Fig. 5: Organization and sequence composition of the ape acrocentric chromosomes.

a, Sequence identity heatmaps and satellite annotations for the NOR⁺ short arms of both HSA22 haplotypes across all the great apes and siamang chromosome 21 (the only NOR⁺ chromosome in siamang) drawn with ModDotPlot¹²⁰. The short-arm telomere is oriented at the top of the plot, with the entirety of the short arm drawn to scale up to but not including the centromeric α-satellite. Heatmap colours indicate self-similarity in the chromosome, and large blocks indicate tandem repeat arrays (rDNA and satellites) with their corresponding annotations given in between. Human is represented by the diploid HG002 genome. b, Estimated number of rDNA units per haplotype for each species. HSA chromosome numbers are given in the first column, with the exception of s-21 for siamang chromosome 21, which is NOR⁺ but has no single human homologue. c, Sum of satellite and rDNA sequences across all short arms for which one haplotype is NOR⁺ in each species. ‘Unlabelled’ indicates sequences without a satellite annotation, which mostly comprise SDs. The total number of SD bases is given for comparison, with some overlap between regions annotated as SDs and satellites. Colours for sequence classes are as for a. d, Top tracks, chromosome 22 in the T2T-CHM13v2.0 reference genome displaying various gene-annotation metrics and the satellite annotation. Bottom tracks, for each primate haplotype, including the human HG002 genome, the chromosome that best matches each 10 kb window of T2T-CHM13 chromosome 22 is colour coded, as determined by MashMap¹²¹. On the right side of the centromere (towards the long arm), HSA22 is syntenic across all species; however, on the short arm, synteny rapidly degrades, with very few regions mapping uniquely to a single chromosome, a result reflective of extensive recombination on the short arms. Even the human HG002 genome does not consistently align to T2T-CHM13 chromosome 22 in the most distal (left-most) regions. acro, acrocentric; mat, maternal; pat, paternal.