboring outlier to the C. bovis genomes (n = 21). Six clusters are color-coded in the left dendrogram (black, green, blue, dark blue, red, and dark red). When the genomes are clustered into just four groups, the blue and dark blue clusters collapse into one group, and the red and dark red clusters merge as well. ANI percentages shown for three select groups represent arithmetic means and standard deviations of bi-directional pairs.
Fig 3.
Phylogenetic tree for 21 C. bovis genomes.
The tree was built of a core of 1,354 genes per genome, 28,434 in total. The core has 598,172 amino acid-residues/bp per genome, 12,519,612 in total. Tree re-rooted.
Fig 4.
Comparative genomic map of 21 C. bovis isolates using the CGView Comparison Tool (CCT).
All isolates were aligned using C. falsenii DSM 44353T’s complete genome as a reference. From the inner to the outer circle: C. bovis 7894, CUAMC1-Small, DSM 20582T, CUAMC1-Large, 16-1683-Large, 16-1683-Small, 17-0240-Large, MI 82–1021, WCM3-Small, WCM3-Large, WCM1, 4828, 4826, 17-0240-Small, 16–3465, 16–2004, 13–1426, WCM4, 12–5346, WCM5, F6900, C. falsenii DSM 44353T (black circle). These rings represent regions of sequence similarity detected by BLAST comparisons of DNA sequences using BLASTn searches and CDS feature translations using BLASTp conducted between the reference genome and the 21 C. bovis comparison genomes. Colored arrows represent COG functional categories. Blue arrows represent sequence features. Direction of the arrows represent either the forward or the reverse strand. CDS, coding sequences; tRNA, transfer RNA; rRNA, ribosomal RNA.
Fig 5.
Pan-genome development of C. bovis.
Pan-genome development using permutations of all 21 isolates of C. bovis (left); the pan-genome development of the C. bovis isolates obtained from humans and cows (upper right); and, the pan-genome development of the C. bovis isolates obtained from rodents (upper right). The red curve shows the fitted exponential Heap’s law function, blue and green curves indicate the upper and lower boundary of the 95% confidence interval.
Fig 6.
C. bovis’ core genome and singleton development.
The core genome development using permutations of all 21 isolates of C. bovis (upper left); the core genome development of the C. bovis isolates obtained from humans and cattle (upper-center); the core genome development of the C. bovis isolates obtained from rodents (mice and a rat) (upper-right); the singleton using permutations of all 21 isolates of C. bovis (lower left); the singleton development of the C. bovis isolates obtained from humans and cattle (lower-center); and, the singleton development of the C. bovis isolates obtained from rodents (mice and a rat) upper-right).
Fig 7.
Plot of the pan-genome vs. core-genome for each of the 21 C. bovis isolates.
The number of core genes is reflected in blue and the pan-genome in black for each of the isolates.
Fig 8.
Venn diagram depicting the number of core genes in segregated groups of C. bovis isolates.
All genomes, the number of genes composing the core genome of all 21 isolates; Humans/Cows, the number of genes of the core genome of the C. bovis isolates obtained from humans and cows, which were absent in one or more of the C. bovis isolates obtained from rodents; Rodents, the number of genes of the core genome of the C. bovis isolates obtained from mice and a rat, which were absent in one or more of the C. bovis isolates obtained from humans or cows.
Fig 9.
Number of genes classified in various COG categories for C. bovis isolates obtained from humans and cows vs. isolates obtained from rodents.
Table 3.
Number of genomic islands, putative virulence factors, and CRISPR-Cas systems in 21 C. bovis isolates.
Fig 10.
Virulence proteins in C. bovis based on the host from which it was isolated: Humans and cows (n = 10) and rodents (n = 11).
*p <0.001, unpaired t-test one-tailed. Error bars represent standard error of the mean.
Table 4.
Virulence factors found in 3 or more C. bovis isolates, their function, and associated microorganisms where these factors have been found.