Abstract
BackgroundFreshwater 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.ResultsIn 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.ConclusionsWe 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.
Highlights
Freshwater planarians are an attractive model for regeneration and stem cell research and have become a promising tool in the field of regenerative medicine
Irradiation destroys planarian neoblasts within 1-2 days, and the animals die within a few weeks because they cannot sustain normal cell turnover
Our 454 sequence reads were assembled together with the ~10,000 S. mediterranea UniGene set available at NCBI, using the 90% similarity criteria
Summary
Freshwater planarians are an attractive model for regeneration and stem cell research and have become a promising tool in the field of regenerative medicine. Freshwater planarians are a classic model for studying the fascinating process of regeneration [1,2,3,4] because they are capable of re-building a complete organism from almost any small body fragment This is made possible by a unique population of adult somatic stem cells called neoblasts. A step towards this end was taken when the S. mediterranea genome and EST information were integrated and approximately 30,000 genes were predicted using an annotation pipeline called MAKER [16] Those gene models, together with ~9,000 mRNAs generated using next-generation sequencing technology, were mapped on the planarian genome and used to improve the assembly [17]. These are accessible, together with the MAKER annotation data, in the S. mediterranea genome database (SmedGD; [17])
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
