2024-03-19T06:08:47Zhttp://digital.csic.es/dspace-oai/requestoai:digital.csic.es:10261/1552242021-12-27T15:33:18Zcom_10261_77com_10261_8com_10261_13col_10261_330col_10261_266
A practical guide to build de-novo assemblies for single tissues of non- model organisms: the example of a Neotropical frog
Montero-Mendieta, Santiago
Grabherr, Manfred
Lantz, Henrik
De la Riva, Ignacio
Leonard, Jennifer A.
Webster, Matthew T.
Vilà, Carles
Genomics, Transcriptomics
RNA-seq
Frog transcriptome
Trinity
Gene ontology
Protein domain identification
Clusters of Orthologous Groups
Kyoto encyclopedia of genes and genomes
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. 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/wiki
2017-09-19T06:08:12Z
2017-09-19T06:08:12Z
2017
artículo
PeerJ, 5:e3702 (2017)
http://hdl.handle.net/10261/155224
10.7717/peerj.3702
28879061
eng
Publisher's version
htpp://dx.doi.org/10.7717/peerj.3702
Sí
Creative Commons Attribution License 4.0
openAccess
PeerJ