Evolutionary rewiring of the endomesoderm gene regulatory networks specify skeleton secreting cells in stony corals.
Stony corals are the eponymous keystone organisms for the most diverse marine ecosystems on earth: coral reefs. Despite their importance, little is known about the developmental genetic programs that drive their embryonic development and subsequent emergence of coral-specific traits. Like all developmental processes, coral development is governed by a series of genetic interactions collectively termed a gene regulatory network. Evolutionary changes in these gene regulatory networks are key sources of biological innovation, but how these networks operate in corals and how they have changed over time remains poorly understood. Here, we integrate chromatin profiling and transcriptomics to define the cis-regulatory architecture of early development in stony corals using the emerging model, Astrangia poculata. We find that key elements of the deeply conserved cnidarian endomesoderm gene regulatory network have been co-opted into a novel subnetwork that specifies secretory cells in corals. Using transgenic reporter assays, we found that a proximal cis-regulatory element of the endomesodermal gene Brachyury is sufficient to drive coral-specific expression patterns in the sea anemone Nematostella vectensis, demonstrating these elements as a key evolvable unit in stony corals. Collectively these findings establish a gene-regulatory framework for coral development and cell specification and suggest that evolutionary rewiring of ancestral developmental programs is a key driver in the evolution and diversification of stony corals.