Coral adapts to its surrounding environment by expressing stress-responsive genes. Thus, it is expected that these genes can serve as helpful biomarkers for investigating the coral reef environment. We evaluated appropriate reference genes for accurately analyzing gene expression using quantitative real-time PCR (qPCR). In this study, we examined each appropriate reference gene for Montipora digitata, Pocillopora damicornis and Acropora nasuta. We employed analytical methods, including 2^–ΔCt, geNorm, NormFinder and BestKeeper, and searched for appropriate reference genes for elongation factor 1 alpha (EF1A), beta-tubulin (TUBB), beta-actin (ACTB), 18S rRNA (18S) and TATA box binding protein (TBP). The most stable genes of M. digitata were EF1A, TUBB and TBP; the most stable genes of P. damicornis and A. nasuta were EF1A and TBP. Additionally, we verified that coral heat shock protein 70 family (HSP70) gene expression was accurately quantified under thermal stress conditions using our suggested reference genes. Collectively, we recommend evaluating reference genes for each coral species and each experimental condition.

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