Rapid evolution of gained essential developmental functions of a young gene via interactions with other essential genes

New genes originated relatively recently and are only present in a subset of species in a phylogeny. Accumulated evidence suggests that new genes, like old genes that are conserved across species, can also take on important functions and be essential for the survival and reproductive success of organisms. While there are detailed analyses of the mechanisms underlying gained fertility functions by new genes, how new genes rapidly became essential for viability remains unclear. We focused on a young retro-duplicated gene (CG7804, which we named Cocoon) in Drosophila that originated three million years ago. We found that, unlike its evolutionarily conserved and broadly expressed parental gene, Cocoon has evolved rapidly under positive selection since its birth and accumulates many amino acid divergences at functional sites from the parental gene. Despite its young age, Cocoon is essential for the survival of D. melanogaster at multiple developmental stages, including the critical embryonic stage, and its expression is essential in different tissues from its parental gene. Functional genomic analyses found that Cocoon gained multiple DNA binding targets, which regulates the expression of genes that have other essential functions and/or have multiple gene-gene interactions. Our observations suggest that Cocoon acquired essential function to survival through forming interactions that have large impacts on the gene interaction network. Our study is an important step towards deciphering the evolutionary trajectory by which new genes functionally diverge from the parental gene and become essential.