aCGH. (A) Gene copy number of the two parental wild isolate haploids. CBS999.97(1-2, wt) genomic DNA was used as a reference to measure DNA copy number changes of CBS999.97(1-1, re) and vice versa. Each line in the histogram represents one oligonucleotide and its position in the CBS999.97(1-2, re) and CBS999.97(1-2, wt) genomic sequence. The CBS999.97(1-2, wt) genome, such as that of QM6a(1-2, wt) , comprises 89 scaffolds. Moreover, three contiguous scaffolds (27, 28, 36) were reassembled into a much larger scaffold, scaffold M. The length of scaffold M is slightly shorter than that of scaffold 11. Normalized means of gene copy number for the oligonucleotides covering the 87 scaffolds are shown. The 87 scaffolds are ordered from left to right according to their length. (B) Gene copy number of four representative ascospores (numbers 1, 5, 9, and 13) of asci III (Figure 1B) with 16 viable ascospores. (C) Gene copy number of two representative ascospores (numbers 1 and 9) of asci IV (Figure 1B) with eight inviable ascospores. (D) Gene copy number of two representative ascospores (numbers 1, 9, and 13) of asci I (Figure 1B) with 12 inviable ascospores. The three strains with duplicated segments (D1-SAN, D2-SAN, and D3-SAN) and the three euploid control strains (N0-Euploidy, N1-Euploidy, and N2-Euploidy) are also indicated.