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Case Reports
. 2018 Oct 10:13:21.
doi: 10.1186/s40793-018-0325-z. eCollection 2018.

First genome sequencing and comparative analyses of Corynebacterium pseudotuberculosis strains from Mexico

Doglas Parise #  1 , Mariana T D Parise #  1 , Marcus V C Viana  1 , Adrian V Muñoz-Bucio  2 , Yazmin A Cortés-Pérez  2 , Beatriz Arellano-Reynoso  2 , Efrén Díaz-Aparicio  2 , Fernanda A Dorella  3 , Felipe L Pereira  3 , Alex F Carvalho  3 , Henrique C P Figueiredo  3 , Preetam Ghosh  4 , Debmalya Barh  1   5   6 , Anne C P Gomide  1 , Vasco A C Azevedo  1
Affiliations
Case Reports

First genome sequencing and comparative analyses of Corynebacterium pseudotuberculosis strains from Mexico

Doglas Parise et al. Stand Genomic Sci. .

Abstract

Corynebacterium pseudotuberculosis is a pathogenic bacterium which has been rapidly spreading all over the world, causing economic losses in the agricultural sector and sporadically infecting humans. Six C. pseudotuberculosis strains were isolated from goats, sheep, and horses with distinct abscess locations. For the first time, Mexican genomes of this bacterium were sequenced and studied in silico. All strains were sequenced using Ion Personal Genome Machine sequencer, assembled using Newbler and SPAdes software. The automatic genome annotation was done using the software RAST and in-house scripts for transference, followed by manual curation using Artemis software and BLAST against NCBI and UniProt databases. The six genomes are publicly available in NCBI database. The analysis of nucleotide sequence similarity and the generated phylogenetic tree led to the observation that the Mexican strains are more similar between strains from the same host, but the genetic structure is probably more influenced by transportation of animals between farms than host preference. Also, a putative drug target was predicted and in silico analysis of 46 strains showed two gene clusters capable of differentiating the biovars equi and ovis: Restriction Modification system and CRISPR-Cas cluster.

Keywords: CRISPR-Cas; Drug target; Genomic sequencing; Phylogenetics; Restriction-modification systems.

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Conflict of interest statement

The authors declare that they have no competing interests.Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Figures

Fig. 1
Fig. 1
Phylogenetic tree of new Corynebacterium pseudotuberculosis strains of this work inside the rectangles, with other strains of the group CMNR. The blue rectangles highlight the biovar ovis strains and the red rectangle highlights the biovar equi strains of this work. The numbers near the nodes indicate bootstrap values
Fig. 2
Fig. 2
Circular map of C. pseudotuberculosis strain MEX1 (biovar ovis) in comparison with the other strains of this study. The cluster of methylation type III, which is only present in biovar ovis strains, is highlighted in blue
Fig. 3
Fig. 3
Circular map of C. pseudotuberculosis strain MEX30 (biovar equi) in comparison with the other strains of this study. The cluster of CRISPR-Cas, which is only present in biovar equi strains, is highlighted in blue. The nitrate reductase gene cluster is highlighted by a black rectangle
Fig. 4
Fig. 4
Alignment generated using Gegenees software showing the percentage similarity among the strains, based on the accessory genome. The blue rectangle highlights the grouping of the biovar ovis. The red rectangle highlights the grouping of the biovar equi
See this image and copyright information in PMC

References

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