title: A reference transcriptome and inferred proteome for the salamander Notophthalmus viridescens.
abstract: Salamanders have a remarkable capacity to regenerate complex tissues, such as limbs and brain, and are therefore an important comparative model system for regenerative medicine. Despite these unique properties among adult vertebrates, the genomic information for amphibians in general, and salamanders in particular, is scarce. Here, we used massive parallel sequencing to reconstruct a de novo reference transcriptome of the red spotted newt (Notophthalmus viridescens) containing 118,893 transcripts with a N50 length of 2016 nts. Comparisons to other vertebrates revealed a newt transcriptome that is comparable in size and characteristics to well-annotated vertebrate transcriptomes. Identification of putative open reading frames (ORFs) enabled us to infer a comprehensive proteome, including the annotation of 19,903 newt proteins. We used the identified domain architectures (DAs) to assign ORFs phylogenetic positions, which also revealed putative salamander specific proteins. The reference transcriptome and inferred proteome of the red spotted newt will facilitate the use of systematic genomic technologies for regeneration studies in salamanders and enable evolutionary analyses of vertebrate regeneration at the molecular level.
authors: Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden.
authors: Ilgar
authors: I
authors: Abdullayev
authors: Matthew
authors: M
authors: Kirkham
authors: Åsa K
authors: ÅK
authors: Björklund
authors: András
authors: A
authors: Simon
authors: Rickard
authors: R
authors: Sandberg
mesh_terms: D000818:Animals; D016000:Cluster Analysis; D019295:Computational Biology / Q000379:methods; D019143:Evolution, Molecular; D020869:Gene Expression Profiling / Q000592:standards*; D058977:Molecular Sequence Annotation; D009673:Notophthalmus viridescens / Q000235:genetics* / Q000378:metabolism* / Q000502:physiology; D016366:Open Reading Frames / Q000235:genetics; D020543:Proteome / Q000032:analysis* / Q000378:metabolism; D040901:Proteomics / Q000379:methods; D012015:Reference Standards; D012038:Regeneration / Q000235:genetics; D059467:Transcriptome / Q000502:physiology*; D014562:Caudata / Q000235:genetics / Q000378:metabolism / Q000502:physiology; D054928:Validation Studies as Topic
chemical_list: D020543:Proteome