Single molecule long-read eccDNA sequencing reveals unambiguous and selective transposon activation in Arabidopsis in response to stress, cellular state, and epigenetic processes

Abstract Extrachromosomal circular DNA (eccDNA) has been described in a number of eukaryotic species, and their presence has been shown to enable gene amplification in phenomena as diverse as cancer and herbicide tolerance. A potential role for eccDNA is to serve as a means for transposon mobilization within the genome. However, most eccDNA studies in plants to date have been based on short-read sequencing data which fails at unambiguously identifying true eccDNA forms of genetic and transposable elements. Here, we report the first atlas of full-length eccDNAs for Arabidopsis using the Cider-Seq pipeline based on long-read sequencing of single molecules. Our dataset was validated by analysing eccDNAs of heat-stressed plants, thereby sequencing full-length eccDNA forms of the well-known heat-responsive ONSEN transposon. Our results show that more evolutionarily recent loci of ONSEN transposon produce greater numbers of eccDNAs upon heat-stress. We identified eccDNAs generated from loci of the transposon superfamily RC/Helitron as the most abundant eccDNAs in Arabidopsis. Profiling of eccDNAs from two cell types displaying altered DNA methylation patterns enabled the identification of new active TE loci such as VANDAL5A, ATCOPIA58 and ATREP19 in the shoot apical meristem, and ATCOPIA53, ENDOVIR1 and TA11 in calli tissues. Unexpectedly analysis of mutants in the DNA methylation pathways revealed that eccDNA formation from several retrotransposon loci is induced in the absence of active DNA demethylase ROS1. Together, our study provides an important resource to investigate the function of eccDNAs and the impact of DNA methylation in their regulation.