Figure 3. All copy number breakpoints resulting in segmental aneuploidy occur at repeat sequences.

(A) Whole genome sequence data plotted as a log2 ratio and converted to chromosome copy number (Y-axis) and chromosome location (X-axis) using YMAP. The source of each isolate is indicated in color: in vivo evolution experiments in a murine model of oropharyngeal candidiasis (OPC) (green), in vitro evolution experiments in the presence of azole antifungal drugs (red), and clinical isolates (blue). Ploidy, determined by flow cytometry, is indicated on the far right. Every copy number breakpoint occurred at a repeat sequence (red arrow), additional details are in Supplementary file 3. Location of the Major Repeat Sequences (black circle) and rDNA array (blue circle) are shown below. Example copy number breakpoints for two isolates (B–C). (B) Isolate AMS3053 underwent a complex rearrangement on Chr3L at a long inverted repeat (Repeat 124, red lines). Read depth (top panel) and allele frequency (IGV panel) data indicate the copy number breakpoint coincided with LOH (blue region) telomere proximal to the breakpoint. The inverted repeat copies (~3.2 kb, 99.5% sequence identity, separated by ~11.3 kb) each contain four complete ORFs and intergenic sequences. (C) Read depth (top panel) and allele frequency (IGV panel) data for isolate CEC2871 shows an internal chromosome deletion on ChrR with copy number breakpoints (red lines) and LOH (blue) that occur between a long tandem repeat (Repeat family 201, red arrows). The tandem repeat copies (~1.4 kb, 93.8% sequence identity, separated by ~55 kb) each contain one ORF.

Figure 3—figure supplement 1. Segmental aneuploidies occur at previously characterized and uncharacterized long repeat sequences.

Representative segmental aneuploidy breakpoints from Figure 3. Whole genome sequence data plotted as a log2 ratio and converted to chromosome copy number (Y-axis) and chromosome location (X-axis) using YMAP. Copy number variation breakpoints (red and green arrowheads) are indicated. Each breakpoint is associated with a long repeat sequence (red or green arrow) shown in the gene track, and annotated genomic features are indicated with black arrows, below the gene track (A-J, Supplementary file 3). Segmental chromosome aneuploidies from the indicated isolates occur within (A) Chr1 repeat family 14, containing ORFs HGT1 and HGT2; (B) Chr2 repeat family 93, containing two uncharacterized ORFs; (C) Chr3 repeat family 124 containing eight ORFs and associated intergenic sequences; (D) CEN4 repeat family 151; (E) CEN5 repeat family 161, containing two ORFs; (F) Chr6 repeat family 137, containing the ALS gene family; (G) a complex repeat region on Chr7 with both inverted and tandem repeat sequences containing five uncharacterized ORFs; and (H) ChrR repeat region containing the rDNA array. Two examples of complex segmental aneuploidies involving more than one repeat family (I and J). (I) Chr1 repeat family 65 is associated with a centromere proximal amplification, while repeat family 40 is associated with a chromosome truncation event. (J) Example of a segmental aneuploidy flanked by two different repeat families. An internal deletion is flanked by repeat family 14 and family 9 in clinical isolate FH5. Family 9 is the only inter-chromosomal repeat associated with any observed copy number breakpoint.