Extended Data Fig. 1: Strain selection and genotyping.
a) Selection of in vitro and in vivo evolved isolates for genotyping based on resistance [RR(AUC) > 1] and susceptibility ranges (BDA MIC range 2 ≤ MIC < 16 µg/ml and ETEST® MIC range of 1.5 ≤ MIC < 32 µg/ml) observed in clinical AMB resistant C. auris strains. Pie chart shows proportions of strains containing ERG6, ERG11 and/or ERG3 variation in 50 selected strains (targeted sequencing and WGS). Details of all genotyped strains can be found in Supplementary Table 2 (Supplementary). b) Graphic representation of variations found in genes involved in ergosterol biosynthesis in selected WGS strains. Lollipop pictograms indicate mutations, indels or frameshifts (nucleotide deletion or insertion), brackets indicate larger deletions (more details see Table 1). A partial translocation in NCP1 in strain 14 is not displayed here but is shown separately in Supplementary Fig. 3 (Supplementary). Colors of lolipops indicate clade origin (legend see Fig. 1b,/c). Functional domains are annotated as GHMPK(N/C): galacto-homoserine, mevalonate and phosphomevalonate kinases (N/C)-terminal domain, SSD: sterol sensing domain, HMG-CoA R: HMG-CoA reductase catalytic domain, ACAT(N/C)D: acetyl-coenzyme A acetyltransferases (N/C)-terminal domain, FNOS: flavodoxin/NO synthase, BD: binding domain, FAH: fatty acid hydrοxylase, SAM: S-adenosyl-methionine, SMC: Sterol methyltransferase C-terminal, a: active site, b: conserved site, g: iron binding site (C465), d: SAM binding residues (129-135,152,153,179-181). c–f) Sequencing read coverage of Clade I (C), III (D), IV (E) and V (F) strains. Relative coverage is plotted per chromosome position based on a fully assembled genome of each clade as described in the Methods section. Columns represent the different chromosomes (Chr) and rows indicate different strains. Strain 1, 10, 18 and 30 are the parental strains of Clade I, III, IV and V respectively, indicated as ‘wt’ (wild type).
