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.解析动物体色形成的机制与遗传基础，对于理解色素生成的代价与限制，以及表型变异的演化与维持机制至关重要。然而，除黑色素外，与结构色（structural colour）及多数广泛分布的色素类群相关的基因仍未得到充分解析，这在一定程度上源于研究的分类学聚焦范围较窄。本研究结合液相色谱-质谱联用技术（liquid chromatography-mass spectrometry）与RNA测序（RNA-seq）基因表达分析，对多态性蜥蜴澳洲岩蜥（*Ctenophorus decresii*）的皮肤体色相关色素与基因进行了表征。雄性澳洲岩蜥的喉部体色可由橙色、黄色、灰色或紫外蓝色组合而成。本研究证实，所有皮肤色型均含有两类生化特性不同的色素：蝶啶类色素（pteridines，自身合成）与类胡萝卜素（carotenoids，从饮食中获取）。橙色皮肤中的蝶啶类色素含量最高，而黄色皮肤的类胡萝卜素含量往往更高；其中作为维生素A前体的β-胡萝卜素（β-carotene）与β-隐黄质（β-cryptoxanthin），此前尚未在爬行动物中被证实存在。基因表达分析验证了上述结果：该分析共鉴定出489个在不同皮肤色型间差异表达的基因，其中包括与蝶啶合成、维生素A原类胡萝卜素代谢、虹彩细胞（iridophore）特异性合成、黑色素合成以及类固醇激素通路相关的基因。然而，在这489个基因中，绝大多数与脊椎动物体色形成的关联均为本研究首次揭示。本研究数据为解析脊椎动物体色变异的遗传基础提供了重要支撑，同时也为后续相关研究提供了宝贵的科研资源。