Identification of housekeeping genes suitable for gene expression analysis in the pearl mussel, Hyriopsis cumingii, during biomineralization

Mol Genet Genomics. 2014 Aug;289(4):717-25. doi: 10.1007/s00438-014-0837-1. Epub 2014 Mar 18.


Quantitative real-time polymerase chain reaction is a sensitive technique for quantifying gene expression levels. One or more appropriate reference genes must be selected to accurately compare mRNA transcript levels across different samples and tissues. The freshwater pearl, Hyriopsis cumingii (Lea), is an important economic species cultured in China. To date, no reference genes for gene expression analysis in this species have been validated. This study aimed to compare the relative expression of seven housekeeping genes across different tissue types and in the mantle or pearl sac during three biomineralization processes: seasonal shell growth, shell healing and pearl-sac formation in H. cumingii. Three programs evaluated the expression stabilities of the seven genes: BestKeeper, geNorm and NormFinder. The beta actin gene (ACTB), commonly used as a housekeeping gene in many studies, was the least stable. The expressions of Ubiquitin (Ubi) and Ribosomal protein L18 (Rpl18) and Elongation factor 1-alpha (EF1α) were more stable than the remaining four genes. Therefore, we suggest that Ubi, Rpl18 and EF1α are suitable reference genes. The three selected reference genes are expected to facilitate analysis of gene expressions during shell or pearl formation in H. cumingii.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Actins / genetics
  • Animal Shells / growth & development*
  • Animals
  • Calcification, Physiologic / genetics
  • Calcification, Physiologic / physiology*
  • DNA Primers / genetics
  • DNA, Complementary / chemistry
  • DNA, Complementary / genetics
  • Environment
  • Gene Expression Profiling
  • Gene Expression Regulation*
  • Genes, Essential / genetics
  • Peptide Elongation Factor 1 / genetics
  • RNA, Messenger / genetics
  • Real-Time Polymerase Chain Reaction
  • Ribosomal Proteins / genetics
  • Seasons
  • Ubiquitin / genetics
  • Unionidae / genetics*
  • Unionidae / physiology


  • Actins
  • DNA Primers
  • DNA, Complementary
  • Peptide Elongation Factor 1
  • RNA, Messenger
  • Ribosomal Proteins
  • Ubiquitin
  • ribosomal protein L18