Fig. 1: High eccDNA load in Arabidopsis thaliana epigenetic mutants is associated with new TE insertions in the genome. | Nature Communications

Fig. 1: High eccDNA load in Arabidopsis thaliana epigenetic mutants is associated with new TE insertions in the genome.

From: Extrachromosomal circular DNA and structural variants highlight genome instability in Arabidopsis epigenetic mutants

Fig. 1

a Scheme depicting the experimental design: from Arabidopsis plants both linear and circular DNA were extracted and sequenced using Illumina and Nanopore (ONT) platforms in order to characterize the eccDNA repertoire and the genomic SVs. b Heat map showing the abundance of TE-eccDNAs detected for 318 Arabidopsis TE families in ddm1, polIV, rdr6, ddm1 polIV, ddm1 rdr6 and ddm1 rdr6 polIV triple mutant plants using Illumina mobilome-seq. The number of eccDNA is normalized by the number of mapped reads per million per library and compared to the WT. c Mobilome-seq data using Illumina and Nanopore sequencing (ONT) showing the coverage at an EVD locus (Chr5:5630538-5634764). ONT reads result in clearer boundaries and uniform coverage. d Number of insertions for 7 mobilized TE families in the genome of ddm1, ddm1 rdr6, ddm1 polIV and ddm1 rdr6 polIV mutants. Note that single plants were sequenced except for the triple mutant where a pool of 5 plants was used, because of the dwarf phenotype. e Target site preferences for different TE families in ddm1 rdr6 polIV mutant plants. Source data are provided as a Source Data file.

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