Selection of a reference gene for studies on lipid‐related aquatic adaptations of toothed whales (Grampus griseus). Issue 23 (26th November 2021)

• Record Type: Journal Article
• Authors: Senevirathna, Jayan D. M.; Yonezawa, Ryo; Saka, Taiki; Igarashi, Yoji; Funasaka, Noriko; Yoshitake, Kazutoshi; Kinoshita, Shigeharu; Asakawa, Shuichi
• Is Part Of: Ecology and evolution. Volume 11:Issue 23(2021)
• Page Start: 17142
• Page End: 17159
• Publication Date: 2021-11-26
• Subjects: cetacean -- gene expression -- gene stability -- qPCR -- reference gene -- transcriptomics; Ecology -- Periodicals; Evolution -- Periodicals; 577.05
• DOI: 10.1002/ece3.8354
• Languages: English
• ISSNs: 2045-7758

Abstract

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. Abstract : The lipid metabolism of toothed whales is an interesting topic to study. RT‐qPCR‐based gene expression and stability study was conducted using various lipid tissues in Risso's dolphin and the LGALS1 gene was identified as the most stable reference gene for further transcriptomic studies.