“Up-regulated and down-regulated genes were defined as differentially expressed genes (DESeq2; p < 0.05) where the log2FC > 0 and log2FC < 0, respectively. Log2FC stands for the number calculated by the DESeq2 software using THS30 as reference strain (TNJ92 untreated cultures vs. THS30 untreated cultures or TNJ92 Cd treated cultures vs. THS30 Cd treated cultures) or untreated cultures as reference conditions (THS30 Cd treated cultures vs. THS30 untreated cultures or TNJ92 Cd treated cultures vs. TNJ92 untreated cultures). Up-regulated and down-regulated genes identified in the CdCl2-treated vs. untreated and in the ΔatfA mutant vs. reference strain comparisons were regarded as stress responsive and AtfA-dependent genes, respectively”.

Gene groups containing functionally related genes were defined as follows:

“Antioxidative enzyme” genes: Genes of known or putative catalases, peroxidases, superoxide dismutases, or of the glutathione/glutaredoxin/thioredoxin system collected from the Aspergillus Genome Database (AspGD; http://www.aspergillusgenome.org; accessed on 2 July 2021).

“Autophagy” genes, “DNA repair” genes, and “P-type ATPase” genes: Genes with “autophagy”, “role in DNA repair”, or “P-type ATPase” feature, respectively, in their general description according to the AspGD.

“Cd2+ efflux pump” genes: Cation transporter genes of “cadmium ion import into vacuole”, “cadmium ion transport”, and “cellular detoxification of cadmium ion” GO terms (AspGD) as well as ygA (AN3624, [41]), an ortholog of A. fumigatus pcaA (Afu1g16130) putative cadmium transporter [8,10].

“Cell wall biosynthesis and degradation genes as well as cell wall integrity pathway” genes: Genes encoding enzymes of cell wall polysaccharide biosynthesis and degradation as well as of the cell wall integrity (protein kinase C) MAPK pathway according to De Groot et al. [42].

“Cys, Met and GSH metabolism” genes: Genes of GSH synthesis and degradation, Cys and Met biosynthesis, transsulfuration pathway, Met cycle., and Met salvage pathway according to the KEGG Pathway Database (https://www.genome.jp/kegg/pathway.html, accessed on 2 July 2021).

“Cys rich protein” genes: Gene encoding proteins with more than 10% Cys content according to the AspGD.

“ER to Golgi vesicle-mediated transport” genes: Genes of the “endoplasmic reticulum to Golgi vesicle-mediated transport” GO term according to the AspGD.

“Fe-S cluster binding protein” genes: Genes of the “iron-sulfur cluster binding” GO term according to the AspGD.

“Folate cycle” genes and “Glyoxylate pathway”genes: Genes of the folate cycle as well as of the glyoxalate cycle according to the KEGG Pathway Database.

“Glycolysis genes”: Genes described by Flipphi et al. [43].

“Phosphorelay response regulator” genes: Genes of the “phosphorelay response regulator activity” and “osmosensory signaling via phosphorelay pathway” GO terms in the AspGD.

“Ribosome biosynthesis” genes: Genes of the “ribosome biogenesis” Aspergillus GO-slim process category (http://www.aspergillusgenome.org/cgi-bin/GO/goTermMapper, accessed on 2 July 2021).

“Secondary metabolism cluster” genes: Manually or experimentally identified secondary metabolite cluster genes according to Inglis et al. [44].

“Squalene-ergosterol pathway” genes: Orthologs of A. fumigatus squalene–ergosterol pathway genes [45].

“Zinc transporter” genes: Genes of the “zinc ion transmembrane transporter activity”, “zinc ion transport”, and “zinc ion transmembrane transport” GO terms in the AspGD.

The enrichment of genes from the above defined genes groups within the up-regulated, down-regulated, stress responsive, and AtfA-dependent gene sets was tested with the “fisher.test” function (Fisher’s exact test; p < 0.05) of the R project (www.R-project.org, accessed on 2 July 2021).

Gene set enrichment analyses with FunCat, GO, and KEGG pathway terms were carried out with the FungiFun2 package (https://elbe.hki-jena.de/fungifun/fungifun.php, accessed on 2 July 2021) using default settings. Hits with adjusted p < 0.05 were taken into consideration during the evaluation process.

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