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

Authors
  • Parise, Doglas1
  • Parise, Mariana T D1
  • Viana, Marcus V C1
  • Muñoz-Bucio, Adrian V2
  • Cortés-Pérez, Yazmin A2
  • Arellano-Reynoso, Beatriz2
  • Díaz-Aparicio, Efrén2
  • Dorella, Fernanda A3
  • Pereira, Felipe L3
  • Carvalho, Alex F3
  • Figueiredo, Henrique C P3
  • Ghosh, Preetam4
  • Barh, Debmalya1, 5, 6
  • Gomide, Anne C P1
  • Azevedo, Vasco A C1
  • 1 Federal University of Minas Gerais, Laboratory of Cellular and Molecular Genetics, Institute of Biologic Sciences, Belo Horizonte, MG, Brazil , Belo Horizonte (Brazil)
  • 2 National Autonomous University of Mexico, Department of Microbiology and Immunology, Faculty of Veterinary Medicine and Zootechnics, Mexico City, Mexico , Mexico City (Mexico)
  • 3 Federal University of Minas Gerais, Aquacen - National Reference Laboratory for Aquatic Animal Diseases, Belo Horizonte, MG, Brazil , Belo Horizonte (Brazil)
  • 4 Virginia Commonwealth University, Department of Computer Science, Richmond, VA-23284, USA , Richmond (United States)
  • 5 Institute of Integrative Omics and Applied Biotechnology (IIOAB), Centre for Genomics and Applied Gene Technology, Nonakuri, Purba Medinipur, West Bengal, 721172, India , Purba Medinipur (India)
  • 6 NITTE University Center for Science Education and Research (NUCSER), NITTE (Deemed to be University), Division of Bioinformatics and Computational Genomics, Deralakatte, Mangaluru, Karnataka, India , Mangaluru (India)
Type
Published Article
Journal
Standards in Genomic Sciences
Publisher
Springer (Biomed Central Ltd.)
Publication Date
Oct 10, 2018
Volume
13
Issue
1
Identifiers
DOI: 10.1186/s40793-018-0325-z
Source
Springer Nature
Keywords
License
Green

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.

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