Fig. 2

An overview of SDs characteristics and the study motivation. Based on the most recent T2T human genome assembly: A A contour plot of the SD abundance given their sequence identity (90–100%, x axis) and the total length (Mb, y-axis, log-scale), where the blue colour intensifies with the increasing number of SDs; B A barplot of the SDs total length (Mb, log-scale, y-axis) given the total number of SDs copies (x-axis) located at the interstitial (top, blue) and non-interstitial (bottom, yellow) genomic regions; C An area plot of the SDs’ total length (Mb, log-scale, y-axis) for SDs with at least given number of copies (x-axis) and the minimal percent of sequence identity (area colour). Here, the number of stacked SDs per base is the number of reads overlapping a given base position of the reference genome. D A normalised depth-of-coverage histogram of the aligned whole-genome circular consensus sequencing (CCS) reads in the human (NA12878), two chimpanzees (Clint, Chaos), bonobo (Mhudilbu), and gorilla (Kamilah) genomic regions syntenic to those flanking the HSA2 fusion site. For bonobo and both chimpanzees two depth-of-coverage tracks are shown. The top track presents the full scale of all data, whereas the bottom track zooms-in the coverage of values excluding the extremely high coverage region. The red line on each of the top tracks indicates the y-axis limit of the bottom track. Note the high coverage of the ~31 kb fragment previously found to be amplified about 400 times in the chimp genome [19]. E Optical genome mapping was used to assess the current incompleteness of the subtelomeric assemblies in chimpanzee and bonobo genomes (panTro5, panTro6, and panPan3). Each of the subtelomeric ends was estimated to lack at least 0.3 Mb of the DNA sequence