Ion Torrent and lllumina, two complementary RNA-seq platforms for constructing the holm oak (Quercus ilex) transcriptome.
Algorithms
Gene Expression Profiling
/ methods
Gene Ontology
Genome, Plant
High-Throughput Nucleotide Sequencing
/ methods
Molecular Sequence Annotation
Plant Proteins
/ genetics
Proteome
/ genetics
Quercus
/ classification
RNA, Plant
/ genetics
Sequence Alignment
Sequence Analysis, RNA
/ methods
Species Specificity
Transcriptome
Trees
/ genetics
Journal
PloS one
ISSN: 1932-6203
Titre abrégé: PLoS One
Pays: United States
ID NLM: 101285081
Informations de publication
Date de publication:
2019
2019
Historique:
received:
26
07
2018
accepted:
20
12
2018
entrez:
17
1
2019
pubmed:
17
1
2019
medline:
12
10
2019
Statut:
epublish
Résumé
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 MIRA-Illumina 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.
Identifiants
pubmed: 30650136
doi: 10.1371/journal.pone.0210356
pii: PONE-D-18-22118
pmc: PMC6334949
doi:
Substances chimiques
Plant Proteins
0
Proteome
0
RNA, Plant
0
Types de publication
Comparative Study
Evaluation Study
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
e0210356Déclaration de conflit d'intérêts
The authors have declared that no competing interests exist.
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