title: Screening for Suitable Reference Genes for Quantitative Real-Time PCR in Heterosigma akashiwo (Raphidophyceae).
abstract: The raphidophyte Heterosigma akashiwo is a globally distributed harmful alga that has been associated with fish kills in coastal waters. To understand the mechanisms of H. akashiwo bloom formation, gene expression analysis is often required. To accurately characterize the expression levels of a gene of interest, proper reference genes are essential. In this study, we assessed ten of the previously reported algal candidate genes (rpL17-2, rpL23, cox2, cal, tua, tub, ef1, 18S, gapdh, and mdh) for their suitability as reference genes in this species. We used qRT-PCR to quantify the expression levels of these genes in H. akashiwo grown under different temperatures, light intensities, nutrient concentrations, and time points over a diel cycle. The expression stability of these genes was evaluated using geNorm and NormFinder algorithms. Although none of these genes exhibited invariable expression levels, cal, tub, rpL17-2 and rpL23 expression levels were the most stable across the different conditions tested. For further validation, these selected genes were used to normalize the expression levels of ribulose-1, 5-bisphosphate carboxylase/oxygenase large unite (HrbcL) over a diel cycle. Results showed that the expression of HrbcL normalized against each of these reference genes was the highest at midday and lowest at midnight, similar to the diel patterns typically documented for this gene in algae. While the validated reference genes will be useful for future gene expression studies on H. akashiwo, we expect that the procedure used in this study may be helpful to future efforts to screen reference genes for other algae.
authors.affiliation: State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, Fujian 361005, China.
authors.forename: Nanjing
authors.initials: N
authors.lastname: Ji
authors.affiliation: State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, Fujian 361005, China.
authors.forename: Ling
authors.initials: L
authors.lastname: Li
authors.affiliation: State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, Fujian 361005, China.
authors.forename: Lingxiao
authors.initials: L
authors.lastname: Lin
authors.affiliation: State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, Fujian 361005, China; Department of Marine Sciences, University of Connecticut, Groton, Connecticut 06340, United States of America.
authors.forename: Senjie
authors.initials: S
authors.lastname: Lin
mesh_terms: D000465:Algorithms; D018076:DNA, Complementary / Q000235:genetics; D018744:DNA, Plant / Q000235:genetics; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant / Q000528:radiation effects; D017343:Genes, Plant; D056726:Genetic Association Studies; D057097:Harmful Algal Bloom; D008027:Light; D012333:RNA, Messenger / Q000235:genetics / Q000302:isolation & purification; D018749:RNA, Plant / Q000235:genetics / Q000302:isolation & purification; D060888:Real-Time Polymerase Chain Reaction / Q000379:methods*; D058009:Stramenopiles / Q000235:genetics* / Q000528:radiation effects; D013696:Temperature; D013997:Time Factors
chemical_list: D018076:DNA, Complementary; D018744:DNA, Plant; D012333:RNA, Messenger; D018749:RNA, Plant