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Evodevo. 2019 Aug 8;10:16. doi: 10.1186/s13227-019-0129-2. eCollection 2019.

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

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1Institut de Systématique, Evolution et Biodiversité, UMR 7205 (CNRS, MNHN, Sorbonne Université, EPHE), Muséum National d'Histoire Naturelle CP50, 57 rue Cuvier, 75005 Paris, France.
2Laboratoire Ecologie, Evolution, Interactions Des Systèmes Amazoniens (LEEISA), USR 3456, CNRS Guyane, Université De Guyane, 275 route de Montabo, 97334 Cayenne, French Guiana.
Genomic Facility, Institut de Biologie de l'Ecole normale superieure (IBENS), École normale supérieure, CNRS, INSERM, PSL Université Paris, 75005 Paris, France.
4Centre d'Ecologie Fonctionnelle et Evolutive, UMR 5175 CNRS-Université de Montpellier, École Pratique des Hautes Études, Université Paul Valéry, 34293 Montpellier 5, France.
Contributed equally



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.


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.


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.


Gene expression; Heliconius butterflies; Lepidoptera; RNA sequencing; Supergene; Transcriptome; Wing pattern

Conflict of interest statement

Competing interestsThe authors declare that they have no competing interests.

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