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BMC genetics
09 17, 2020;21 (1): 107.

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

Wenbin Liu, Xiudan Yuan, Shuli Yuan, Liuye Dai, Shenghua Dong, Jinhui Liu, Liangyue Peng, Minmeng Wang, Yi Tang, Yamei Xiao
Author Information
  1. Wenbin Liu: State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, P.R. China.
  2. Xiudan Yuan: State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, P.R. China.
  3. Shuli Yuan: State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, P.R. China.
  4. Liuye Dai: State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, P.R. China.
  5. Shenghua Dong: State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, P.R. China.
  6. Jinhui Liu: State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, P.R. China.
  7. Liangyue Peng: State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, P.R. China.
  8. Minmeng Wang: State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, P.R. China.
  9. Yi Tang: State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, P.R. China.
  10. Yamei Xiao: State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, P.R. China. yameix@hunnu.edu.cn. ORCID
PMID: 32943013 DOI: 10.1186/s12863-020-00915-6

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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MeSH Term

Animals
Carps
Fish Proteins
Gene Expression Profiling
Goldfish
Polyploidy
Real-Time Polymerase Chain Reaction
Reference Standards
Ribosomal Proteins
Software
Transcriptome

Chemicals

Fish Proteins
Ribosomal Proteins
ribosomal protein S18
ribosomal protein S5
Journal Article Research Support, Non-U.S. Gov't

Word Cloud

Created with Highcharts 10.0.0genesreferenceexpressionfishgenetissuesdifferentpolyploidReferencecellsreportedthreeploidy12candidateribosomalproteinRPS5RPS18CyprinuscarpioCarassiusauratusBACKGROUND:usuallystablyexpressedvariousHowevermaydistinctspeciesstudyintendanswerwhethertraditionalchangesRESULTS:retrievingmRNAsequencingdataNCBISRAdatabaseselectedexaminedlevels10fourcelllinesreal-timePCRprofilessystematicallyevaluatedusingsoftwareplatforms:BestKeeperNormFindergeNormCONCLUSION:28SS5S18suitabledemonstratedculturedOptimalanalysisPolyploid

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