title: Comparative transcriptomics of early dipteran development.
abstract: BACKGROUND
  Modern sequencing technologies have massively increased the amount of data available for comparative genomics. Whole-transcriptome shotgun sequencing (RNA-seq) provides a powerful basis for comparative studies. In particular, this approach holds great promise for emerging model species in fields such as evolutionary developmental biology (evo-devo).
  
  
  RESULTS
  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. In this paper, we provide a comparative analysis of early embryonic transcriptomes across species, and use our data for a phylogenomic re-evaluation of dipteran phylogenetic relationships.
  
  
  CONCLUSIONS
  We show how comparative transcriptomics can be used to create useful resources for evo-devo, 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 to investigate deep dipteran phylogenetic relationships. Our results, based on a concatenation of 160 orthologous genes, provide support for the traditional view of Clogmia being the sister group of Brachycera (Megaselia, Episyrphus, Drosophila), rather than that of Culicomorpha (which includes mosquitoes and blackflies).
authors: EMBL/CRG Research Unit in Systems Biology, Centre de Regulació Genòmica (CRG), and Universitat Pompeu Fabra (UPF), Barcelona, Spain.
authors: Eva
authors: E
authors: Jiménez-Guri
authors: Jaime
authors: J
authors: Huerta-Cepas
authors: Luca
authors: L
authors: Cozzuto
authors: Karl R
authors: KR
authors: Wotton
authors: Hui
authors: H
authors: Kang
authors: Heinz
authors: H
authors: Himmelbauer
authors: Guglielmo
authors: G
authors: Roma
authors: Toni
authors: T
authors: Gabaldón
authors: Johannes
authors: J
authors: Jaeger
mesh_terms: D000818:Animals; D001499:Bayes Theorem; D055028:Comparative Genomic Hybridization; D004175:Diptera / Q000145:classification / Q000235:genetics*; D004331:Drosophila melanogaster / Q000235:genetics; D047108:Embryonic Development / Q000235:genetics; D020440:Gene Duplication; D023281:Genomics; D010802:Phylogeny; D012313:RNA / Q000235:genetics / Q000378:metabolism; D017423:Sequence Analysis, RNA; D059467:Transcriptome
chemical_list: D012313:RNA