Table 1.
Metadata information and biological characterization of Candida auris strains isolated in Japan.
Table 2.
Genetic features of chromosomal DNA draft sequences and complete mitochondrial DNA in C. auris JCM 15448.
Fig 1.
Comparative whole genome analysis of C. auris among seven Japanese strains and 126 strains deposited in SRA database.
Phylogenetic analysis with SNVs on core genome regions. 168,815 SNVs were detected in 133 strains. The maximum-likelihood phylogenetic tree was constructed using RAxML version 8.2.0. The clade, metadata, and mapping analysis results are described in the color schemes on the right of the phylogenetic tree.
Fig 2.
Pangenomic analysis of C. auris strains.
(A) The abundance ratio of the accessory gene among the C. auris clades determined using hierarchical cluster analysis. The relative abundance is shown using color gradients. Sixty-one genes were determined to be specific unidentified genes in clade II. (B) Functional prediction analysis in specific unidentified genes of clade II. A pie chart showing the ratio of the 61 genes categorized by protein domain information and/or gene ontology terms. (C) List of specific unidentified genes, which are related to cell wall proteins, in clade II. The predicted functional domains of the amino acid sequences are described in schematic illustrations. In the pangenome of C. auris, ten and three proteins were predicted to be cell wall protein domain-containing proteins and agglutinin domain-containing proteins, respectively. Eight genes coding cell wall-related proteins remain unidentified in only clade II.
Fig 3.
Comparison of copy number variations (CNVs) among four C. auris clades.
(A) A graphic representing the CNV data excluding 22 high variance samples is merged in each clade. A high copy region was defined as having more than 1.6 copies. The conserved CNV regions in each clade are labeled with colored boxes as follows: orange: clade I, yellow: clade II, green: clade IV. Alphabets of small letter indicate the positions of conserved CNVs. CNVs greater than four copies are shown as four copies for ease of interpretation. (B) Phylogenetic tree analysis with conserved CNVs among four clades. The positions of CNV are displayed by alphabets as described above. The copy numbers are showed by a color gradient with black, orange and red. The detailed information of conserved CNVs are described in Table 3.
Table 3.
Unique conserved copy number variations on chromosomal DNA among each C. auris cluster.
Fig 4.
Comparative whole genome analysis of nine strains of clade II C. auris.
(A) Core genome SNV phylogenetic tree of strains belonging to clade II. All-against-all comparisons of SNV counts are shown by a lower triangular matrix using a color gradient with black and yellow. (B) Comparative CNV analysis among strains in clade II. Unique CNV regions are labeled by yellow and light green boxes, and base range is noted on each contig.