From Bioinformatics Core Wiki

Title Comparative transcriptomics of early dipteran development

Authors Eva Jiménez-Guri, Jaime Huerta-Cepas, Luca Cozzuto, Karl R. Wotton, Hui Kang, Heinz Himmelbauer, Guglielmo Roma, Toni Gabaldón, Johannes Jaeger
Date 2013-02-24

Publisher BMC genomics
DOI 10.1186/1471-2164-14-123
Tag Animals, Bayes Theorem, Comparative Genomic Hybridization, Diptera, Drosophila melanogaster, Embryonic Development, Gene Duplication, Genomics, Phylogeny, RNA, Sequence Analysis, RNA, Transcriptome


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).

Annotation The BioCore collaborated with the group of Dr. Yogi Jaeger (CRG) to publish the de novo transcriptomes of three non-drosophilid diptera, Clogmia albipunctata, Megaselia abdita, and Episyrphus balteatus.
Bioinformatics Core Facility @ CRG — 2011-2019