eccDNA profiling in Arabidopsis indicates shift in transposon population in response to stress, cellular state, and epigenetic processes

Extrachromosomal circular DNA (eccDNA) sequencing data was generated using CIDER-Seq on Arabidopsis accession Columbia (Col-0) under various conditions and in various mutants. Prior to germination, Arabidopsis thaliana seeds were surface sterilized and stratified for 2 days at 4 °C. Before and during stress treatments plants were grown under controlled conditions in a Panasonic MLR-352-PE growth chamber on solid ½ MS medium (1% sucrose, 0.8% agar, pH 5.8) at 21 °C with 12/12 hr (day/night) light cycle. For the heat-stress, a prechilling step was performed. Seedlings were first placed at 4° for 24 hr within the growth chamber. This chilling pretreatment was followed by 24 h with the chamber set to 37° for the heat-stressed (HS) plants; control stressed (CS) plants were moved to 21°C. All Arabidopsis mutants used in this study, ddm1, dcl3, rdr6, and ros1, are in the Col-0 background. Calli tissues were induced from Arabidopsis leaf explant as described before (J.-J. Wang et al., 2015). Fluorescence-activated nuclear sorting (FANS) was performed as previously described (Gutzat & Mittelsten Scheid, 2020). Samples were prepared for CIDER-Seq and PacBio sequencing reads (ccs reads) were processed on deconcat (https://github.com/devang-mehta/ciderseq2) as described before (Mehta et al., 2020).