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A practical guide to build de-novo assemblies for single tissues of non-model organisms: the example of a Neotropical frog
CSIC, Donana Biol Stn EBD, Dept Integrat Ecol, Conservat & Evolutionary Genet Grp, Seville, Spain..
Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
CSIC, Museo Nacl Ciencias Nat, Dept Biodivers & Evolutionary Biol, Madrid, Spain..
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2017 (English)In: PeerJ, ISSN 2167-8359, E-ISSN 2167-8359, Vol. 5, article id e3702Article in journal (Refereed) Published
Abstract [en]

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. Weused 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/TRANSCRIPTOMEASSEMBLY- PIPELINE/wiki.

Place, publisher, year, edition, pages
PEERJ INC , 2017. Vol. 5, article id e3702
Keywords [en]
Genomics, Transcriptomics, RNA-seq, Frog transcriptome, Trinity, Gene ontology, Protein domain identification, Clusters of Orthologous Groups, Kyoto encyclopedia of genes and genomes
National Category
Biological Sciences
Identifiers
URN: urn:nbn:se:uu:diva-336834DOI: 10.7717/peerj.3702ISI: 000411957600001PubMedID: 28879061OAI: oai:DiVA.org:uu-336834DiVA, id: diva2:1167231
Available from: 2017-12-18 Created: 2017-12-18 Last updated: 2017-12-18Bibliographically approved

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Grabherr, ManfredLantz, HenrikWebster, Matthew Thomas
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