First de-novo transcriptome assembly of a South American frog, Oreobates cruralis, enables population genomic studies of Neotropical amphibians
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Abstract
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
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2017. First de-novo transcriptome assembly of a South American frog, Oreobates cruralis, enables population genomic studies of Neotropical amphibians. PeerJ Preprints 5:e2980v1 https://doi.org/10.7287/peerj.preprints.2980v1note This preprint is not peer-reviewed. You may wish to reference the subsequent peer-reviewed version of this article.
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This is a submission to PeerJ for review.
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Competing Interests
The authors declare that they have no competing interests.
Author Contributions
Santiago Montero-Mendieta conceived and designed the experiments, performed the experiments, analyzed the data, wrote the paper, prepared figures and/or tables, reviewed drafts of the paper.
Manfred Grabherr wrote the paper, reviewed drafts of the paper.
Henrik Lantz wrote the paper, reviewed drafts of the paper.
Ignacio De la Riva contributed reagents/materials/analysis tools, wrote the paper, reviewed drafts of the paper.
Jennifer A Leonard contributed reagents/materials/analysis tools, wrote the paper, reviewed drafts of the paper.
Matthew T Webster conceived and designed the experiments, wrote the paper, reviewed drafts of the paper.
Carles Vilà conceived and designed the experiments, performed the experiments, wrote the paper, reviewed drafts of the paper.
Animal Ethics
The following information was supplied relating to ethical approvals (i.e., approving body and any reference numbers):
The Spanish Government (Ministerio de Economía y Competitividad) provided full approval for this study.
Field Study Permissions
The following information was supplied relating to field study approvals (i.e., approving body and any reference numbers):
Field experiments were approved by the Dirección General de la Biodiversidad, Ministerio de Medio Ambiente y Agua, La Paz, Bolivia
DNA Deposition
The following information was supplied regarding the deposition of DNA sequences:
Raw RNA-seq data in FASTQ format has been deposited at the NCBI Sequence Read Archive database (SRA) under the accession SRP106442. The transcriptome assembly in FASTA format has been deposited at DDBJ/EMBL/GenBank under the accession GFNJ00000000. The version described in this paper is the first version, GFNJ01000000. All the data is available at NCBI BioProject under the accession PRJNA384528.
Data Deposition
The following information was supplied regarding data availability:
NCBI BioProject: PRJNA384528 (https://www.ncbi.nlm.nih.gov/bioproject/PRJNA384528)
Funding
This work was supported by grants from the Spanish Government (Ministerio de Economía y Competitividad) to CV (CGL2013-47547-P) and to IDlR (CGL2011-30393), as well as a “FPI” (Formación de Personal Investigador) fellowship (BES-2014-069006) and a travel grant (EEBB-I-2016-10576) to SMM. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
