Open Access Highly Accessed Research article

Comparative transcriptomics of early dipteran development

Eva Jiménez-Guri1, Jaime Huerta-Cepas2, Luca Cozzuto3, Karl R Wotton1, Hui Kang456, Heinz Himmelbauer4, Guglielmo Roma37, Toni Gabaldón28* and Johannes Jaeger18*

Author affiliations

1 EMBL/CRG Research Unit in Systems Biology, Centre de Regulació Genòmica (CRG), and Universitat Pompeu Fabra (UPF), Barcelona, Spain

2 Bioinformatics and Genomics Programme, Centre de Regulació Genòmica (CRG), and Universitat Pompeu Fabra (UPF), Barcelona, Spain

3 CRG Bioinformatics Core, Centre de Regulació Genòmica (CRG), and Universitat Pompeu Fabra (UPF), Barcelona, Spain

4 CRG Genomics Unit, Centre de Regulació Genòmica (CRG), and Universitat Pompeu Fabra (UPF), Barcelona, Spain

5 Max Planck Institute for Molecular Genetics, Berlin, Germany

6 Present address: ICFC Life Technologies, Bld #2, 218 Yindu Road, Shanghai, 200231, P. R. China

7 Present address: Developmental and Molecular Pathways, Novartis Institute for Biomedical Research, Basel, Switzerland

8 Centre de Regulació Genòmica (CRG), Dr. Aiguader 88, Barcelona, 08003, Spain

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Citation and License

BMC Genomics 2013, 14:123  doi:10.1186/1471-2164-14-123

Published: 24 February 2013



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).


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.


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).

Non-drosophilid diptera; Clogmia albipunctata; Megaselia abdita; Episyrphus balteatus; Comparative transcriptomics; RNA-seq; De novo assembly; Automated annotation; Evolutionary developmental biology; Phylogenomics