pgen.1011864.t001 -

Comparing organ-specific gene regulatory networks (GRNs) across large evolutionary distances remains a major challenge, particularly when the species under study differ in data resolution. This applies to the GRN controlling compound eye development in insects, which is well characterized in Drosophila melanogaster but less well understood in other lineages. Here, we introduce the marmalade fly Episyrphus balteatus (Syrphidae), which diverged from Drosophila approximately 90 million years ago, as a comparative model to study eye development in Diptera. Using RNA-seq and ATAC-seq datasets, we reconstruct the first eye GRN in Episyrphus. Many genes involved in early Drosophila eye specification and differentiation are also active in Episyrphus. Among these, both species share a set of 22 transcription factors (TFs). The GRN built from these TFs and their DNA-binding motifs displays a high degree of internal connectivity. Link conservation analysis, followed by experimental testing in Drosophila, further identifies the AML1/Runx transcription factor lozenge (lz) as a negative regulator of the retinal determination gene dachshund (dac). Within the eye GRN, the degree of regulatory link conservation varies among genes, and both the number and position of regulatory regions often differ across orthologous loci. These results expand the eye GRN of Diptera and suggest extensive network rewiring over the evolutionary span separating Episyrphus and Drosophila.