Fig. 1

Chromosome arms with low recombination frequency. The hg38 subtelomere reference sequences are shown as light blue bars; the dark blue vertical ticks within these bars indicate in silico Nt.BspQI nick-label sites. Individual single-molecule maps were de novo assembled into the consensus maps (yellow lines), which were then aligned with the hg38 reference (light blue bars). The green lines on the consensus maps are Nt.BspQI (GCTCTTC) sites that align to the corresponding reference site. Those that do not align with the reference are designated with light blue lines. Chromosome arms without a consensus map were mapped to the hg38 reference instead of de novo assembled. The location of the telomere is shown with a red “T”. Representative examples of raw images of single molecules that were imaged are shown below the references. The DNA backbone is blue, and both the labeled subtelomeric Nt.BspQI sites and the telomere (TTAGGG) n tracts are green. a Representative data for three chromosome arms (2q U2OS, 2p SK-MEL-2, 3p Saos-2) that have heterogenous end telomere length. b A 5q molecule from U2OS with an end telomere and directly below, a 5q end recombined with an unknown genomic fragment with retention of a long internal telomere-like sequence (ITS). 16q molecules from SK-MEL-2, one with recombination and one without. c Molecules of 15q from U2OS aligned to hg38; two display end telomere (TTAGGG) n loss. Likewise, molecules from 8p SK-MEL-2, 1 displays telomere loss. d U2OS chromosome 2p molecules aligned to hg38 with short end telomeres