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Background  Unravelling the genetic basis of polymorphic characters is central to our understanding of the origins and diversification of living organisms. Recently, supergenes have been implicated in a wide range of complex polymorphisms, from adaptive colouration in butterflies and fish to reproductive strategies in birds and plants. The concept of a supergene is now a hot topic in biology, and identification of its functional elements is needed to shed light on the evolution of highly divergent adaptive traits. Here, we apply different gene expression analyses to study the supergene  P  that controls polymorphism of mimetic wing colour patterns in the neotropical butterfly  Heliconius numata .    Results  We performed de novo transcriptome assembly and differential expression analyses using high-throughput Illumina RNA sequencing on developing wing discs of different  H. numata  morphs. Within the  P  interval, 30 and 17 of the 191 transcripts were expressed differentially in prepupae and day-1 pupae, respectively. Among these is the gene  cortex , known to play a role in wing pattern formation in  Heliconius  and other Lepidoptera. Our in situ hybridization experiments confirmed the relationship between  cortex  expression and adult wing patterns.    Conclusions  This study found the majority of genes in the  P  interval to be expressed in the developing wing discs during the critical stages of colour pattern formation, and detect drastic changes in expression patterns in multiple genes associated with structural variants. The patterns of expression of  cortex  only partially recapitulate the variation in adult phenotype, suggesting that the remaining phenotypic variation could be controlled by other genes within the  P  interval. Although functional studies on  cortex  are now needed to determine its exact developmental role, our results are in accordance with the classical supergene hypothesis, whereby several genes inherited together due to tight linkage control a major developmental switch.    Electronic supplementary material  The online version of this article (10.1186/s13227-019-0129-2) contains supplementary material, which is available to authorized users.

Unravelling the genes forming the wing pattern supergene in the polymorphic butterfly Heliconius numata