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dc.contributor.authorJiménez-Guri, E
dc.contributor.authorHuerta-Cepas, J
dc.contributor.authorCozzuto, L
dc.contributor.authorWotton, KR
dc.contributor.authorKang, H
dc.contributor.authorHimmelbauer, H
dc.contributor.authorRoma, G
dc.contributor.authorGabaldón, T
dc.contributor.authorJaeger, J
dc.date.accessioned2017-02-15T10:06:11Z
dc.date.issued2013-02-24
dc.description.abstractBACKGROUND: 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).en_GB
dc.description.sponsorshipToni Hermoso Pulido from the CRG Bioinformatics Core provided help and support with the diptex database. We thank Debayan Datta, Maik Zehnsdorf, and Anna Menoyo (CRG Genomics Unit) for technical help. We gratefully acknowledge Urs Schmidt-Ott, for providing fly cultures, for sharing Episyrphus balteatus transcriptome data, for crucial advice on sequencing strategy, fly husbandry, and other experimental protocols, as well as for useful comments on the manuscript. Victor Jiménez-Guri drew the embryo pictures in Figure 1. This research was funded by the MEC/EMBL agreement for the EMBL/CRG Research Unit in Systems Biology, by AGAUR SGR grant 406, and by Grants BFU2009-10184 and BFU2009-09168 from the Spanish Ministry of Science and Innovation (MICINN). EJG is supported by ERASysBio+ Grant P#161 (MODHEART). LC was supported by grant PTA2011-6729-I from the Spanish Ministry of Science and Innovation (MICINN). JHC is supported by a Juan de la Cierva postdoctoral fellowship from the Spanish Ministry of Science and Innovation (JCI2010-07614). HK was supported by GABI-FUTURE grant BeetSeq (0315069A) by the German Federal Ministry of Education and Research.en_GB
dc.identifier.citationVol. 14, pp. 123 -en_GB
dc.identifier.doi10.1186/1471-2164-14-123
dc.identifier.other1471-2164-14-123
dc.identifier.urihttp://hdl.handle.net/10871/25866
dc.language.isoenen_GB
dc.publisherBioMed Centralen_GB
dc.relation.urlhttps://www.ncbi.nlm.nih.gov/pubmed/23432914en_GB
dc.rights© 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.en_GB
dc.subjectAnimalsen_GB
dc.subjectBayes Theoremen_GB
dc.subjectComparative Genomic Hybridizationen_GB
dc.subjectDipteraen_GB
dc.subjectDrosophila melanogasteren_GB
dc.subjectEmbryonic Developmenten_GB
dc.subjectGene Duplicationen_GB
dc.subjectGenomicsen_GB
dc.subjectPhylogenyen_GB
dc.subjectRNAen_GB
dc.subjectSequence Analysis, RNAen_GB
dc.subjectTranscriptomeen_GB
dc.titleComparative transcriptomics of early dipteran development.en_GB
dc.typeArticleen_GB
dc.date.available2017-02-15T10:06:11Z
exeter.place-of-publicationEnglanden_GB
dc.descriptionPublished onlineen_GB
dc.descriptionJournal Articleen_GB
dc.descriptionResearch Support, Non-U.S. Gov'ten_GB
dc.descriptionThis is the final version of the article. Available from BioMed Central via the DOI in this record.en_GB
dc.identifier.eissn1471-2164
dc.identifier.journalBMC Genomicsen_GB


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