Genomic resources for the scuttle fly <i>Megaselia abdita</i> : 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 Drosophila melanogaster and the ability to cost-effectively rear many species in laboratories. One of these dipteran species, the scuttle fly Megaselia abdita (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 de novo chromosome-level assembly and annotation of M. abdita and transcriptomes of nine embryonic and four post-embryonic stages. We also compare nine stage-matched embryonic transcriptomes between M. abdita and D. melanogaster. Our analysis of these resources reveals extensive chromosomal synteny with D. melanogaster; 24 orphan genes with embryo-specific expression, including a novel F-box LRR gene in M. abdita; and conserved and diverged features of gene expression dynamics between M. abdita and D. melanogaster. Collectively, our results provide a new resource for studying the diversification of developmental processes in flies.