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. 2020 Sep 17;21(1):107.
doi: 10.1186/s12863-020-00915-6.

Optimal reference genes for gene expression analysis in polyploid of Cyprinus carpio and Carassius auratus

Wenbin Liu  1   2 , Xiudan Yuan  1   2 , Shuli Yuan  1   2 , Liuye Dai  1   2 , Shenghua Dong  1   2 , Jinhui Liu  1   2 , Liangyue Peng  1   2 , Minmeng Wang  1   2 , Yi Tang  1   2 , Yamei Xiao  3   4
Affiliations

Optimal reference genes for gene expression analysis in polyploid of Cyprinus carpio and Carassius auratus

Wenbin Liu et al. BMC Genet. .

Abstract

Background: Reference genes are usually stably expressed in various cells and tissues. However, it was reported that the expression of some reference genes may be distinct in different species. In this study, we intend to answer whether the expression of reported traditional reference genes changes or not in the polyploid fish RESULTS: By retrieving the mRNA sequencing data of three different ploidy fish from the NCBI SRA database, we selected 12 candidate reference genes, and examined their expression levels in the 10 tissues and in the four cell lines of three different ploidy fish by real-time PCR. Then, the expression profiles of these 12 candidate reference genes were systematically evaluated by using the software platforms: BestKeeper, NormFinder and geNorm.

Conclusion: The 28S ribosomal protein S5 gene (RPS5) and the ribosomal protein S18 gene (RPS18) are the most suitable reference genes for the polyploid of Cyprinus carpio and Carassius auratus, demonstrated by both of the tissues and the cultured cells.

Keywords: Polyploid fish; RPS18; RPS5; Reference gene.

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Conflict of interest statement

The authors declare that they have no competing interests.

Figures

Fig. 1
Fig. 1
The qPCR cycle threshold (Ct) values of candidate reference genes in tissues (Left) and cultured cells (Right) of different ploidy fish. The red area represented the range of Ct value variation
Fig. 2
Fig. 2
The expression stability of candidate reference genes in the tissues (Left) and cultured cells (Right) of different ploidy fish assessed by the NormFinder software
Fig. 3
Fig. 3
The stability of candidate reference genes in tissues (Left) and cultured cells (Right) of different ploidy fish determined by GeNorm analysis
Fig. 4
Fig. 4
Optimal number of reference genes for normalization of gene expression in tissues (Left) and cultured cells (Right). The geNorm was used to calculate the pairwise variation (Vn/Vn + 1, the “n” represents the number of reference genes)
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