Abstract:Quantitative real-time PCR (qRT-PCR) is a powerful and commonly used method for in-depth analysis of gene expression that offers increased sensitivity and specificity over other methods. However, in order to obtain accurate results when using qRT-PCR to study gene expression, one or several internal control genes for normalization are needed. Housekeeping genes are known as such a class of genes that their expression levels are expected to remain constant in the cells or tissues in response to any environmental or physiological stress. But, in fact, no any housekeeping gene always stably expressed under all physiological conditions as ideal reference genes. Glyceraldehyde-3-phosphate dehydrogenase (GAPDH), a classic key glycolysis enzyme presented in all tissues, is one of the most common housekeeping genes used in the analysis of comparing gene expression levels as reference genes. Nowadays, the role of as the reference gene was being questioned and challenged by accumulated experiment evidences. To investigate the stability of as a reference gene, the full-length cDNA sequence was cloned from the ridgetail white prawn, , which mRNA was measured in different tissues and at different post-molt times. The obtained full-length cDNA of was 1514bp, including 69 bp of 5'-untranslated region (UTR), 1002 bp of open reading frame (ORF), 443 bp of 3'-UTR containing a canonical polyadenylation signal sequence AATAAA prior to a poly A tail. The ORF of encoded 333 amino acids without signal peptide analyzed by SignalP software which is highly conserved across the phylogenetic scale. The molecular mass was calculated to be 35.71 kDa, and the pI was estimated to be 6.61. By alignment, the amino acid sequence of binding domain (amino acids 3-149) and the catalytic domain (amino acids 154-311). In order to compare the expression stability of three endogenous candidate genes (18S rRNA, ) in qRT-PCR analysis in different tissues and different post-molt times, eight tissues (eyestalk, gill, heart, hepatopancreas, ovary, stomach, instestines and abdominal muscle) and 4 different post-molt times (1, 5, 10 and 15 min) of E. carinicauda were collected for qRT-PCR. Comprehensive analysis of the results using delta Ct method and the software packages geNorm, NormFinder and BestKeeper revealed that 18S rRNA was the most stable reference gene in both different tissues and different post-molt times, then was the -actin in decreasing order. In conclusion, the best choice for single reference gene is 18S rRNA, and 18S rRNA and E. carinicauda.