Identifying CGRs in strain 118. (A) CGH microarray analysis, displaying results for Chromosomes II and III. The large green region corresponds to the deletion surrounding the repeats, whereas the red region corresponds to the duplication surrounding the SCT1 locus. By examining the hybridization values for individual oligonucleotides on the microarrays, we found that the small red and green regions depicted in this figure do not represent true duplications and deletions, respectively. (B) Nanopore sequencing coverage maps of Chromosomes III and II, generated via UGENE, with a red arrow highlighting the deletion boundaries, and a green arrow indicating a duplication. (C) Ribbon single-read view highlighting a long read that captured the entire gene conversion event, showing a ∼20-kb insertion of Chromosome II in place of the deleted region on Chromosome III. (D) Single base pair resolution of the 5′ and 3′ junctions between Chromosomes III and II. The 5′ junction shows that the break and repair occurred within the (GAA)n repeats. The 3′ junction shows that the recombination event occurred within Ty elements on Chromosomes II and III. The gray region represents a 23-bp window of identity, with SNPs on either side identifying the specific Ty element (Supplemental Fig. S5D). The unannotated Ty1 element is adjacent to YCLWTy2-1 (Supplemental Fig. S3). (E) Diagram of the CGR event resulting in a gene conversion. Chromosome maps have the same format as in Figure 1A. Relevant features are labeled. Purple arrows indicate sites of HR invasion. The top portion displays the broken Chromosome III, processed to expose ends for HR, and the donor Chromosome II. The bottom portion displays the final chromosome products. See main text for details.
