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Open Access Open Badges Research article

The use of reference gene selection programs to study the silvering transformation in a freshwater eel Anguilla australis: a cautionary tale

Alvin N Setiawan* and P Mark Lokman

Author Affiliations

Department of Zoology, University of Otago, 340 Great King Street, P. O. Box 56, Dunedin 9054, New Zealand

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BMC Molecular Biology 2010, 11:75  doi:10.1186/1471-2199-11-75

Published: 22 September 2010



Quantitative real-time PCR (qPCR) has been the method of choice for the quantification of mRNA. Due to the various artifactual factors that may affect the accuracy of qPCR, internal reference genes are most often used to normalize qPCR data. Recently, many studies have employed computer programs such as GeNorm, BestKeeper and NormFinder in selecting reference genes, but very few statistically validate the outcomes of these programs. Thus, in this study, we selected reference genes for qPCR of liver and ovary samples of yellow (juvenile), migratory (silver) and 11-KT treated juveniles of New Zealand shortfinned eels (Anguilla australis) using the three computer programs and validate the selected genes statistically using REST 2009 software and the Mann-Whitney test. We also tested for the repeatability of use for the best reference genes by applying them to a data set obtained in a similar experiment conducted the previous year.


Out of six candidate genes, the combination of 18 s and eef1 was found to be the best statistically validated reference for liver, while in ovary it was l36. However, discrepancies in gene rankings were found between the different programs. Also, statistical validation procedures showed that several genes put forward as being the best by the programs were in fact, regulated, making them unsuitable as reference genes. Additionally, eef1 which was found to be a suitable - though not the top ranked - reference gene for liver tissues in one year, was regulated in another.


Our study highlights the need for external validations of reference gene selections made by computer programs. Researchers need to be vigilant in validating and reporting the rationale for the use of reference gene in published studies.