Ion Torrent and lllumina, two complementary RNA-seq platforms for constructing the holm oak (Quercus ilex) transcriptome
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Author
Guerrero-Sánchez, Victor M.
Amil-Ruiz, Francisco
Verardi, Andrea
Jorrín-Novo, Jesús V.
Rey Santome, María Dolores
Maldonado-Alconada, Ana M.
Publisher
Public Library of ScienceDate
2019Subject
Quercus ilexGenomic analysis
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Show full item recordAbstract
Transcriptome 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.