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Ion torrent-based transcriptional assessment of a Corynebacterium pseudotuberculosis equi strain reveals denaturing high-performance liquid chromatography a promising rRNA depletion method
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Castro, Thiago L. P., Seyffert, Nubia, Ramos, Rommel T. J., Barbosa, Silvanira, Carvalho, Rodrigo D. O., Pinto, Anne Cybelle, Carneiro, Adriana Ribeiro, Silva, Wanderson Marques, Pacheco, Luis G. C., Downson, Christopher G., Schneider, Maria P. C., Miyoshi, Anderson, Azevedo, V. (Vasco) and Silva, Artur (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, Volume 6 (Number 2). pp. 168-177. doi:10.1111/1751-7915.12020 ISSN 1751-7907.
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WRAP_Dowson_mbt12020.pdf - Published Version Available under License Creative Commons Attribution. Download (730Kb) | Preview |
Official URL: http://dx.doi.org/10.1111/1751-7915.12020
Abstract
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.
| Item Type: | Journal Article | ||||
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| Subjects: | Q Science > QH Natural history > QH301 Biology Q Science > QH Natural history > QH426 Genetics Q Science > QR Microbiology |
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| Divisions: | Faculty of Science, Engineering and Medicine > Science > Life Sciences (2010- ) | ||||
| Library of Congress Subject Headings (LCSH): | Corynebacterium, Horses -- Diseases, RNA , Genomics , Microbial genomics | ||||
| Journal or Publication Title: | Microbial Biotechnology | ||||
| Publisher: | Wiley-Blackwell Publishing Ltd. | ||||
| ISSN: | 1751-7907 | ||||
| Official Date: | March 2013 | ||||
| Dates: |
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| Volume: | Volume 6 | ||||
| Number: | Number 2 | ||||
| Page Range: | pp. 168-177 | ||||
| DOI: | 10.1111/1751-7915.12020 | ||||
| Status: | Peer Reviewed | ||||
| Publication Status: | Published | ||||
| Access rights to Published version: | Open Access (Creative Commons) | ||||
| Date of first compliant deposit: | 25 December 2015 | ||||
| Date of first compliant Open Access: | 25 December 2015 | ||||
| Funder: | Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq), Brazil. Coordenação do Aperfeiçoamento de Pessoal de Nível Superior (CAPES) |
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