Functional genomic basis of the Papilio alphenor doublesex supergene

The development of complex phenotypes requires the coordinated action of many genes across space and time, yet many species have evolved the ability to develop multiple discrete, alternate phenotypes. Such polymorphisms are often controlled by supergenes, sets of tightly-linked mutations in one or more genes that function together to produce a complex phenotype4. Although theories of supergene evolution are well-established, the mutations that cause functional differences between supergene alleles remain essentially unknown. doublesex is the master regulator of insect sexual differentiation but functions as a supergene in multiple Papilio swallowtail butterflies, where divergent dsx alleles control development of discrete non-mimetic or mimetic female wing color patterns. This project comprises ATAC-seq and CUT&RUN sequencing data for Papilio alphenor that enable identification of cis-regulatory elements (CREs), DSX binding locations, and H3K4me3 locations genome-wide.