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dc.contributor.authorMontero-Mendieta, Santiagoes_ES
dc.contributor.authorGrabherr, Manfredes_ES
dc.contributor.authorLantz, Henrikes_ES
dc.contributor.authorDe la Riva, Ignacioes_ES
dc.contributor.authorLeonard, Jennifer A.es_ES
dc.contributor.authorWebster, Matthew T.es_ES
dc.contributor.authorVilà, Carleses_ES
dc.date.accessioned2017-09-19T06:08:12Z-
dc.date.available2017-09-19T06:08:12Z-
dc.date.issued2017-
dc.identifier.citationPeerJ, 5:e3702 (2017)es_ES
dc.identifier.urihttp://hdl.handle.net/10261/155224-
dc.description.abstractWhole 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. Nonmodel 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/wikies_ES
dc.language.isoenges_ES
dc.publisherPeerJes_ES
dc.relation.isversionofPublisher's versiones_ES
dc.rightsopenAccesses_ES
dc.subjectGenomics, Transcriptomicses_ES
dc.subjectRNA-seqes_ES
dc.subjectFrog transcriptomees_ES
dc.subjectTrinityes_ES
dc.subjectGene ontologyes_ES
dc.subjectProtein domain identificationes_ES
dc.subjectClusters of Orthologous Groupses_ES
dc.subjectKyoto encyclopedia of genes and genomeses_ES
dc.titleA practical guide to build de-novo assemblies for single tissues of non- model organisms: the example of a Neotropical froges_ES
dc.typeartículoes_ES
dc.identifier.doi10.7717/peerj.3702-
dc.description.peerreviewedPeer reviewedes_ES
dc.relation.publisherversionhtpp://dx.doi.org/10.7717/peerj.3702es_ES
dc.rights.licenseCreative Commons Attribution License 4.0es_ES
dc.relation.csices_ES
oprm.item.hasRevisionno ko 0 false*
dc.identifier.pmid28879061-
dc.type.coarhttp://purl.org/coar/resource_type/c_6501es_ES
item.openairetypeartículo-
item.cerifentitytypePublications-
item.fulltextWith Fulltext-
item.languageiso639-1en-
item.openairecristypehttp://purl.org/coar/resource_type/c_18cf-
item.grantfulltextopen-
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