RT Journal Article
SR Electronic
T1 <em>De novo</em> transcriptome analysis of dermal tissue from the rough-skinned newt, <em>Taricha granulosa</em>, enables investigation of tetrodotoxin expression
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 653238
DO 10.1101/653238
A1 Haley C. Glass
A1 Amanda D. Melin
A1 Steven M. Vamosi
YR 2019
UL http://biorxiv.org/content/early/2019/05/30/653238.abstract
AB Background Tetrodotoxin (TTX) is a potent neurotoxin used in anti-predator defense by several aquatic species, including the rough-skinned newt, Taricha granulosa. While several possible biological sources of newt TTX have been investigated, mounting evidence suggests a genetic, endogenous origin. We present here a de novo transcriptome assembly and annotation of dorsal skin samples from the tetrodotoxin-bearing species T. granulosa, to facilitate the study of putative genetic mechanisms of TTX expression.Findings Approximately 211 million read pairs were assembled into 245,734 transcripts using the Trinity de novo assembly method. Of the assembled transcripts, we were able to annotate 34% by comparing them to databases of sequences with known functions, suggesting that many transcripts are unique to the rough-skinned newt. Our assembly has near-complete sequence information for an estimated 83% of genes based on Benchmarking Universal Single Copy Orthologs. We also utilized other comparative methods to assess the quality of our assembly. The T. granulosa assembly was compared with that of the Japanese fire-belly newt, Cynops pyrrhogaster, and they were found to share a total of 30,556 orthologous sequences (12.9% gene set).Conclusions We provide a reference assembly for Taricha granulosa that will enable downstream differential expression and comparative transcriptomics analyses. This publicly available transcriptome assembly and annotation dataset will facilitate the investigation of a wide range of questions concerning amphibian adaptive radiation, and the elucidation of mechanisms of tetrodotoxin defense in Taricha granulosa and other TTX-bearing species.TTXTetrodotoxinRNA-seqRNA sequencingbpbase pairsBUSCOBenchmarking Universal Single Copy OrthologsGOGene OntologyNCBINational Center for Biotechnology InformationSRAShort Read ArchiveTSATranscriptome Shotgun Assembly