Open Access Highly Accessed Research article

Comparative transcriptomics of early dipteran development

Eva Jiménez-Guri1, Jaime Huerta-Cepas2, Luca Cozzuto3, Karl R Wotton1, Hui Kang456, Heinz Himmelbauer4, Guglielmo Roma37, Toni Gabaldón28* and Johannes Jaeger18*

Author Affiliations

1 EMBL/CRG Research Unit in Systems Biology, Centre de Regulació Genòmica (CRG), and Universitat Pompeu Fabra (UPF), Barcelona, Spain

2 Bioinformatics and Genomics Programme, Centre de Regulació Genòmica (CRG), and Universitat Pompeu Fabra (UPF), Barcelona, Spain

3 CRG Bioinformatics Core, Centre de Regulació Genòmica (CRG), and Universitat Pompeu Fabra (UPF), Barcelona, Spain

4 CRG Genomics Unit, Centre de Regulació Genòmica (CRG), and Universitat Pompeu Fabra (UPF), Barcelona, Spain

5 Max Planck Institute for Molecular Genetics, Berlin, Germany

6 Present address: ICFC Life Technologies, Bld #2, 218 Yindu Road, Shanghai, 200231, P. R. China

7 Present address: Developmental and Molecular Pathways, Novartis Institute for Biomedical Research, Basel, Switzerland

8 Centre de Regulació Genòmica (CRG), Dr. Aiguader 88, Barcelona, 08003, Spain

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BMC Genomics 2013, 14:123  doi:10.1186/1471-2164-14-123

Published: 24 February 2013

Additional files

Additional file 1:

Transcriptome sequencing, assembly, and annotation. Describes sequence data sets, de novo assembly, and automatic annotation in detail. Analyses are summarized in Tables S1–S3. Contains supplementary Figures S1–5, which show length distribution plots for 454 raw reads, contigs, and isotigs, and well as Trinity transcripts (contigs) for all assemblies and species. Figure S6 shows a comparative analysis of annotations between species and assembly strategies. (PDF 535 kb)

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Additional file 2:

Verification of annotation. Describes details of manual verification of transcriptome annotation not shown in the main text. Includes an analysis of predicted alternative splicing events. Contains supplementary Tables S4 and S5 summarizing manual curation and presenting a detailed list of manually curated candidate genes. Figure S7 and Table S6 show details of the verification of alternative splice isoforms as predicted by Newbler- and Trinity-based assemblies. (PDF 4599 kb)

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Additional file 3:

GO term enrichment analysis. Describes details of the enrichment analysis for GO terms associated with sets of genes present in different species, and for genes specific to subsets of species. Contains supplementary Table S7, with details of enriched GO categories between species. (XLSX 35 kb)

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Additional file 4:

Principal component analysis (PCA) of compositional bias. Contains Figure S8 showing the results of a PCA for amino acid distributions from concatenated sequences in all 21 species considered in our phylogenomic analysis. (PDF 112 kb)

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Additional file 5:

List of gene-tree phylogenies. Text file containing all gene trees obtained from the combination of the four phylomes reconstructed in this study. (7Z 10204 kb)

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Additional file 6:

List of species-trees topologies. Text file containing all topologies which are represented in the combined set of gene-tree phylogenies. (GZ 284 kb)

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