This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ Preprints) and either DOI or URL of the article must be cited.
Cite this article
Montero-Mendieta S, Grabherr M, Lantz H, De la Riva I, Leonard JA, Webster MT, Vilà C.2017. First de-novo transcriptome assembly of a South American frog, Oreobates cruralis, enables population genomic studies of Neotropical amphibians. PeerJ Preprints5:e2980v1https://doi.org/10.7287/peerj.preprints.2980v1
Whole genome sequencing is opening the door to novel insights into the population structure and evolutionary history of poorly known species. In organisms with large genomes, which includes most amphibians, whole-genome sequencing is excessively challenging and transcriptome sequencing (RNA-seq) represents a cost-effective tool to explore genome-wide variability. Non-model organisms do not usually have a reference genome to facilitate assembly and the transcriptome sequence must be assembled de-novo. We used RNA-seq to obtain the transcriptome profile for Oreobates cruralis, a poorly known South American direct-developing frog. In total, 550,871 transcripts were assembled, corresponding to 422,999 putative genes. Of those, we identified 23,500, 37,349, 38,120 and 45,885 genes present in the Pfam, EggNOG, KEGG and GO databases, respectively. Interestingly, our results suggested that genes related to immune system and defense mechanisms are abundant in the transcriptome of O. cruralis. We also present a workflow to assist with pre-processing, assembling, evaluating and functionally annotating a de-novo transcriptome from RNA-seq data of non-model organisms. Our workflow guides the inexperienced user in an intuitive way through all the necessary steps to build de-novo transcriptome assemblies using readily available software and is freely available at: https://github.com/biomendi/PRACTICAL-GUIDE-TO-BUILD-DE-NOVO-TRANSCRIPTOME-ASSEMBLIES-FOR-NON-MODEL-ORGANISMS/wiki