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dc.contributor.authorGuerrero-Sánchez, Victor M.
dc.contributor.authorAmil-Ruiz, Francisco
dc.contributor.authorVerardi, Andrea
dc.contributor.authorJorrín-Novo, Jesús V.
dc.contributor.authorRey Santome, María Dolores
dc.contributor.authorMaldonado-Alconada, Ana M.
dc.date.accessioned2019-02-05T10:49:11Z
dc.date.available2019-02-05T10:49:11Z
dc.date.issued2019
dc.identifier.urihttp://hdl.handle.net/10396/17765
dc.description.abstractTranscriptome analysis is widely used in plant biology research to explore gene expression across a large variety of biological contexts such as those related to environmental stress and plant-pathogen interaction. Currently, next generation sequencing platforms are used to obtain a high amount of raw data to build the transcriptome of any plant. Here, we compare Illumina and Ion Torrent sequencing platforms for the construction and analysis of the holm oak (Quercus ilex) transcriptome. Genomic analysis of this forest tree species is a major challenge considering its recalcitrant character and the absence of previous molecular studies. In this study, Quercus ilex raw sequencing reads were obtained from Illumina and Ion Torrent and assembled by three different algorithms, MIRA, RAY and TRINITY. A hybrid transcriptome combining both sequencing technologies was also obtained in this study. The RAY-hybrid assembly generated the most complete transcriptome (1,116 complete sequences of which 1,085 were single copy) with a E90N50 of 1,122 bp. The MIRAIllumina and TRINITY-Ion Torrent assemblies annotated the highest number of total transcripts (62,628 and 74,058 respectively). MIRA-Ion Torrent showed the highest number of shared sequences (84.8%) with the oak transcriptome. All the assembled transcripts from the hybrid transcriptome were annotated with gene ontology grouping them in terms of biological processes, molecular functions and cellular components. In addition, an in silico proteomic analysis was carried out using the translated assemblies as databases. Those from Ion Torrent showed more proteins compared to the Illumina and hybrid assemblies. This new generated transcriptome represents a valuable tool to conduct differential gene expression studies in response to biotic and abiotic stresses and to assist and validate the ongoing Q. ilex whole genome sequencing.es_ES
dc.format.mimetypeapplication/pdfes_ES
dc.language.isoenges_ES
dc.publisherPublic Library of Sciencees_ES
dc.rightshttps://creativecommons.org/licenses/by-nc-nd/4.0/es_ES
dc.sourcePLoS ONE 14(1): e0210356 (2019)es_ES
dc.subjectQuercus ilexes_ES
dc.subjectGenomic analysises_ES
dc.titleIon Torrent and lllumina, two complementary RNA-seq platforms for constructing the holm oak (Quercus ilex) transcriptomees_ES
dc.typeinfo:eu-repo/semantics/articlees_ES
dc.relation.publisherversionhttps://doi.org/10.1371/journal.pone.0210356es_ES
dc.relation.projectIDGobierno de España. FJCI-2016-28296es_ES
dc.rights.accessRightsinfo:eu-repo/semantics/openAccesses_ES


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