Figure 3.

28S subtypes found by haplotype analysis

(A) Correlation coefficient (Pearson’s r²) heatmap between positions across H7-hESC 28S rDNA with variant frequency >10%. x axis and y axis are annotated by regions. Helix regions are annotated by light blue, and ES regions are annotated by yellow. Individual positions with higher r² between regions are also indicated.

(B) Same as (A) for the Genome In A Bottle (GIAB) dataset.

(C) Haplotype digit code to variant sequence conversion at the three positions with higher r² in (A) and (B).

(D) Bray-Curtis principal coordinate analysis (PCoA) of 386 H7-hESC 28S rDNA sequences (upper panel) and 386 28S rDNA sequences from each GIAB sample (lower panel). Each dot is a complete 28S rDNA sequence with similarity between sequences measured on 6-mers. The colors correspond to coloring an rDNA sequence by its 3-position haplotype described in (C). Numbers in the x and y labels represent the PCoA explained variance.

(E) Telomere-to-telomere (T2T) haplotype distribution across the five acrocentric chromosomes. The rDNA acrocentric arms are presented in a schematic cartoon with proportions of rDNA haplotypes in different colors as found in the matching table below. Haplotypes match the 3-position haplotypes in (C). We indicate the rDNA copy number of each haplotype in every chromosome.