PMC5282893_01
Transmission Electron Micrograph of three strains sequenced in this study. The electron micrographs of a MB11, b MB30 and c MB66, demonstrate the pleomorphic morphology of the species
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Fig1
C. pseudotuberculosis bv. equi is a facultative intracellular, beta-hemolytic, pleomorphic (Fig. 1), non-sporulating, unencapsulated, non-mobile, facultative anaerobic, Gram-positive pathogen..
Dendrogram of the representative genomes in the CMNR group. The analysis was performed using MEGA 5.10. Only bootstraps greater than 50% are shown in the branches of the dendrogram. The accession numbers for the sequences used in the analysis are: C. pseudotuberculosis MB11 (CP013260), C. pseudotuberculosis MB14 (CP013261), C. pseudotuberculosis MB30 (CP013262), C. pseudotuberculosis MB66 (CP013263), C. pseudotuberculosis 316 (CP003077), C. pseudotuberculosis 258 (CP003540), C. pseudotuberculosis 1002 (CP001809), C. pseudotuberculosis C231 (CP001829), C. diphtheriae NCTC 13129 (BX248353), C. glutamicum ATCC 13032 (BA000036), C. striatum ATCC 6940 (GCA_000159135), C. accolens ATCC 49725 (GCA_000159115), C. pseudogenitalium ATCC 33035 (NZ_ABYQ00000000), C. jeikeium K411 (NC_007164), N. brasiliensis ATCC 700358 (CP003876), N. farcinica IFM 10152 (NC_006361), M. bovis AF2122/97 (BX248333), M. ulcerans Agy99 (CP000325), M. smegmatis MC2 155 (CP000480), R. equi 103S (FN563149), R. fascians NBRC 12155 (GCA_001894785), R. erythropolis PR4 (NC_012490), R. jostii RHA1 (NC_008268)
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Fig2
The analysis was performed using the NCBI reference sequence for the species, retrieving from the database at least one representative from each genus in the Corynebacterium, Mycobacterium, Nocardia , and Rhodococcus group (Fig. 2). The dendrogram in Fig. 2 shows the phylogenetic proximity between the sequenced biovars of the species C. pseudotuberculosis.
Optical map of Corynebacterium pseudotuberculosis MB11. The figure shows the alignment of the KpnI sites observed in the optical map (bottom scale bar) with those predicted by the in silico assembly (top scale bar). Vertical lines connect identical restriction sites observed in the optical map and those predicted by the assembly, demonstrating that the genome was assembled in the correct order
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Fig3
An optical map using KpnI restriction sites was generated to evaluate the quality of the genome assembly for the MB11 strain (Fig. 3). Figure 3 shows that the in silico assembly for strain MB11 was very satisfactory; the positions of the restriction sites were corroborated by the optical map analysis. 
Circular map of the genome for the sequenced Corynebacterium pseudotuberculosis strains. The outermost ring in blue shows the features extracted from the MB11 genome using a .gbk file. The next ring shows the CDSs predicted on the forward strand of MB11 in red, followed by the CDSs on the reverse strand with their features in blue. The other three rings in red, green, and blue show proteins predicted by blastx for the MB14, MB30, and MB66 genomes, respectively, compared to the MB11 genome. The two innermost rings show the GC content and GC skew, followed by the size of the genome in base pairs
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Fig4
A circular map was generated using the CGView web tool that shows the relationship of the predicted proteins in the MB14, MB30, and MB66 genomes compared to strain MB11, in which the in silico assembly was corroborated by the optical map (Fig. 4).
Comparison of C. pseudotuberculosis genome structures using blastn. The names of the strains are indicated at the side of the gray bars showing the size of each genome. Red bars show conserved regions between two genomes using an e-value of 1-e05, while blue bars show inverted regions
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Fig5
Tool. The MB11 and MB14 strains showed extensive structural similarity, while MB30 had a large inversion of approximately 1.2 Mbp compared to MB14 (Fig. 5). However, MB66 had the largest number of structural rearrangements (Fig. 5).