Early embryonic transcriptome sequences of diptera (flies and midges)

Modern sequencing technologies have massively increased the amount of data available for comparative genomics. However, de novo assembly and automated annotation of genomes remains a challenge. Comparative transcriptomics offers a way around this problem, since transcriptomes are more straightforward to assemble and annotate, while still providing a powerful basis for comparative studies. This approach holds great promise for emerging model species in fields such as evolutionary developmental biology, but so far we lack examples that showcase its usefulness. We have sequenced early embryonic transcriptomes of two non-drosophilid dipteran species: the moth midge Clogmia albipunctata, and the scuttle fly Megaselia abdita. Our analysis includes a third, published, transcriptome for the hoverfly Episyrphus balteatus. These emerging models for comparative developmental studies close an important phylogenetic gap between Drosophila melanogaster and other insect model systems. We compare the performance of sequencing platforms (454/Illumina) and pipelines for de novo assembly (Newbler/Trinity). We assess the quality of automatic annotation by manual curation and in situ hybridization. Finally, we provide a comparative analysis of transcriptomes across species, and use our data for a phylogenomic reconstruction of dipteran phylogenetic relationships. We show how comparative transcriptomics can be used to create useful resources for evolutionary developmental biology, and to investigate phylogenetic relationships. Our results demonstrate that de novo assembly of short (Illumina) reads yields high-quality, high-coverage transcriptomic data sets. We use these data sets to investigate deep dipteran phylogenetic relationship, which remain difficult to resolve. Further comparative transcriptomic analyses will be required to tackle this problem.