Selection of a reference gene for studies on lipid‐related aquatic adaptations of toothed whales (Grampus griseus)

Ecology and Evolution

Noriko Funasaka¹  Yoji Igarashi²  Jayan D. M. Senevirathna³  Kazutoshi Yoshitake³  Ryo Yonezawa³  Shuichi Asakawa³  Taiki Saka³  Shigeharu Kinoshita³ 

[1] Department of Life Sciences Graduate School of Bioresources Mie University Mie Japan;Department of Life Sciences and Chemistry Graduate School of Bioresources Mie University Mie Japan;Laboratory of Aquatic Molecular Biology and Biotechnology Department of Aquatic Bioscience Graduate School of Agricultural and Life Sciences The University of Tokyo Tokyo Japan;

关键词: cetacean;    gene expression;    gene stability;    qPCR;    reference gene;    transcriptomics;   

DOI  :  10.1002/ece3.8354

来源: DOAJ

【 摘 要 】

Abstract Toothed whales are one group of marine mammals that has developed special adaptations, such as echolocation for predation, to successfully live in a dynamic aquatic environment. Their fat metabolism may differ from that of other mammals because toothed whales have acoustic fats. Gene expression in the metabolic pathways of animals can change with respect to their evolution and environment. A real‐time quantitative polymerase chain reaction (RT‐qPCR) is a reliable technique for studying the relative expressions of genes. However, since the accuracy of RT‐qPCR data is totally dependent on the reference gene, the selection of the reference gene is an essential step. In this study, 10 candidate reference genes (ZC3H10, FTL, LGALS1, RPL27, GAPDH, FTH1, DCN, TCTP, NDUS5, and UBIM) were initially tested for amplification efficiency using RT‐qPCR. After excluding DCN, the remaining nine genes, which are nearly 100% efficient, were selected for the gene stability analysis. Stable reference genes across eight different fat tissue, liver, and muscle samples from Grampus griseus were identified by four algorithms, which were provided in Genorm, NormFinder, BestKeeper, and Delta CT. Finally, a RefFinder comprehensive ranking was performed based on the stability values, and the nine genes were ranked as follows: LGALS1 > FTL > GAPDH > ZC3H10 > FTH1 > NDUS5 > TCTP > RPL27 > UBIM. The LGALS1 and FTL genes were identified as the most stable novel reference genes. The third‐ranked gene, GAPDH, is a well‐known housekeeping gene for mammals. Ultimately, we suggest the use of LGALS1 as a reliable novel reference gene for genomics studies on the lipid‐related aquatic adaptations of toothed whales.

【 授权许可】

Unknown