Comparative transcriptomics of early dipteran development

BMC Genomics

Research Article

Jaime Huerta-Cepas¹  Toni Gabaldón²  Luca Cozzuto³  Guglielmo Roma⁴  Heinz Himmelbauer⁵  Hui Kang⁶  Eva Jiménez-Guri⁷  Karl R Wotton⁷  Johannes Jaeger⁸ 

[1] Bioinformatics and Genomics Programme, Centre de Regulació Genòmica (CRG), and Universitat Pompeu Fabra (UPF), Barcelona, Spain;Bioinformatics and Genomics Programme, Centre de Regulació Genòmica (CRG), and Universitat Pompeu Fabra (UPF), Barcelona, Spain;Centre de Regulació Genòmica (CRG), Dr. Aiguader 88, 08003, Barcelona, Spain;CRG Bioinformatics Core, Centre de Regulació Genòmica (CRG), and Universitat Pompeu Fabra (UPF), Barcelona, Spain;CRG Bioinformatics Core, Centre de Regulació Genòmica (CRG), and Universitat Pompeu Fabra (UPF), Barcelona, Spain;Developmental and Molecular Pathways, Novartis Institute for Biomedical Research, Basel, Switzerland;CRG Genomics Unit, Centre de Regulació Genòmica (CRG), and Universitat Pompeu Fabra (UPF), Barcelona, Spain;CRG Genomics Unit, Centre de Regulació Genòmica (CRG), and Universitat Pompeu Fabra (UPF), Barcelona, Spain;Max Planck Institute for Molecular Genetics, Berlin, Germany;ICFC Life Technologies, Bld #2, 218 Yindu Road, 200231, Shanghai, P. R. China;EMBL/CRG Research Unit in Systems Biology, Centre de Regulació Genòmica (CRG), and Universitat Pompeu Fabra (UPF), Barcelona, Spain;EMBL/CRG Research Unit in Systems Biology, Centre de Regulació Genòmica (CRG), and Universitat Pompeu Fabra (UPF), Barcelona, Spain;Centre de Regulació Genòmica (CRG), Dr. Aiguader 88, 08003, Barcelona, Spain;

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

DOI  :  10.1186/1471-2164-14-123

 received in 2012-08-14, accepted in 2013-02-19,  发布年份 2013

来源: Springer

【 摘 要 】

BackgroundModern 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).ResultsWe 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.ConclusionsWe 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).

【 授权许可】

Unknown   
© Jiménez-Guri et al.; licensee BioMed Central Ltd. 2013. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.