Fig. 3

ACRs are associated with transcriptional regulation in autotetraploid rice. a Heatmap showing the distribution of ACR read counts from 2 × and 4 × rice that were arranged in descending order based on FPKM values. The transition from white to red corresponds to ACR read intensities from low to high levels. Expressed genes with the top 20% (blue) and bottom 20% (green) transcriptional levels are shown. b Numbers of leaf ACRs and its associated genes. The ACRs are defined based on their distance to the nearest gene and are categorized as genic (gACRs; overlapping at least 1b with a gene), proximal (pACRs; within 2 kb of a gene, light blue), distal (dACRs; > 2 kb from a gene, dark red), or intergenic (iACR; the sum of pACRs and dACRs, no overlapping genes). c Boxplots of the expression levels of different types of associated ACRs. Only gACR- and only iACR-associated genes overlapped with gACRs and iACRs, respectively; igACR-associated genes were associated with both intergenic and genic ACRs; and nonACR-associated genes (neither gACR nor iACR) did not overlap with genes. Asterisks indicate significance of differences at a P value < 0.05 by Wilcoxon rank sum test. The five statistical values of the boxplot from top to bottom are the maximum, third quartile, median, first quartile, and minimum. The centerline is the median, the box limits are the upper and lower quartiles, and the whiskers are the 1.5-times interquartile ranges. d Numbers of up-regulated and down-regulated genes associated with gACRs and iACRs, which were only detected in 2× (2×-specific) or 4× (4×-specific) rice. e Snapshots of ACR distributions and gene expression (Scaffold: Chr1, 30,095–30,120 kb). The ACR density and expression levels are observed and scaled by the y-axis