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).补充图S0：白色念珠菌（C. albicans）探索性泛基因组分析的完整流程工作流，包含各关联生物信息学工具及其参数设置。所有工具的版本均在正文中说明。 补充图S1：白色念珠菌双端测序读段（paired-end reads）修剪前后的质量分数。展示了各碱基位置的平均Phred质量分数，其中(S1A)为原始读段，(S1B)为经Trimmomatic进行质量过滤后的双端读段。 补充图S2：针对14株白色念珠菌基因组的组装质量评估指标中，基于碱基对（bp）长度统计的重叠群（contig）数量汇总。该分析通过QUAST完成评估，并由MultiQC进行可视化展示。 补充图3：(S3A)展示了每个样本中鉴定得到的基因总数，(S3B)详细呈现了各样本的基因长度（碱基对，以log10为刻度）分布情况。 补充图S4：(S4A)展示了划分为核心、附属及单例三类的直系同源簇（orthogroups）数量，(S4B)呈现了各基因组中不同类别直系同源簇的分布情况。 补充图S5：丰度排名前20的Pfam结构域（Pfam domains）数量汇总(S5B)，以及利用eggNOG mapper对白色念珠菌泛基因组分析中排名前15的物种进行的直系同源基因注释结果。 补充表1：通过OrthoFinder完成的直系同源基因推断分析结果，展示了基于GCA的直系同源簇存在/缺失表，其中0表示缺失，1表示存在。 补充表2：通过Funannotate完成的功能注释分析结果，展示了每个基因及其所归属的功能类别（如存在对应类别）。