Publication detail

Identification and validation of reference genes in Clostridium beijerinckii NRRL B-598 for RT-qPCR using RNA-Seq data

JUREČKOVÁ, K. RASCHMANOVÁ, H. KOLEK, J. VASYLKIVSKA, M. BRANSKÁ, B. PATÁKOVÁ, P. PROVAZNÍK, I. SEDLÁŘ, K.

Original Title

Identification and validation of reference genes in Clostridium beijerinckii NRRL B-598 for RT-qPCR using RNA-Seq data

Type

journal article in Web of Science

Language

English

Original Abstract

Gene expression analysis through reverse transcription-quantitative real-time polymerase chain reaction (RT-qPCR) depends on correct data normalization by reference genes with stable expression. Although Clostridium beijerinckii NRRL B-598 is a promising Gram-positive bacterium for the industrial production of biobutanol, validated reference genes have not yet been reported. In this study, we selected 160 genes with stable expression based on an RNA sequencing (RNA-Seq) data analysis, and among them, seven genes (zmp, rpoB1, rsmB, greA, rpoB2, topB2, and rimO) were selected for experimental validation by RT-qPCR and gene ontology enrichment analysis. According to statistical analyses, zmp and greA were the most stable and suitable reference genes for RT-qPCR normalization. Furthermore, our methodology can be useful for selection of the reference genes in other strains of Clostridium beijerinckii and it also suggests that the RNA-Seq data can be used for the initial selection of novel reference genes, however their validation is required.

Keywords

HKG; housekeeping genes; non-model organisms; biofuel; Clostridium

Authors

JUREČKOVÁ, K.; RASCHMANOVÁ, H.; KOLEK, J.; VASYLKIVSKA, M.; BRANSKÁ, B.; PATÁKOVÁ, P.; PROVAZNÍK, I.; SEDLÁŘ, K.

Released

4. 3. 2021

Publisher

Frontiers

ISBN

1664-302X

Periodical

Frontiers in Microbiology

Year of study

12

Number

1

State

Swiss Confederation

Pages from

1

Pages to

10

Pages count

10

URL

https://www.frontiersin.org/articles/10.3389/fmicb.2021.640054/full

Full text in the Digital Library

http://hdl.handle.net/11012/196506

BibTex

@article{BUT169963,
  author="Kateřina {Šabatová} and Hana {Raschmanová} and Jan {Kolek} and Maryna {Vasylkivska} and Barbora {Branská} and Petra {Patáková} and Valentine {Provazník} and Karel {Sedlář}",
  title="Identification and validation of reference genes in Clostridium beijerinckii NRRL B-598 for RT-qPCR using RNA-Seq data",
  journal="Frontiers in Microbiology",
  year="2021",
  volume="12",
  number="1",
  pages="1--10",
  doi="10.3389/fmicb.2021.640054",
  issn="1664-302X",
  url="https://www.frontiersin.org/articles/10.3389/fmicb.2021.640054/full"
}