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
Coppe, Alessandro, Pujolar, Jose Martin, Maes, Gregory E., Larsen, Peter F., Hansen, Michael M., Bernatchez, Louis, Zane, Lorenzo, and Bortoluzzi, Stefania (2010) 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. BMC Genomics, 11. 635. pp. 1-13.
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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. 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.
| Item ID: | 27632 |
|---|---|
| Item Type: | Article (Research - C1) |
| ISSN: | 1471-2164 |
| Additional Information: | © 2010 Coppe et al; licensee BioMed Central Ltd. 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. |
| Funders: | Marine Genomics Europe, University of Padova, Danish Council for Independent Research, Natural Sciences, Fund for Scientific Research |
| Projects and Grants: | Marine Genomics Europe network of excellence grant (Bid 45), University of Padova grant CPDA085158/08, University of Padova grant CPDR074285/07, Danish Council for Independent Research, Natural Sciences grant 09-072120 |
| Date Deposited: | 07 Jun 2013 09:37 |
| FoR Codes: | 06 BIOLOGICAL SCIENCES > 0604 Genetics > 060405 Gene Expression (incl Microarray and other genome-wide approaches) @ 50% 06 BIOLOGICAL SCIENCES > 0604 Genetics > 060408 Genomics @ 30% 07 AGRICULTURAL AND VETERINARY SCIENCES > 0704 Fisheries Sciences > 070405 Fish Physiology and Genetics @ 20% |
| SEO Codes: | 83 ANIMAL PRODUCTION AND ANIMAL PRIMARY PRODUCTS > 8302 Fisheries - Wild Caught > 830204 Wild Caught Fin Fish (excl. Tuna) @ 50% 96 ENVIRONMENT > 9608 Flora, Fauna and Biodiversity > 960808 Marine Flora, Fauna and Biodiversity @ 50% |
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