Deciphering extrachromosomal circular DNA in Arabidopsis

Graphical abstract
Highlights • 743 eccDNAs were detected in Arabidopsis leaf, flower, stem and root tissues. • A large number of tRNAs and transposons were hosted by the eccDNAs. • eccDNAs have inverted repeats at upstream and downstream of the boundaries.
Extrachromosomal circular DNA (eccDNA) is independent of the chromosome and exists in many eukaryotes. However, the nature and origin of eccDNA in plants remains unclear. In this study, we sequenced 12 samples from four tissues (leaf, flower, stem and root) with three biological replicates. In total, we found 743 eccDNAs found in at least two samples. Most of eccDNA have inverted repeats ranging from 4 to 12 bp in the boundaries. Interestingly, eccDNA is not only related to transposon activity, but also hosts tRNA genes, suggesting that the eccDNAs may be associated with tRNA abundance which controls protein synthesis under conditions of stress. Our results provide an unprecedented view of eccDNA, which is still naïve in scope.