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Evaluation of potential reference genes for use in gene expression studies in the conifer pathogen (Heterobasidion annosum)

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Abstract

The basidiomycete Heterobasidion annosum is the causative agent of butt and root rot disease of conifer trees and it’s one of the most destructive conifer pathogen in the northern hemisphere. Because of the intrinsic difficulties in genome manipulation in this fungus, most studies have been focused on gene expression analysis using quantitative real time polymerase chain reaction (qPCR). qPCR is a powerful technique but its reliability resides in the correct selection of a set of reference genes used in the data normalization. In this study, we determined the expression stability of 11 selected reference genes in H. annosum. Almost nothing has so far been published about validation of a set of reference genes to be used in gene expression experiments in this fungus. Eleven reference genes were validated in H. annosum which was grown on three different substrates: pine bark, pine heartwood, and pine sapwood. Bestkeeper and NormFinder Excel-based software were used to evaluate the reference gene transcripts’ stability. The results from these two programs indicated that three reference genes namely Tryp metab, RNA Pol3 TF, and Actin were stable in H. annosum in the conditions studied. Interestingly, the GAPDH transcript which has been extensively used in qPCR data normalization is not the best choice when a wide reference gene selection is available. This work represents the first extensive validation of reference genes in H. annosum providing support for gene expression studies and benefits for the wider forest pathology community.

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Acknowledgments

We thank Dr Sébastien Duplessis, Dr Kirk Overmyer and Luis Orlando Morales for their help and critical discussion. Academy of Finland and Viikki Doctoral Programme in Molecular Biosciences are gratefully acknowledged for research funding.

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Authors and Affiliations

  1. Department of Forest Sciences, University of Helsinki, Helsinki, Finland

    Tommaso Raffaello & Fred O. Asiegbu

  2. Viikki Doctoral Programme in Molecular Biosciences (VGSB), Helsinki, Finland

    Tommaso Raffaello & Fred O. Asiegbu

Authors
  1. Tommaso Raffaello
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  2. Fred O. Asiegbu
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Correspondence to Tommaso Raffaello.

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Raffaello, T., Asiegbu, F.O. Evaluation of potential reference genes for use in gene expression studies in the conifer pathogen (Heterobasidion annosum). Mol Biol Rep 40, 4605–4611 (2013). https://doi.org/10.1007/s11033-013-2553-z

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  • DOI: https://doi.org/10.1007/s11033-013-2553-z

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