Format

Send to

Choose Destination
PeerJ. 2017 Sep 1;5:e3702. doi: 10.7717/peerj.3702. eCollection 2017.

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

Author information

1
Conservation and Evolutionary Genetics Group, Department of Integrative Ecology, Doñana Biological Station (EBD-CSIC), Consejo Superior de Investigaciones Científicas, Seville, Spain.
2
Department of Medical Biochemistry and Microbiology, National Bioinformatics Infrastructure Sweden (BILS), Uppsala Universitet, Uppsala, Sweden.
3
Department of Biodiversity and Evolutionary Biology, Museo Nacional de Ciencias Naturales, Consejo Superior de Investigaciones Científicas, Madrid, Spain.
4
Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala Universitet, Uppsala, Sweden.

Abstract

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.

KEYWORDS:

Clusters of Orthologous Groups; Frog transcriptome; Gene ontology; Genomics; Kyoto encyclopedia of genes and genomes; Protein domain identification; RNA-seq; Transcriptomics; Trinity

Conflict of interest statement

The authors declare there are no competing interests.

Supplemental Content

Full text links

Icon for PeerJ, Inc. Icon for PubMed Central
Loading ...
Support Center