eccDNA in Arabidopsis thaliana epigenetic mutants

The presence of abundant extrachromosomal circular DNA (eccDNA) is associated with high transposable element (TE) activity, notably in plant epigenetic mutants. However, the epigenetic control of the eccDNA compartment is still poorly described and the relationships between eccDNA and plant genome stability are not documented. In wild-type plants, three layers prevent TE activity: maintenance of DNA methylation, RNA-directed DNA methylation and post-transcriptional gene silencing. Here we show that Arabidopsis thaliana plants combining mutations in these three pathways have a high eccDNA load associated with new integration of TEs. By sequencing both the eccDNA and the corresponding genomic compartment using short and long reads, we document (1) the presence of truncated TEs both as eccDNAs and at new integration loci and (2) the presence of chimeric eccDNA. At the genomic level, complex rearrangements were detected using long read sequencing in a triple mutant in Decrease DNA methylation 1 (DDM1), RNA dependent RNA polymerase 6 (RDR6) and RNA polymerase IV (PolIV), suggesting that SVs could have been overlooked in these mutant backgrounds. We propose that plants having a high level of eccDNA may have altered DNA repair pathways leading to genome instability and the accumulation of structural variation.