Functional characterization of Aspergillus nidulans clinical isolates Supplemental Information
Creators: name: Bastos, Rafael Wesley
name: Valero, Clara
name: Silva, Lilian Pereira
name: Schoen, Taylor
name: Drott, Milton
name: Verônica Brauer
name: Silva-Rocha, Rafael
name: Lind, Abigail
name: Steenwyk, Jacob
name: Rokas, Antonis
name: Rodrigues, Fernando
name: Lagrou, Katrien
name: Marcet-Houben, Marina
name: Gabaldón, Toni
name: McDonnell, Erin
name: Reid, Ian
name: Tsang, Adrian
name: Berl R. Oakley
name: Loures, Flávio Vieira
name: Almeida, Fausto
name: Huttenlocher, Anna
name: Keller, Nancy P.
name: Ries, Laure Nicolas Annick
name: Goldman, Gustavo H.
Publisher: name: figshare
Year: 2020
Subjects: subject: 60505 Mycology
subject: FOS: Biological sciences
subject: FOS: Biological sciences

description: Supplementary Figure S1. The clinical isolates MO80069 and SP-2605-48 are metabolically different from the FGSC-A4 reference strain. Principal component analysis (PCA) of the levels of quantified metabolites identified in biological replicates of all three strains when grown for 16 h in minimal medium supplemented with glucose (A), ethanol (B), acetate (C) and mucin (D).<br><br>Supplementary Figure S2. The clinical isolates MO80069 and SP-2605-48 are metabolically different from the FGSC-A4 reference strain. Hierarchical component analysis (HCA) of the levels of quantified metabolites identified in biological replicates of all three strains when grown for 16 h in minimal medium supplemented with glucose (A), ethanol (B), acetate (C) and mucin (D). <br><br>Supplementary Figure S3. The A. nidulans clinical isolates are sensitive to hydrogen peroxide-induced oxidative stress but not to other physiological-relevant stresses. Strains were grown in tenfold serial dilutions in complete medium supplemented with increasing concentrations of H2O2 for 48 h at 37°C (A), or they were grown from 105spores on glucose minimal medium (GMM) supplemented with increasing concentrations of menadione (B), in the presence of iron-depleted GMM supplemented with the iron chelators BPS and ferrozine (C) and on GMM in the presence of different temperatures (D) for 5 days at 37°C. Standard deviations represent biological triplicates with *p&lt;0.05;**p&lt;0.01; ***p&lt;0.001; ****p&lt;0.0001 in a 2-way ANOVA test when comparing growth of the clinical isolates to the FGSC-A4 reference strain.<br><br>Supplementary Figure S4. The clinical isolates MO80069 and SP-2605-48 are true A. nidulans strains. The phylogenetic tree was constructed based on the CaM, BenA, RPB2 and ITS rDNA sequencing data, which was compared to sequences from other species in the Aspergillus section of Nidulantes.<br><br>Supplementary Table S1. Identified metabolites in the A. nidulansclinical isolates MO80069 and SP-2605-48 and the reference strain FGSC-A4 when grown for 24 h in minimal medium (MM) supplemented with fructose and after transfer to MM supplemented with either glucose, acetate, ethanol or mucin for 16 h. Also shown are the average and standard deviations for normalised (divided by fungal dryweight) metabolite quantities measured in 4 biological replicates and corresponding p-values (p-value &lt; 0.05 was considered significant in ) when comparing metabolite quantity in each clinical isolate to the quantity in the reference strain. In addition fold change of metabolite quantity between the clinical isolates and the reference strain was calculated for all significantly different metabolite quantities. <br><br>Supplementary Table S2. Single nucleotide polymorphisms (SNPs) detected in the genomes of the A. nidulans clinical isolates MO80069 and SP-2605-48 in comparison to the reference strain FGSC A4 and to each other. Nucleotide and amino acid details of each SNP are shown as well as the impact of the resulting SNP mutation. <br><br>Supplementary Table S3. Large scale insertions and deletions (indels) detected in the genomes of the A. nidulans clinical isolates MO80069LAB and SP-2605-48. Genomes were compared to the reference genome of strain FGSC A4. Gene IDs are given if the indels span predicted open reading frames (ORFs). Also shown are the chromosomal location of the indel, the DNA sequence in the reference strain, the DNA sequence of the indel ("=" signifies that the sequence in the clinical isolate is the same as in the reference strain) and the number of basepairs for each indel ("imprecise" denotes all sequences containing an "N", which is a base that could not be identified during sequencing). Individual tabs show indels that are specific to either strain or that are present in both strains. <br>Supplementary Table S4. Number and type of mutation in genes encoding enzymes involved in carbohydrate (C) metabolism, sexual reproduction and cell wall biosynthesis and degradation. Also indicated is the clinical isolate in which the mutation occurs and the resulting nucleotide and amino acid changes.