Supplementary data: The pangenome of Candida albicans as a genomic window into eukaryotic biodiversity

Supplementary Figure S0. Complete pipeline workflow of the exploratory pangenome analysis of C. albicans with each associated bioinformatic tools and their parameters. Every version of each tool is addressed in the main text. Supplementary Figure S1. Quality scores of C. albicans paired-end reads before and after trimming. Mean Phred quality scores per base position are shown for (S1A) raw reads and (S1B) paired reads after quality filtering with Trimmomatic. Supplementary Figure S2. Summary of contig number according to bp size in the assembly quality metrics for 14 C. albicans genomes evaluated with QUAST and visualized through MultiQC. Supplementary Figure 3. (S3A) illustrates the total number of genes identified per sample, (S3B) details the distribution of gene lengths (bp, log10 scale) for each sample. Supplementary Figure 4. (S4A) Shows the amount of orthogroups classified into the categories: core, accessory, and singleton. (S4B) Distribution of orthogroups by category in individual genomes. Supplementary Figure S5. Summary count of the top 20 most abundant Pfam domains (S5B), and ortholog assignment for top 15 species in the C. albicans pangenome analysis using eggNOGG mapper. Supplementary Table 1. Results obtained from the orthology inference analysis done with OrthoFinder, shown a presence/absence table of the orthogroups by GCA. 0 represents absence, and 1 means presence. Supplementary Table 2. Results obtained from the functional annotation analysis done with Funannotate, showing each gene with its assigned category (if any).