Supplemental Material for Mixão et al., 2020

Figure S1. Frequency of 27-mers coverage (k-mer multiplicity) in C. stellatoidea genomic reads. The proportion of 27-mers which are absent (black) or at 1x coverage (red) in C. albicans SC5314 haplotype A is represented in the fill of the density line. The number of k-mers including heterozygous positions (levels of heterozygosity) determine the height of the peaks. The fraction of k-mers not included in the reference relates with the levels of heterozygosity, as they correspond to the alternative haplotype that is not represented in the reference genome.

Figure S2. Distribution of heterozygous variants in C. stellatoidea genome (CBS1905). a) Patterns of heterozygosity and homozygosity in chromosome 6 of C. stellatoidea, C. africana and C. albicans. Two different methodologies to define heterozygous and homozygous genomic regions are shown. In the first three lanes a 100bp distance approach is used, and heterozygous and LOH blocks are marked in light and dark blue, respectively. In the second group of three lanes a 10kb window-based approach is used, and the density in heterozygous SNPs is represented by a yellow to red gradient. b) IGV screenshot of C. stellatoidea read coverage when aligned to C. albicans haplotype A chromosome 6 (635,000 to 645,000bp). Heterozygous blocks separated by homozygous regions can be observed. The differences in the methodologies for definition of heterozygous and homozygous regions can be compared with the IGV screenshot.

Figure S3. Density plot of the haplotype divergence in C. stellatoidea, where the x-axis represents the percentage of haplotype divergence (calculated by the number of heterozygous SNPs divided by the heterozygous block size), and the y-axis corresponds to the blocks density.