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Comparative transcriptomics of early dipteran development

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dc.contributor.author Jiménez Guri, Eva
dc.contributor.author Huerta Cepas, Jaime
dc.contributor.author Cozzuto, Luca
dc.contributor.author Wotton, Karl R.
dc.contributor.author Kang, Hui
dc.contributor.author Himmelbauer, Heinz
dc.contributor.author Roma, Guglielmo
dc.contributor.author Gabaldón Estevan, Juan Antonio, 1973-
dc.contributor.author Jaeger, Johannes, 1973-
dc.date.accessioned 2014-05-14T07:34:13Z
dc.date.available 2014-05-14T07:34:13Z
dc.date.issued 2013
dc.identifier.citation Jiménez-Guri E, Huerta-Cepas J, Cozzuto L, Wotton KR, Kang H, Himmelbauer H et al. Comparative transcriptomics of early dipteran development. BMC Genomics. 2013; 14:123. DOI: 10.1186/1471-2164-14-123
dc.identifier.issn 1471-2164
dc.identifier.uri http://hdl.handle.net/10230/22482
dc.description.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).
dc.description.sponsorship 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/nMinistry of Science and Innovation (MICINN). EJG is supported by ERASys Bio+ Grant P#161 (MODHEART). LC was supported by grant PTA2011-6729-I from the Spanish Ministry of Science and Innovation (MICINN). JHC is/nsupported 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
dc.format.mimetype application/pdf
dc.language.iso eng
dc.publisher BioMed Central
dc.relation.ispartof BMC Genomics. 2013;14:123
dc.rights © 2013 Eva Jiménez Guri et al. This article is distributed under a Creative Commons Attribution License
dc.rights.uri http://creativecommons.org/licenses/by/2.0/
dc.subject.other Genètica
dc.subject.other Genòmica
dc.subject.other Dípters
dc.title Comparative transcriptomics of early dipteran development
dc.type info:eu-repo/semantics/article
dc.identifier.doi http://dx.doi.org/10.1186/1471-2164-14-123
dc.relation.projectID info:eu-repo/grantAgreement/ES/3PN/BFU2009-10184
dc.relation.projectID info:eu-repo/grantAgreement/ES/3PN/BFU2009-09168
dc.relation.projectID info:eu-repo/grantAgreement/ES/3PN/PTA2011-6729
dc.relation.projectID info:eu-repo/grantAgreement/ES/3PN/JCI2010-07614
dc.rights.accessRights info:eu-repo/semantics/openAccess
dc.type.version info:eu-repo/semantics/publishedVersion

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