title: Ion Torrent-based transcriptional assessment of a Corynebacterium pseudotuberculosis equi strain reveals denaturing high-performance liquid chromatography a promising rRNA depletion method.
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.
authors: Institute of Biological Sciences, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil.
authors: Thiago L P
authors: TL
authors: Castro
authors: Nubia
authors: N
authors: Seyffert
authors: Rommel T J
authors: RT
authors: Ramos
authors: Silvanira
authors: S
authors: Barbosa
authors: Rodrigo D O
authors: RD
authors: Carvalho
authors: Anne Cybelle
authors: AC
authors: Pinto
authors: Adriana Ribeiro
authors: AR
authors: Carneiro
authors: Wanderson Marques
authors: WM
authors: Silva
authors: Luis G C
authors: LG
authors: Pacheco
authors: Christopher
authors: C
authors: Downson
authors: Maria P C
authors: MP
authors: Schneider
authors: Anderson
authors: A
authors: Miyoshi
authors: Vasco
authors: V
authors: Azevedo
authors: Artur
authors: A
authors: Silva
mesh_terms: D000818:Animals; D001426:Bacterial Proteins / Q000235:genetics / Q000378:metabolism; D002851:Chromatography, High Pressure Liquid / Q000379:methods*; D003354:Corynebacterium Infections / Q000382:microbiology / Q000662:veterinary; D016925:Corynebacterium pseudotuberculosis / Q000145:classification / Q000235:genetics / Q000378:metabolism*; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006734:Horse Diseases / Q000382:microbiology; D006736:Horses / Q000382:microbiology; D009691:Nucleic Acid Denaturation / Q000235:genetics*; D012329:RNA, Bacterial / Q000235:genetics / Q000378:metabolism; D012335:RNA, Ribosomal / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D013045:Species Specificity; D059467:Transcriptome
chemical_list: D001426:Bacterial Proteins; D012329:RNA, Bacterial; D012335:RNA, Ribosomal