Open Access Highly Accessed Research article

Sequencing, de novo annotation and analysis of the first Anguilla anguilla transcriptome: EeelBase opens new perspectives for the study of the critically endangered european eel

Alessandro Coppe1, Jose Martin Pujolar1, Gregory E Maes2, Peter F Larsen3, Michael M Hansen3, Louis Bernatchez4, Lorenzo Zane1* and Stefania Bortoluzzi1

Author Affiliations

1 Biology Department, University of Padova, Via G. Colombo 3, I-35131 Padova, Italy

2 Katholieke Universiteit Leuven, Laboratory of Animal Diversity & Systematics, B-3000 Leuven, Belgium

3 Aarhus University, Department of Biological Sciences, Ny Munkegade 114, DK-8000 Aarhus C, Denmark

4 University of Laval, IBIS, Quebec City, PQ G1V 0A6 Canada

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BMC Genomics 2010, 11:635  doi:10.1186/1471-2164-11-635

Published: 16 November 2010

Additional files

Additional file 1:

Additional Figure. Distribution of average quality (A), length (B) and number of reads (C) in the set of 28,229 contigs obtained by the first run of reads assembly.

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Additional file 2:

Additional Figure. Pair-wise relationships between main properties (sequence length, number of reads per contig, average sequence quality, and average sequence coverage) characterizing the set of 28,229 contigs obtained by the first run of reads assembly.

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Additional file 3:

Additional Figure. Distribution of sequence length (A) and relationship between length and average quality (B) in the set of 19,631 contigs of the European eel transcriptome.

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Additional file 4:

Additional Table. Mapping of the 122,193 GO terms associated to the European eel contigs to a total of 124 GO-Slim ancestor terms by single count.

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Additional file 5:

Additional Table. Genes encoding heat shock proteins represented in EeelBase. The table summarizes a total of 92 GO terms associated to 26 contigs belonging to 11 different heat shock protein genes. The 55 non-redundant terms are also reported in a word cloud form, with character size proportional to the number of occurrences of the functional term.

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Additional file 6:

Additional Figures. Mapping of zebrafish genes homologous to European eel transcripts to three KEGG pathways: ribosome (37 genes), oxidative phosphorylation (34 genes) and proteasome (15 genes). Green boxes represent KEGG nodes specific to the considered organism; Red stars indicate enriched nodes, which may represent one or more genes.

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