Data from: Revealing the biochemical and genetic basis of color variation in a polymorphic lizard

Determining the mechanistic and genetic basis of animal coloration is essential to understand the costs and constraints on colour production, and the evolution and maintenance of phenotypic variation. However, genes underlying structural colour and widespread pigment classes apart from melanin remain largely uncharacterised, in part due to restricted taxonomic focus. We combined liquid chromatography-mass spectrometry and RNA-seq gene expression analyses to characterise the pigments and genes associated with skin colour in the polymorphic lizard, Ctenophorus decresii. Throat coloration in male C. decresii may be a combination of orange, yellow, grey or ultra-violet blue. We confirmed the presence of two biochemically different pigment classes, pteridines (self-synthesised) and carotenoids (acquired through the diet), in all skin colours. Orange skin had the highest levels of pteridine pigments while yellow skin tended to have higher levels of carotenoids, of which the vitamin A precursors β-carotene and β-cryptoxanthin have not been previously confirmed in reptiles. These results were confirmed by gene expression analyses, which detected 489 genes differentially expressed between the skin colours, including genes associated with pteridine production, provitamin A carotenoid metabolism, iridophore-specific synthesis, melanin synthesis and steroid hormone pathways. For the majority of these 489 genes, however, our study reveals a new association with colour production in vertebrates. These data represent a significant contribution to understanding the genetic basis of colour variation in vertebrates and a rich resource for further studies.