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Detection of active transposable elements in Arabidopsis thaliana using Oxford
Nanopore Sequencing technology
#MMPMID28715998
Debladis E
; Llauro C
; Carpentier MC
; Mirouze M
; Panaud O
BMC Genomics
2017[Jul]; 18
(1
): 537
PMID28715998
show ga
BACKGROUND: Transposables elements (TEs) contribute to both structural and
functional dynamics of most eukaryotic genomes. Because of their propensity to
densely populate plant and animal genomes, the precise estimation of the impact
of transposition on genomic diversity has been considered as one of the main
challenges of today's genomics. The recent development of NGS (next generation
sequencing) technologies has open new perspectives in population genomics by
providing new methods for high throughput detection of Transposable
Elements-associated Structural Variants (TEASV). However, these have relied on
Illumina platform that generates short reads (up to 350 nucleotides). This
limitation in size of sequence reads can cause high false discovery rate (FDR)
and therefore limit the power of detection of TEASVs, especially in the case of
large, complex genomes. The newest sequencing technologies, such as Oxford
Nanopore Technologies (ONT) can generate kilobases-long reads thus representing a
promising tool for TEASV detection in plant and animals. RESULTS: We present the
results of a pilot experiment for TEASV detection on the model plant species
Arabidopsis thaliana using ONT sequencing and show that it can be used
efficiently to detect TE movements. We generated a ~0.8X genome coverage of a
met1-derived epigenetic recombinant inbred line (epiRIL) using a MinIon device
with R7 chemistry. We were able to detect nine new copies of the
LTR-retrotransposon Evadé (EVD). We also evidenced the activity of the DNA
transposon CACTA, CAC1. CONCLUSIONS: Even at a low sequence coverage (0.8X), ONT
sequencing allowed us to reliably detect several TE insertions in Arabidopsis
thaliana genome. The long read length allowed a precise and un-ambiguous mapping
of the structural variations caused by the activity of TEs. This suggests that
the trade-off between read length and genome coverage for TEASV detection may be
in favor of the former. Should the technology be further improved both in terms
of lower error rate and operation costs, it could be efficiently used in
diversity studies at population level.
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