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. 2010 Nov 16;11:635. doi: 10.1186/1471-2164-11-635.

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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Anguilla / genetics*
  • Animals
  • Base Sequence
  • Contig Mapping
  • Databases, Nucleic Acid*
  • Databases, Protein
  • Endangered Species*
  • Europe
  • Fish Proteins / chemistry
  • Fish Proteins / genetics
  • Gene Expression Profiling*
  • Genome / genetics
  • Humans
  • MicroRNAs / genetics
  • Molecular Sequence Annotation*
  • Reproducibility of Results
  • Sequence Analysis, DNA / methods*
  • Sequence Homology, Nucleic Acid
  • Smegmamorpha / genetics
  • Species Specificity
  • Zebrafish / genetics

Substances

  • Fish Proteins
  • MicroRNAs