Ion Torrent and lllumina, two complementary RNA-seq platforms for constructing the holm oak (Quercus ilex) transcriptome

• DOI: 10.1371/journal.pone.0210356
• Publication Date: 2019-01-16T18:45:38Z
• Authors: Victor M. Guerrer...; Ana M. Maldonado-...; Francisco Amil-Ruiz; Andrea Verardi; Jesús V. Jorrín-Novo; María-Dolores Rey
• Keywords: Ion semiconductor sequencing; Illumina dye sequencing

Transcriptome analysis is widely used in plant biology research to explore gene expression across a large variety of biological contexts such as those related environmental stress and plant-pathogen interaction. Currently, next generation sequencing platforms are obtain high amount raw data build the transcriptome any plant. Here, we compare Illumina Ion Torrent for construction holm oak (Quercus ilex) transcriptome. Genomic this forest tree species major challenge considering its recalcitrant character absence previous molecular studies. In study, Quercus ilex reads were obtained from assembled by three different algorithms, MIRA, RAY TRINITY. A hybrid combining both technologies was also study. The RAY-hybrid assembly generated most complete (1,116 sequences which 1,085 single copy) with E90N50 1,122 bp. MIRA-Illumina TRINITY-Ion assemblies annotated highest number total transcripts (62,628 74,058 respectively). MIRA-Ion showed shared (84.8%) All ontology grouping them terms processes, functions cellular components. addition, an silico proteomic carried out using translated databases. Those more proteins compared assemblies. This new represents valuable tool conduct differential studies response biotic abiotic stresses assist validate ongoing Q. whole genome sequencing.