Fig. 1: Genome-wide distribution and global characterization of rice eccDNAs.
From: Adaptive dynamics of extrachromosomal circular DNA in rice under nutrient stress
a Size distribution (kb) of eccDNAs (blue bars) and eccDNAs that overlap with genes (red bars) detected in all 16 samples. Only the most abundant eccDNas ranging from 200 bp to 6 kb are shown. b Karyoplot displaying the chromosomal distribution of eccDNAs found in all samples. c Density distribution (in 100 kb windows) of eccDNAs in all samples, TEs, methylated positions, genes, non-coding RNAs, and motifs across the 12 chromosomes of rice. d Proportion of overall eccDNAs overlapping with genes (ecGenes), upstream 2 kb regions (up2kb), downstream 2 kb regions (down2kb), and intergenic regions. e Proportion of overall eccDNAs overlapping with Transposable Elements (ecTEs). f Proportion of overall eccDNAs overlapping with non-coding RNAs (ecNon-codingRNAs). g Proportion of all ecGenes overlapping with unique 5’UTR, unique CDS, unique 3’UTR, 5’UTR together with CDS (5’UTR + CDS), CDS together with 3’UTR (CDS + 3’UTR), and all together with 5’UTR, CDS, and 3’UTR (5’UTR + CDS + 3’UTR) regions. h Venn diagram showing all ecGenes (Genes in red), ecTEs (TEs in green), and ecNon-codingRNAs (Non-coding RNAs in pink). i Venn diagram showing overall eccDNAs overlapping with upstream 2 kb regions (up2kb in orange), ecTEs (TEs in green), and ecNon-codingRNAs (Non-coding RNAs in pink). j Venn diagram showing overall eccDNAs overlapping with downstream 2 kb regions (down2kb in yellow), ecTEs (TEs in green), and ecNon-codingRNAs (non-coding RNAs in pink).
