Genome-Wide Identification and Evaluation of New Reference Genes for Gene Expression Analysis Under Temperature and Salinity Stresses in Ciona savignyi

Frontiers in Genetics
Xuena HuangAibin Zhan

Abstract

Rapid adaptation/accommodation to changing environments largely contributes to maximal survival of invaders during biological invasions, usually leading to success in crossing multiple barriers and finally in varied environments in recipient habitats. Gene expression is one of the most important and rapid ways during responses to environmental stresses. Selection of proper reference genes is the crucial prerequisite for gene expression analysis using the common approach, real-time quantitative PCR (RT-qPCR). Here we identified eight candidate novel reference genes from the RNA-Seq data in an invasive model ascidian Ciona savignyi under temperature and salinity stresses. Subsequently, the expression stability of these eight novel reference genes, as well as other six traditionally used reference genes, was evaluated using RT-qPCR and comprehensive tool RefFinder. Under the temperature stress, two traditional reference genes, ribosomal proteins S15 and L17 (RPS15, RPL17), and one novel gene Ras homolog A (RhoA), were recommended as the top three stable genes, which can be used to normalize target genes with a high and moderate expression level, respectively. Under the salinity stress, transmembrane 9 superfamily member (TMN), MOB...Continue Reading

References

Mar 14, 2001·Trends in Ecology & Evolution·C S. Kolar, D M. Lodge
Nov 10, 2001·Annual Review of Genomics and Human Genetics·E V Koonin
Apr 28, 2004·Trends in Genetics : TIG·Alexander E Vinogradov
Sep 20, 2007·PloS One·Hendrik J M de JongeArja ter Elst
Apr 10, 2009·Cellular and Molecular Life Sciences : CMLS·A CorduanF Desmots
Jan 5, 2011·Molecular Ecology·Brent L Lockwood, George N Somero
Nov 4, 2011·Nature Reviews. Genetics·Eulàlia de NadalFrancesc Posas
Aug 15, 2012·Trends in Ecology & Evolution·Daniel SimberloffMontserrat Vilà
Jul 3, 2013·Trends in Genetics : TIG·Eli Eisenberg, Erez Y Levanon
Nov 19, 2015·Plant, Cell & Environment·Sira Echevarría-ZomeñoM Mar Castellano
Nov 26, 2015·Molecular Immunology·Annegret BitzerMarcus Groettrup
Aug 26, 2016·Nature Protocols·Mihaela PerteaSteven L Salzberg
Aug 5, 2017·International Journal of Molecular Sciences·Stephen S C ChimTak-Yeung Leung

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Datasets Mentioned

BETA
SRP152910

Methods Mentioned

BETA
PCR
environmental stress
RNA-Seq
electrophoresis

Software Mentioned

geNorm
FastQC
BestKeeper
NormFinder
HISAT2
Delta Ct
Ensemble
RefFinder
Primer Premier
StringTie

Related Concepts