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Smed454 dataset: unravelling the transcriptome of Schmidtea mediterranea
- Source :
- Recercat. Dipósit de la Recerca de Catalunya, instname, BMC Genomics, Dipòsit Digital de la UB, Universidad de Barcelona, BMC Genomics, Vol 11, Iss 1, p 731 (2010)
- Publisher :
- BioMed Central
-
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.
- Subjects :
- lcsh:QH426-470
DNA Repair
lcsh:Biotechnology
Receptors, Cell Surface
Eye
Genètica molecular
lcsh:TP248.13-248.65
Consensus Sequence
Databases, Genetic
Genetics
Planària
Animals
Molecular genetics
Homeodomain Proteins
Base Composition
Internet
Neurotransmitter Agents
Genome
Base Sequence
Reverse Transcriptase Polymerase Chain Reaction
Regeneració (Biologia)
Gene Expression Profiling
Cell Cycle
Membrane Proteins
Reproducibility of Results
Molecular Sequence Annotation
Planaria
Planarians
Sequence Analysis, DNA
lcsh:Genetics
Regeneration (Biology)
RNA Splice Sites
Cell Division
Biotechnology
Research Article
DNA Damage
Subjects
Details
- Database :
- OpenAIRE
- Journal :
- Recercat. Dipósit de la Recerca de Catalunya, instname, BMC Genomics, Dipòsit Digital de la UB, Universidad de Barcelona, BMC Genomics, Vol 11, Iss 1, p 731 (2010)
- Accession number :
- edsair.pmid.dedup....c3061c5d83a443a1f0e10c816531be83