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Background   Pyropia yezoensis , a marine red alga, is an ideal research model for studying the mechanisms of abiotic stress tolerance in intertidal seaweed. Real-time quantitative polymerase chain reaction (RT-qPCR) is the most commonly used method to analyze gene expression levels. To accurately quantify gene expression, selection and validation of stable reference genes is required.    Results  We used transcriptome profiling data from different abiotic stress treatments to identify six genes with relatively stable expression levels:  MAP, ATPase, CGS1, PPK, DPE2,  and  FHP . These six genes and three conventional reference genes,  UBC ,  EF1-α , and  eif4A , were chosen as candidates for optimal reference gene selection. Five common statistical approaches (geNorm, ΔCt method, NormFinder, BestKeeper, and ReFinder) were used to identify the stability of each reference gene. Our results show that:  MAP ,  UBC , and  FHP  are stably expressed in all analyzed conditions;  CGS1  and  UBC  are stably expressed under conditions of dehydration stress; and  MAP ,  UBC , and  CGS1  are stably expressed under conditions of temperature stress.    Conclusion  We have identified appropriate reference genes for RT-qPCR in  P. yezoensis  under different abiotic stress conditions which will facilitate studies of gene expression under these conditions.    Electronic supplementary material  The online version of this article (10.1186/s12864-018-4643-8) contains supplementary material, which is available to authorized users.

Transcriptome-wide identification of optimal reference genes for expression analysis of Pyropia yezoensis responses to abiotic stress