Fig. 2

rDNA cluster-specific expression in natural inbred lines. a The proportion of RNA-seq reads expressing a particular reporter variant (y-axis) against the proportion of DNA-seq reads accounting for the existence of the same variant (x-axis) for five natural inbred lines: Col-0 (6909), Sf-2 (7328), Bur-0 (7058), No-0 (7273), and Ct-1 (7067). Notice that no variants Bur-0 rDNA-2-specific passed the threshold (present in > 5% of copies within an individual) due to the small size of that rDNA cluster (Fig. 2b and [36]). Error bars represent standard deviations of three to seven biological replicates. The dashed line indicates the one-to-one ratio between DNA and RNA. b FISH results for the same accessions as in (a) showing that rDNA clusters carrying actively transcribed rRNA localize in proximity to the nucleolus, while silenced rDNAs are observed elsewhere in the nucleus. Images in black and white show DAPI-stained nuclei. Probes hybridizing the 45S rRNA gene cluster, chromosomes 2 and 4 are highlighted in yellow, red, and green, respectively. The nucleolus is marked by a dashed contour. Bar = 10 μm. For (a) and (b), purple and turquoise colored frames indicate accessions dominant for rDNA-2 and rDNA-4, respectively. c Relative frequency of nuclei with a particular rDNA configuration in relation to the nucleolus for the same parental accessions as in (a) and (b). The colored areas correspond to nuclei displaying exclusively two rDNA-2 (dark purple), one rDNA-2 (mid purple), two rDNA-2 per one rDNA-4 (light purple), two rDNA-4 (dark turquoise), one rDNA-4 (mid turquoise), two rDNA-4 per one rDNA-2 (light turquoise), one rDNA-2 per rDNA-4 (light gray), and two rDNA-2 per two rDNA-4 (light green) hybridization signals localized to the nucleolus. The number of nuclei (n) analyzed per accession is indicated at the top of each bar