title: Smed454 dataset: unravelling the transcriptome of Schmidtea mediterranea.
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.
authors.affiliation: Departament de Genètica, Facultat de Biología, Universitat de Barcelona (UB), Barcelona, Catalunya, Spain.
authors.forename: Josep F
authors.initials: JF
authors.lastname: Abril
authors.forename: Francesc
authors.initials: F
authors.lastname: Cebrià
authors.forename: Gustavo
authors.initials: G
authors.lastname: Rodríguez-Esteban
authors.forename: Thomas
authors.initials: T
authors.lastname: Horn
authors.forename: Susanna
authors.initials: S
authors.lastname: Fraguas
authors.forename: Beatriz
authors.initials: B
authors.lastname: Calvo
authors.forename: Kerstin
authors.initials: K
authors.lastname: Bartscherer
authors.forename: Emili
authors.initials: E
authors.lastname: Saló
mesh_terms: D000818:Animals; D001482:Base Composition / Q000235:genetics; D001483:Base Sequence; D002453:Cell Cycle / Q000235:genetics; D002455:Cell Division / Q000235:genetics; D016384:Consensus Sequence / Q000235:genetics; D004249:DNA Damage / Q000235:genetics; D004260:DNA Repair / Q000235:genetics; D030541:Databases, Genetic; D005123:Eye / Q000378:metabolism; D020869:Gene Expression Profiling; D016678:Genome / Q000235:genetics; D018398:Homeodomain Proteins / Q000235:genetics; D020407:Internet; D008565:Membrane Proteins / Q000235:genetics; D058977:Molecular Sequence Annotation; D018377:Neurotransmitter Agents / Q000235:genetics; D010932:Planarians / Q000166:cytology / Q000235:genetics*; D022821:RNA Splice Sites / Q000235:genetics; D011956:Receptors, Cell Surface / Q000235:genetics; D015203:Reproducibility of Results; D020133:Reverse Transcriptase Polymerase Chain Reaction; D017422:Sequence Analysis, DNA / Q000379:methods*
chemical_list: D018398:Homeodomain Proteins; D008565:Membrane Proteins; D018377:Neurotransmitter Agents; D022821:RNA Splice Sites; D011956:Receptors, Cell Surface