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"The genome, like all biological objects, is subject to a subtle balance between stability and adaptability. Transposable elements are mobile elements that participate in genome evolution, but can also cause harmful mutations. The epigenome helps maintain genome stability by preventing the activity of these transposable elements. During their activity, transposable elements generate circular forms of extrachromosomal DNA (ecDNA), but their impact on the genome is unknown.

We have developed a method called mobilome-seq for full-length sequencing of cDNA using Nanopore technology. By analyzing cDNAs and the genome of plants mutant for major epigenetic regulatory pathways in Arabidopsis thaliana, we were able to show that these plants accumulated a large quantity of cDNAs corresponding to DNA transposons and retrotransposons.

What's more, the cDNA population is much more diverse than expected, with half of the cDNAs being truncated and others chimeric. Unexpectedly, we have also shown that the genome of these plants contains important structural variants, such as gene duplications, which appear spontaneously in a single generation in the laboratory.

One locus in particular, involved in pathogen resistance, is deleted or duplicated in these plants, suggesting that there are "hotspots" of structural variation in the genome."