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The establishment of a (set of) stably expressed reference gene(s) is required to normalize transcription data. Polyploidy is very common in the plant kingdom, but it is not necessarily the case that a reference gene which works well at the diploid level will also work well at the polyploid level. Here, ten candidate reference genes are compared in the context of gene transcription in the genus  Chrysanthemum . The robustness of some, but not all, of these was shown to be high across ploidy levels.  MTP  (metalloprotease) and  ACTIN  (actin) were the most stable in diploid and tetraploid  C. nankingense , while  PSAA  (photosynthesis-related plastid gene representing photosystem I) and  EF-1α  (elongation factor-1 α ) were the most stable in tetraploid and hexaploid  C. zawadskii.   EF-1α  and  PGK  (phosphoglycerate kinase) was the best combination for the complete set of four taxa. These results suggest that when making cross-species comparison of transcript abundance involving different ploidy levels, care needs to be taken in the selection of reference gene(s).

Reference gene selection for cross-species and cross-ploidy level comparisons in Chrysanthemum spp.