The European eel (Anguilla anguilla L.; Anguillidae; Teleostei) is a catadromous fish species with a complex life cycle conditioned by marine (spawning, larval phase and maturation) and continental (feeding, growth) environments. Current available information indicates that the overall stock is at an historical minimum in most of the distribution area and continues to decline, while fishing mortality is still high both on juveniles (glass eels) and adults (yellow and silver eels) . At present, recruitment is dramatically low, with a sharp and widespread reduction by 90-99% as compared to recruitment prior to 1980 . Several hypotheses have been put forward concerning the causes of the eel stock decline, including anthropogenic factors affecting eels during their continental phase of the life-cycle (overfishing, migration barriers, pollution and human-introduced diseases; ) and climatic events affecting eels during the oceanic phase [4, 5]. The European eel was included in 2007 in Appendix II of the Convention on International Trade of Endangered Species (CITES; http://www.cites.org) and was listed in 2008 as critically endangered in the IUCN Red List of Threatened Species http://www.iucnredlist.org. A management framework for the recovery of the European eel stock was established in 2007 by the Council of the European Union through a dedicated regulation (EU 1100/2007) for eel recovery and sustainable use of the stock requiring the preparation of national eel management plans from any Member States. Current demand for eels cannot be met by fisheries and relies on aquaculture instead, based on wild-caught juvenile eels as artificial reproduction of the species is not yet feasible .
From this perspective, an evaluation of European eel population genetic structure, genetic diversity, effective (spawning) population size, and possible evolutionary responses to anthropogenic environmental stress is crucial. Traditionally, these issues have been addressed by studying a limited number of markers due to the shortage of genomic sequence resources available for eels. No genome sequencing have been conducted for any anguillid species so far and all the species within the genus Anguilla are still poorly characterized at the molecular level. For the species A. anguilla only 232 proteins are available. Similarly, only 121 ESTs and 404 nucleotide sequences are known, the latter including the complete mitochondrial genome (NCBI databases 9/25/2010), encoding 13 peptides.
Next-generation sequencing techniques such as 454 pyrosequencing methodology allow for a massive characterization of expressed genes [6–10]. A complete characterization of Expressed Sequence Tags (ESTs) provides an overview of the transcriptome, i.e. those genes expressed in a given tissue at a given time . Initially, pyrosequencing was restricted to model organisms [12–15] because of the short reads (100-200 bp) produced that make de novo genome assembly difficult without a reference genome. However, the more accurate base calling and deeper sequencing coverage of the 454 approach means that transcribed genes of non-model organisms can be characterized without a pre-existing sequence reference. Recently, 454 pyrosequencing has been successfully applied to large-scale EST sequencing in non-model organisms , including insects [17, 18], plants [19–21] and corals . In fish, characterized transcriptomes include the whitefish Corenogus clupeaformis , the eelpout Zoarces viviparus , the lake sturgeon Acipenser fulvescens  and the cichlid Amphilophus sp. . Pyrosequencing of ESTs can be used to characterize gene expression, discover and identify new genes, providing a rich data resource for identification of novel Type I genetic markers (microsatellites and SNPs) for quantitative trait locus (QTL) and population genomic analyses. Up till now, only 196 ESTs are available for the Japanese eel  and 121 ESTs for the European eel . More recently, EST sequencing of a normalized A. anguilla cDNA library produced by the European Marine Genomics Network of Excellence allowed to obtain 4,893 ESTs (795 contigs and 4,008 singletons), used for the identification of putatively selected microsatellites markers [29, 30].
The non-coding portion of the transcriptome has been largely neglected in studies focusing on non-model organisms despite its emerging biological importance and the continuous discovery of novel classes of functional non-coding RNAs [31, 32]. As an example, microRNAs (miRNAs) are small non-coding RNAs playing an important role in the regulation of gene expression in a wide range of biological processes, including cell differentiation, organogenesis and development, which have been found in a wide range of organisms, from plants to viruses and vertebrates (reviewed in ). The majority of fish miRNAs have been characterised in model species (360 for Danio rerio, 131 for Fugu rubripes and 132 for Tetraodon nigroviridis), with the exception of rainbow trout .
Here we present the European eel transcriptome, obtained by 454 FLX Titanium sequencing of over 300,000 ESTs from a normalized cDNA library, and assembly of reads in about 19,000 contigs, representing bona fide individual transcripts. An innovative aspect of our study is the identification of putative European eel miRNA sequences, by comparing reconstructed contig sequences with known Metazoan miRNAs hairpin precursor sequences. In summary, 36% of contigs were annotated by similarity to known protein or nucleotide sequences, plus 35 contigs matching miRNAs sequences known in different species were identified. A database (EeelBase) has been established that provides the first picture of the genomic transcriptional activity of this economically important but endangered species. The database will be updated in the future, if additional data becomes available.