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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

Abstract

Background

Once highly abundant, the European eel (Anguilla anguilla L.; Anguillidae; Teleostei) is considered to be critically endangered and on the verge of extinction, as the stock has declined by 90-99% since the 1980s. Yet, the species is poorly characterized at molecular level with little sequence information available in public databases.

Results

The first European eel transcriptome was obtained by 454 FLX Titanium sequencing of a normalized cDNA library, produced from a pool of 18 glass eels (juveniles) from the French Atlantic coast and two sites in the Mediterranean coast. Over 310,000 reads were assembled in a total of 19,631 transcribed contigs, with an average length of 531 nucleotides. Overall 36% of the contigs were annotated to known protein/nucleotide sequences and 35 putative miRNA identified.

Conclusions

This study represents the first transcriptome analysis for a critically endangered species. EeelBase, a dedicated database of annotated transcriptome sequences of the European eel is freely available at http://compgen.bio.unipd.it/eeelbase webcite. Considering the multiple factors potentially involved in the decline of the European eel, including anthropogenic factors such as pollution and human-introduced diseases, our results will provide a rich source of data to discover and identify new genes, characterize gene expression, as well as for identification of genetic markers scattered across the genome to be used in various applications.