Genomic Resources for the Scuttle Fly Megaselia abdita: 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, <i>Drosophila melanogaster</i>, and the ability to cost-effectively rear many species in laboratories. One of them, the scuttle fly <i>Megaselia abdita</i> (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 <i>de novo</i> chromosome-level assembly and annotation of <i>M. abdita</i> and transcriptomes of 9 embryonic and 4 postembryonic stages. We also compare 9 stage-matched embryonic transcriptomes between <i>M. abdita</i> and <i>D. melanogaster</i>. Our analysis of these resources reveals extensive chromosomal synteny with <i>D. melanogaster</i>, 28 orphan genes with embryo-specific expression including a novel F-box LRR gene in <i>M. abdita</i>, and conserved and diverged features of gene expression dynamics between <i>M. abdita</i> and <i>D. melanogaster</i>. Collectively, our results provide a new reference for studying the diversification of developmental processes in flies.