Composition and structure of Arabidopsis thaliana extrachromosomal circular DNAs revealed by nanopore sequencing

Extrachromosomal circular DNA (eccDNA) are enigmatic DNA molecules that have been detected in range of organisms. In plants, eccDNAs have various genomic origins and may be derived from transposable elements. The information about the structure of individual eccDNA molecules as well as their dynamics in response to stress is poorly understood. In this study, we showed that nanopore sequencing is a useful tool for the detection and structural analysis of eccDNA molecules. By applying nanopore sequencing to eccDNA molecules of epigenetically stressed Arabidopsis plants grown under various stress treatments (heat, abscisic acid, and flagellin), we showed that TE-derived eccDNA quantity and structure vary dramatically between individual TEs. Epigenetic stress alone did not cause eccDNA up-regulation, while its combination with heat stress triggers the generation of full-length and various truncated eccDNAs of the ONSEN element. We showed that the ratio between full-length and truncated eccDNAs is TE- and condition-dependent. Our work paves the way for further elucidation of the structural features of eccDNAs and their connection with various biological processes such as eccDNA transcription and eccDNA-mediated TE silencing.