A practical guide to build de-novo assemblies for single tissues of non-model organisms: the example of a Neotropical frog

Montero-Mendieta S, Grabherr M, Lantz H, De la Riva I, Leonard JA, Webster MT, VilĂ  C

PeerJ 5 (-) e3702 [2017-09-01; online 2017-09-01]

Whole genome sequencing (WGS) is a very valuable resource to understand the evolutionary history of poorly known species. However, in organisms with large genomes, as most amphibians, WGS is still 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 and the transcriptome must be assembled de-novo. We used RNA-seq to obtain the transcriptomic 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 pipeline to assist with pre-processing, assembling, evaluating and functionally annotating a de-novo transcriptome from RNA-seq data of non-model organisms. Our pipeline 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/TRANSCRIPTOME-ASSEMBLY-PIPELINE/wiki.

Bioinformatics Compute and Storage [Service]

Bioinformatics Support and Infrastructure [Collaborative]

Bioinformatics Support, Infrastructure and Training [Collaborative]

NGI Uppsala (SNP&SEQ Technology Platform) [Service]

National Genomics Infrastructure [Service]

QC bibliography QC xrefs

PubMed 28879061

DOI 10.7717/peerj.3702

Crossref 10.7717/peerj.3702

SRA: SRP106442
GENBANK: GFNJ00000000 TSA: Oreobates cruralis, transcriptome shotgun assembly
BioProject: PRJNA384528 Oreobates cruralis isolate:MNCN/ADN:65263 Transcriptome or Gene expression