Few weeks ago I posted about a paper from the laboratories of Thomas Braun and his collaborators on a de novo assembly of the transcriptome of Notophthalmus viridescens and their findings of some novel urodele- and newt-specific protein families. Now, another reference transcriptome from this model species has been reported by the laboratories of András Simon and Rickard Sandberg (http://www.ncbi.nlm.nih.gov/pubmed/23454602). Here, the authors provide a dataset of 29,316 ORFs (open reading frames) of which 19,903 have a Blast hit (to UniProt or PfamA domain) and 13,263 correspond to complete ORFs, containing both start and stop codons. Similarly to what was reported in the previous transcriptome, a significant number of proteins with novel (newt-specific) or amphibian-specific domain architectures have been identified. As discussed in the previous post these novel proteins might help understanding the high regenerative capabilities of newts compared to other vertebrates and fuels the debate on the evolution of regeneration. As an example, the authors identified 940 ORFs that show a significant higher expression in the brain compared to other tissues. Among the novel newt-specific ORFs they have found one that appears upregulated during regeneration of dopamine neurons in the adult newt midbrain. It will be interesting to see the functional characterization of that gene.
Finally they also analysed the number of putative miRNA target sites in the 3’UTRs because previous studies in the axolotl Ambystoma mexicanum had suggested that in that species there appears to be an extensive miRNA-mediated gene regulation compared to other vertebrates with much more reduced regenerative capabilities (based on a higher density of putative miRNAs sites in introns compared to humans). However, in the newt N. viridescens the density of miRNAs sites, at least, in the 3’UTR is comparable to that from humans.
In any case, people working in newt regeneration have now an important tool to start characterizing better the process of regeneration in these animals. This transcriptome will be freely available at http://sandberg.cbm.ki.se/redspottednewt