Detection of Active Transposable Elements in Arabidopsis thaliana using Oxford Nanopore Sequencing Technology

Transposables elements (TEs) contribute to both structural and functional dynamics of most eukaryotic genomes. The precise estimation of the impact of transposition on genomic diversity has been considered as a challenge 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). The short reads generated by Illumina platform has been used as a technology of choice for the detection of structural variants in plants and animals, but the short reads that it generates can cause high false discovery rate (FDR) and therefore limit the power of detection of TEASVs, especially in the case of complex genomes. The newest sequencing technologies, such as Oxford Nanopore Technologies (ONT) can generate long reads thus representing a promising tool for TEASV detection in plant and animals.

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^TM device. We were able to detect 9 new copies of the LTR-retrotransposon Evadé (EVD) among the 13 estimated that this line harbors. We also evidenced the activity of three additional TE families, a MULE transposon, an HELITRON and a DNA transposon.

Even at a low sequence coverage, ONT sequencing allowed us to reliably detect several TE insertions. Therefore, it is a promising alternative to other NGS platforms for the detection of structural variants in complex genomes.