Genomic Resources for the Scuttle Fly : A Model Organism for Comparative Developmental Studies in Flies.

The order Diptera (true flies) holds promise as a model taxon in evolutionary developmental biology due to the inclusion of the model organism, , and the ability to cost-effectively rear many species in laboratories. One of them, the scuttle fly (Phoridae) has been used in evolutionary developmental biology for 30 years and is an excellent phylogenetic intermediate between fruit flies and mosquitoes but remains underdeveloped in genomic resources. Here, we present a chromosome-level assembly and annotation of and transcriptomes of 9 embryonic and 4 postembryonic stages. We also compare 9 stage-matched embryonic transcriptomes between and . Our analysis of these resources reveals extensive chromosomal synteny with , 28 orphan genes with embryo-specific expression including a novel F-box LRR gene in , and conserved and diverged features of gene expression dynamics between and . Collectively, our results provide a new reference for studying the diversification of developmental processes in flies.