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Comparative transcriptomics of early dipteran development
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 i...
Autores principales: | , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2013
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3616871/ https://www.ncbi.nlm.nih.gov/pubmed/23432914 http://dx.doi.org/10.1186/1471-2164-14-123 |
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author | Jiménez-Guri, Eva Huerta-Cepas, Jaime Cozzuto, Luca Wotton, Karl R Kang, Hui Himmelbauer, Heinz Roma, Guglielmo Gabaldón, Toni Jaeger, Johannes |
author_facet | Jiménez-Guri, Eva Huerta-Cepas, Jaime Cozzuto, Luca Wotton, Karl R Kang, Hui Himmelbauer, Heinz Roma, Guglielmo Gabaldón, Toni Jaeger, Johannes |
author_sort | Jiménez-Guri, Eva |
collection | PubMed |
description | 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). |
format | Online Article Text |
id | pubmed-3616871 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2013 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-36168712013-04-05 Comparative transcriptomics of early dipteran development Jiménez-Guri, Eva Huerta-Cepas, Jaime Cozzuto, Luca Wotton, Karl R Kang, Hui Himmelbauer, Heinz Roma, Guglielmo Gabaldón, Toni Jaeger, Johannes BMC Genomics Research Article 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). BioMed Central 2013-02-24 /pmc/articles/PMC3616871/ /pubmed/23432914 http://dx.doi.org/10.1186/1471-2164-14-123 Text en Copyright © 2013 Jiménez-Guri et al.; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 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. |
spellingShingle | Research Article Jiménez-Guri, Eva Huerta-Cepas, Jaime Cozzuto, Luca Wotton, Karl R Kang, Hui Himmelbauer, Heinz Roma, Guglielmo Gabaldón, Toni Jaeger, Johannes Comparative transcriptomics of early dipteran development |
title | Comparative transcriptomics of early dipteran development |
title_full | Comparative transcriptomics of early dipteran development |
title_fullStr | Comparative transcriptomics of early dipteran development |
title_full_unstemmed | Comparative transcriptomics of early dipteran development |
title_short | Comparative transcriptomics of early dipteran development |
title_sort | comparative transcriptomics of early dipteran development |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3616871/ https://www.ncbi.nlm.nih.gov/pubmed/23432914 http://dx.doi.org/10.1186/1471-2164-14-123 |
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