title: A de novo assembly of the newt transcriptome combined with proteomic validation identifies new protein families expressed during tissue regeneration.
abstract: BACKGROUND
  Notophthalmus viridescens, an urodelian amphibian, represents an excellent model organism to study regenerative processes, but mechanistic insights into molecular processes driving regeneration have been hindered by a paucity and poor annotation of coding nucleotide sequences. The enormous genome size and the lack of a closely related reference genome have so far prevented assembly of the urodelian genome.
  
  
  RESULTS
  We describe the de novo assembly of the transcriptome of the newt Notophthalmus viridescens and its experimental validation. RNA pools covering embryonic and larval development, different stages of heart, appendage and lens regeneration, as well as a collection of different undamaged tissues were used to generate sequencing datasets on Sanger, Illumina and 454 platforms. Through a sequential de novo assembly strategy, hybrid datasets were converged into one comprehensive transcriptome comprising 120,922 non-redundant transcripts with a N50 of 975. From this, 38,384 putative transcripts were annotated and around 15,000 transcripts were experimentally validated as protein coding by mass spectrometry-based proteomics. Bioinformatical analysis of coding transcripts identified 826 proteins specific for urodeles. Several newly identified proteins establish novel protein families based on the presence of new sequence motifs without counterparts in public databases, while others containing known protein domains extend already existing families and also constitute new ones.
  
  
  CONCLUSIONS
  We demonstrate that our multistep assembly approach allows de novo assembly of the newt transcriptome with an annotation grade comparable to well characterized organisms. Our data provide the groundwork for mechanistic experiments to answer the question whether urodeles utilize proprietary sets of genes for tissue regeneration.
authors: Mario
authors: M
authors: Looso
authors: Jens
authors: J
authors: Preussner
authors: Konstantinos
authors: K
authors: Sousounis
authors: Marc
authors: M
authors: Bruckskotten
authors: Christian S
authors: CS
authors: Michel
authors: Ettore
authors: E
authors: Lignelli
authors: Richard
authors: R
authors: Reinhardt
authors: Sabrina
authors: S
authors: Höffner
authors: Marcus
authors: M
authors: Krüger
authors: Panagiotis A
authors: PA
authors: Tsonis
authors: Thilo
authors: T
authors: Borchardt
authors: Thomas
authors: T
authors: Braun
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D018507:Gene Expression Regulation, Developmental; D006321:Heart / Q000254:growth & development; D007908:Lens, Crystalline / Q000254:growth & development / Q000378:metabolism / Q000502:physiology; D008969:Molecular Sequence Data; D009206:Myocardium / Q000378:metabolism; D020543:Proteome / Q000235:genetics / Q000378:metabolism*; D012038:Regeneration / Q000235:genetics*; D012455:Salamandridae; D059467:Transcriptome
chemical_list: D020543:Proteome