Fig. 2

Landscape of ACRs in diploid and autotetraploid rice. a The distribution of ACRs in diploid (2×) and autotetraploid (4×) rice on chromosomes 1 and 4. The average densities of ACRs per 1 kb bin were calculated (P value < 0.05) and are shown in the vertical bars. Relative density of gene and repetitive DNA were used to defined as euchromatin and heterochromatin. As shown, the black bars represent heterochromatin and grey ones represent euchromatin. The average levels of H3K4me3 (SRR6781461) and 5mC (GSE121274) are shown for comparison. The percentages of ACR density of heterochromatic and euchromatic regions of 2 × and 4 × rice chromosomes are shown in the lower right panel. H3K4me3 is enriched in euchromatin, whereas 5mC marks heterochromatin. In this regard, the chromosomes are colored to illustrate the regions of heterochromatin (dark black) and euchromatin (light black) according to the chromosomal distributions of H3K4me3 and 5mC, respectively. b The proportions of ACR-related genes and repeats (histogram; left) and genomic regions (right) in 2 × and 4 × rice leaves based on ATAC-seq from three biological replications. UTR, untranslated region. c ACR density profile in genes. The 2-kb upstream and downstream flanks are aligned. The average ACR densities per bin, which were calculated from the Tn5 integration frequency within each 100 bp interval, are plotted. TTS transcription termination site