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. 2019 Jun 7;8:e45954. doi: 10.7554/eLife.45954

Figure 4. Many LOH breakpoints occur at long intra- and inter-chromosomal repeat sequences.

Whole genome sequence data plotted as a log2 ratio and converted to chromosome copy number (Y-axis) and chromosome location (X-axis) using YMAP. (A) All long-range homozygous regions (light blue) that are associated with long repeat sequences (colored arrows) are indicated for 20 diverse C. albicans isolates. LOH breakpoints and isolate information are detailed in Supplementary files 1 and 4. The type of long repeat is indicated with colored arrows: intra-chromosomal (red), inter-chromosomal (yellow), both intra- and inter-chromosomal (green), rDNA repeat (blue), and MRS (black). (B–C) Two example LOH breakpoints in isolate CEC723 that occur at long repeats (red arrows) on (B) Chr1 (repeat copy length ~1.1 kb), and (C) ChrR (repeat copy length ~3.3 kb) and continue to the right telomere of the respective chromosomes. Heterozygous and homozygous allele ratios are indicated in the IGV track. The position, orientation, and spacer length of the long repeat sequence is indicated in the gene track. ORFs (black arrows) contained within the long repeat sequences are indicated above the gene track. The LOH breakpoint on ChrR is within a repeat-dense region; additional long repeats in the region are indicated (dashed arrows).

Figure 4.

Figure 4—figure supplement 1. Long-track homozygosis occurs on Chr3L at telomere seed sequences.

Figure 4—figure supplement 1.

(A) Homozygosis of the right arm of Chr3 in SC5314 occurred near a telomere repeat sequence. Chromosome plot indicating the location of homozygosis (light blue) on Chr3R in SC5314. An 8 bp unit of the C. albicans telomere repeat sequence (5’ – AACTTCTT – 3’) indicated by the two red arrows. Read depth and allele ratios above the gene track indicates that homozygosis occurs near the 8 bp telomere seed sequence in the 3’ end of orf19.5880 and continues to the Chr3R telomere. (B) Proposed model of telomere addition and subsequent homozygosis of the right arm of Chr3 in SC5314. (i) A double-strand DNA break occurs on one homolog of Chr3 (blue) near the 8 bp telomere seed sequence (red arrow). (ii) Recombination between the 8 bp telomere seed sequence on Chr3 and a telomere on another chromosome end (iii) leads to the formation of a truncated Chr3 capped with a new telomere. (iv) A secondary break within the newly added telomere sequence and BIR of the opposite Chr3 homolog results in (v) formation of a full-length disomic Chr3 that is homozygous for the right arm.