Retrotransposons are mobile genetic elements abundant in plant and animal 
genomes. While efficiently silenced by the epigenetic machinery, they can be 
reactivated upon stress or during development. Their level of transcription not 
reflecting their transposition ability, it is thus difficult to evaluate their 
contribution to the active mobilome. Here we applied a simple methodology based 
on the high throughput sequencing of extrachromosomal circular DNA (eccDNA) 
forms of active retrotransposons to characterize the repertoire of mobile 
retrotransposons in plants. This method successfully identified known active 
retrotransposons in both Arabidopsis and rice material where the epigenome is 
destabilized. When applying mobilome-seq to developmental stages in wild type 
rice, we identified PopRice as a highly active retrotransposon producing eccDNA 
forms in the wild type endosperm. The mobilome-seq strategy opens new routes for 
the characterization of a yet unexplored fraction of plant genomes.