Funding Information This work was supported by Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) and Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES).
Ion Torrent-based transcriptional assessment of a Corynebacterium pseudotuberculosis equi strain reveals denaturing high-performance liquid chromatography a promising rRNA depletion method
Article first published online: 15 JAN 2013
© 2013 The Authors. Microbial Biotechnology published by Blackwell Publishing Ltd and Society for Applied Microbiology
This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.
Special Issue: The Corynebacterium Cell Factory
Volume 6, Issue 2, pages 168–177, March 2013
How to Cite
Castro, T. L. P., Seyffert, N., Ramos, R. T. J., Barbosa, S., Carvalho, R. D. O., Pinto, A. C., Carneiro, A. R., Silva, W. M., Pacheco, L. G. C., Downson, C., Schneider, M. P. C., Miyoshi, A., Azevedo, V. and Silva, A. (2013), Ion Torrent-based transcriptional assessment of a Corynebacterium pseudotuberculosis equi strain reveals denaturing high-performance liquid chromatography a promising rRNA depletion method. Microbial Biotechnology, 6: 168–177. doi: 10.1111/1751-7915.12020
- Issue published online: 15 FEB 2013
- Article first published online: 15 JAN 2013
- Manuscript Accepted: 14 NOV 2012
- Manuscript Revised: 13 NOV 2012
- Manuscript Received: 1 OCT 2012
- Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) and Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)
Corynebacterium pseudotuberculosis equi is a Gram-positive pathogenic bacterium which affects a variety of hosts. Besides the great economic losses it causes to horse-breeders, this organism is also known to be an important infectious agent to cattle and buffaloes. As an outcome of the efforts in characterizing the molecular basis of its virulence, several complete genome sequences were made available in recent years, enabling the large-scale assessment of genes throughout distinct isolates. Meanwhile, the RNA-seq stood out as the technology of choice for comprehensive transcriptome studies, which may bring valuable information regarding active genomic regions, despite of the still impeditive associated costs. In an attempt to increase the use of generated reads per instrument run, by effectively eliminating unwanted rRNAs from total RNA samples without relying on any commercially available kits, we applied denaturing high-performance liquid chromatography (DHPLC) as an alternative method to assess the transcriptional profile of C. pseudotuberculosis. We have found that the DHPLC depletion method, allied to Ion Torrent sequencing, allows mapping of transcripts in a comprehensive way and identifying novel transcripts when a de novo approach is used. These data encourage us to use DHPLC in future transcriptional evaluations in C. pseudotuberculosis.