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Open Access Highly Accessed Research article

Smed454 dataset: unravelling the transcriptome of Schmidtea mediterranea

Josep F Abril12, Francesc Cebrià12, Gustavo Rodríguez-Esteban12, Thomas Horn3, Susanna Fraguas12, Beatriz Calvo12, Kerstin Bartscherer4 and Emili Saló12*

  • * Corresponding author: Emili Saló esalo@ub.edu

  • † Equal contributors

Author Affiliations

1 Departament de Genètica, Facultat de Biología, Universitat de Barcelona (UB), Av. Diagonal 645, edifici annex, planta 1, 08028, Barcelona, Catalunya, Spain

2 Institut de Biomedicina de la Universitat de Barcelona (IBUB), Av. Diagonal 645, edifici annex, planta 1, 08028, Barcelona, Catalunya, Spain

3 Division of Signaling and Functional Genomics German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, 69120 Heidelberg, Germany

4 Max Planck Research Group Stem Cells and Regeneration Max-Planck-Institute for Molecular Biomedicine, Von-Esmarch-Strasse 54, 48149 Muenster, Germany

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BMC Genomics 2010, 11:731  doi:10.1186/1471-2164-11-731

Published: 31 December 2010

Abstract

Background

Freshwater planarians are an attractive model for regeneration and stem cell research and have become a promising tool in the field of regenerative medicine. With the availability of a sequenced planarian genome, the recent application of modern genetic and high-throughput tools has resulted in revitalized interest in these animals, long known for their amazing regenerative capabilities, which enable them to regrow even a new head after decapitation. However, a detailed description of the planarian transcriptome is essential for future investigation into regenerative processes using planarians as a model system.

Results

In order to complement and improve existing gene annotations, we used a 454 pyrosequencing approach to analyze the transcriptome of the planarian species Schmidtea mediterranea Altogether, 598,435 454-sequencing reads, with an average length of 327 bp, were assembled together with the ~10,000 sequences of the S. mediterranea UniGene set using different similarity cutoffs. The assembly was then mapped onto the current genome data. Remarkably, our Smed454 dataset contains more than 3 million novel transcribed nucleotides sequenced for the first time. A descriptive analysis of planarian splice sites was conducted on those Smed454 contigs that mapped univocally to the current genome assembly. Sequence analysis allowed us to identify genes encoding putative proteins with defined structural properties, such as transmembrane domains. Moreover, we annotated the Smed454 dataset using Gene Ontology, and identified putative homologues of several gene families that may play a key role during regeneration, such as neurotransmitter and hormone receptors, homeobox-containing genes, and genes related to eye function.

Conclusions

We report the first planarian transcript dataset, Smed454, as an open resource tool that can be accessed via a web interface. Smed454 contains significant novel sequence information about most expressed genes of S. mediterranea. Analysis of the annotated data promises to contribute to identification of gene families poorly characterized at a functional level. The Smed454 transcriptome data will assist in the molecular characterization of S. mediterranea as a model organism, which will be useful to a broad scientific community.