Figure 2.

Global sequence motif-dependent nick-labeling distinguishes subtelomeres and identifies subtelomeric structural variants. (A) The subtelomere repeat elements of 1p, 5q, and 8p are shown as colored blocks, with each color indicating a paralogy block of segmentally duplicated subtelomeric repeat elements (SREs) as defined previously (Stong et al. 2014). The telomeres are designated as a red T. The consensus maps of nick-labeled single molecules after de novo assembly and alignment with the hg38 reference are shown as light blue bars; the dark blue vertical ticks within these bars indicate the Nt.BspQI nick-label sites. The single molecules that comprise the respective consensus map are the yellow lines shown directly below each map. The labels on the single molecules that align with the hg38 reference are dark green, and those that do not align are light blue. The dark blue and red bars designate the overlapping regions between the chromosome arms. (B) The major haplotypes of Chromosome 6p detected from eight individuals. The hg38 6p subtelomere reference sequence is shown as a light blue bar; the dark blue vertical ticks within these bars indicate the in silico Nt.BspQI nick-label sites. The black line segment designates a telomere-adjacent gap in the hg38 reference sequence. Each haplotype is represented as a distinct consensus map of single molecules from the designated genome (yellow line) aligned to the hg38 6p reference sequence. The labels on these consensus maps that align with the hg38 reference are dark green, and those that do not align are light blue. (C) The two distinct haplotypes of the cancer genome UMUC3 for Chromosome 6p.