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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