Amos B, Aurrecoechea C, Barba M et al (2022) VEuPathDB: the eukaryotic pathogen, vector and host bioinformatics resource center. Nucleic Acids Res 50:D898–D911. https://doi.org/10.1093/nar/gkab929

CAS  Article  PubMed  Google Scholar 

Barber AE, Sae-Ong T, Kang K et al (2021) Aspergillus fumigatus pan-genome analysis identifies genetic variants associated with human infection. Nat Microbiol 6:1526–1536. https://doi.org/10.1038/s41564-021-00993-x

CAS  Article  PubMed  Google Scholar 

Barker BM, Kroll K, Vödisch M et al (2012) Transcriptomic and proteomic analyses of the Aspergillus fumigatus hypoxia response using an oxygen-controlled fermenter. BMC Genomics 13:62. https://doi.org/10.1186/1471-2164-13-62

CAS  Article  PubMed  PubMed Central  Google Scholar 

Bertuzzi M, van Rhijn N, Krappmann S et al (2021) On the lineage of Aspergillus fumigatus isolates in common laboratory use. Med Mycol 59:7–13. https://doi.org/10.1093/mmy/myaa075

CAS  Article  PubMed  Google Scholar 

Brakhage AA, Liebmann B (2005) Aspergillus fumigatus conidial pigment and cAMP signal transduction: significance for virulence. Med Mycol 43:75–82. https://doi.org/10.1080/13693780400028967

CAS  Article  Google Scholar 

Castresana J (2000) Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol 17:540–552. https://doi.org/10.1093/oxfordjournals.molbev.a026334

CAS  Article  PubMed  Google Scholar 

Chang YC, Khanal Lamichhane A, Garraffo HM et al (2014) Molecular mechanisms of hypoxic responses via unique roles of Ras1, Cdc24 and Ptp3 in a human fungal pathogen Cryptococcus neoformans. PLoS Genet 10:1004292. https://doi.org/10.1371/journal.pgen.1004292

CAS  Article  Google Scholar 

Chen S, Zhou Y, Chen Y, Gu J (2018) fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics 34:i884–i890. https://doi.org/10.1093/bioinformatics/bty560

CAS  Article  PubMed  PubMed Central  Google Scholar 

DeLano W (2002) Pymol: An open-source molecular graphics tool. CCP4 Newsletter on Protein Crystallography 82–92

Denning DW (1998) Invasive aspergillosis. Clin Infect Dis 26:781–803. https://doi.org/10.1086/513943

CAS  Article  PubMed  Google Scholar 

Desai PR, van Wijlick L, Kurtz D et al (2015) Hypoxia and temperature regulated morphogenesis in Candida albicans. PLoS Genet 11:e1005447. https://doi.org/10.1371/journal.pgen.1005447

CAS  Article  PubMed  PubMed Central  Google Scholar 

Fortwendel JR, Panepinto JC, Seitz AE et al (2004) Aspergillus fumigatus rasA and rasB regulate the timing and morphology of asexual development. Fungal Genet Biol 41:129–139. https://doi.org/10.1016/j.fgb.2003.10.004

CAS  Article  PubMed  Google Scholar 

Fortwendel JR, Zhao W, Bhabhra R et al (2005) A fungus-specific Ras homolog contributes to the hyphal growth and virulence of Aspergillus fumigatus. Eukaryot Cell 4:1982–1989. https://doi.org/10.1128/EC.4.12.1982-1989.2005

CAS  Article  PubMed  PubMed Central  Google Scholar 

Fortwendel JR, Juvvadi PR, Rogg LE et al (2012) Plasma membrane localization is required for RasA-mediated polarized morphogenesis and virulence of Aspergillus fumigatus. Eukaryot Cell 11:966–977. https://doi.org/10.1128/EC.00091-12

CAS  Article  PubMed  PubMed Central  Google Scholar 

Grahl N, Dinamarco TM, Willger SD et al (2012) Aspergillus fumigatus mitochondrial electron transport chain mediates oxidative stress homeostasis, hypoxia responses and fungal pathogenesis. Mol Microbiol 84:383–399. https://doi.org/10.1111/j.1365-2958.2012.08034.x

CAS  Article  PubMed  PubMed Central  Google Scholar 

Hagiwara D, Takahashi-Nakaguchi A, Toyotome T et al (2013) NikA/TcsC histidine kinase is involved in conidiation, hyphal morphology, and responses to osmotic stress and antifungal chemicals in Aspergillus fumigatus. PLoS ONE 8:e80881. https://doi.org/10.1371/journal.pone.0080881

CAS  Article  PubMed  PubMed Central  Google Scholar 

Hagiwara D, Takahashi H, Watanabe A et al (2014) Whole-genome comparison of Aspergillus fumigatus strains serially isolated from patients with aspergillosis. J Clin Microbiol 52:4202–4209. https://doi.org/10.1128/JCM.01105-14

CAS  Article  PubMed  PubMed Central  Google Scholar 

Hall A (1998) Rho GTPases and the actin cytoskeleton. Science 279:509–514. https://doi.org/10.1126/science.279.5350.509

CAS  Article  PubMed  Google Scholar 

Harispe L, Portela C, Scazzocchio C et al (2008) Ras GTPase-activating protein regulation of actin cytoskeleton and hyphal polarity in Aspergillus nidulans. Eukaryot Cell 7:141–153. https://doi.org/10.1128/EC.00346-07

CAS  Article  PubMed  Google Scholar 

Howard SJ, Cerar D, Anderson MJ et al (2009) Frequency and evolution of azole resistance in Aspergillus fumigatus associated with treatment failure. Emerg Infect Dis 15:1068–1076. https://doi.org/10.3201/eid1507.090043

CAS  Article  PubMed  PubMed Central  Google Scholar 

Jumper J, Evans R, Pritzel A et al (2021) Highly accurate protein structure prediction with AlphaFold. Nature 596:583–589. https://doi.org/10.1038/s41586-021-03819-2

CAS  Article  PubMed  PubMed Central  Google Scholar 

Katoh K, Standley DM (2013) MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol 30:772–780. https://doi.org/10.1093/molbev/mst010

CAS  Article  PubMed  PubMed Central  Google Scholar 

Kowalski CH, Kerkaert JD, Liu KW et al (2019) Fungal biofilm morphology impacts hypoxia fitness and disease progression. Nat Microbiol 4:2430–2441. https://doi.org/10.1038/s41564-019-0558-7

CAS  Article  PubMed  PubMed Central  Google Scholar 

Kowalski CH, Beattie SR, Fuller KK et al (2016) Heterogeneity among isolates reveals that fitness in low oxygen correlates with Aspergillus fumigatus virulence. mBio 7:e01515-16. https://doi.org/10.1128/mBio.01515-16

Article  PubMed  PubMed Central  Google Scholar 

Latgé JP (1999) Aspergillus fumigatus and aspergillosis. Clin Microbiol Rev 12:310–350. https://doi.org/10.1128/CMR.12.2.310

Article  PubMed  PubMed Central  Google Scholar 

Latgé JP (2001) The pathobiology of Aspergillus fumigatus. Trends Microbiol 9:382–389. https://doi.org/10.1016/S0966-842X(01)02104-7

Article  PubMed  Google Scholar 

Li L, Stoeckert CJ, Roos DS (2003) OrthoMCL: identification of ortholog groups for eukaryotic genomes. Genome Res 13:2178–2189. https://doi.org/10.1101/gr.1224503

CAS  Article  PubMed  PubMed Central  Google Scholar 

Li H, Handsaker B, Wysoker A et al (2009) The Sequence Alignment/Map format and SAMtools. Bioinformatics 25:2078–2079. https://doi.org/10.1093/bioinformatics/btp352

CAS  Article  PubMed  PubMed Central  Google Scholar 

Li H (2013) Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. arXiv:1303.3997. https://doi.org/10.48550/arXiv.1303.3997

Liu W, Xie Y, Ma J et al (2015) IBS: an illustrator for the presentation and visualization of biological sequences. Bioinformatics 31:3359–3361. https://doi.org/10.1093/bioinformatics/btv362

CAS  Article  PubMed  PubMed Central  Google Scholar 

Majima H, Arai T, Kusuya Y et al (2021) Genetic differences between Japan and other countries in cyp51A polymorphisms of Aspergillus fumigatus. Mycoses 64:1354–1365. https://doi.org/10.1111/myc.13370

CAS  Article  PubMed  Google Scholar 

Mayorga ME, Timberlake WE (1992) The developmentally regulated Aspergillus nidulans wA gene encodes a polypeptide homologous to polyketide and fatty acid synthases. Mol Gen Genet 235:205–212. https://doi.org/10.1007/BF00279362

CAS  Article  PubMed  Google Scholar 

Norton TS, Fortwendel JR (2014) Control of Ras-mediated signaling in Aspergillus fumigatus. Mycopathologia 178:325–330. https://doi.org/10.1007/s11046-014-9765-1

CAS  Article  PubMed  PubMed Central  Google Scholar 

Ries LNA, Steenwyk JL, de Castro PA et al (2019) Nutritional heterogeneity among Aspergillus fumigatus strains has consequences for virulence in a strain- and host-dependent manner. Front Microbiol 10:854. https://doi.org/10.3389/fmicb.2019.00854

Article  PubMed  PubMed Central  Google Scholar 

Scheffzek K, Ahmadian MR, Kabsch W et al (1997) The Ras-RasGAP complex: structural basis for GTPase activation and its loss in oncogenic Ras mutants. Science 277:333–338. https://doi.org/10.1126/science.277.5324.333

CAS  Article  PubMed  Google Scholar 

Shimizu K, Keller NP (2001) Genetic involvement of a cAMP-dependent protein kinase in a G protein signaling pathway regulating morphological and chemical transitions in Aspergillus nidulans. Genetics 157:591–600. https://doi.org/10.1093/genetics/157.2.591

CAS  Article  PubMed  PubMed Central  Google Scholar 

Som T, Kolaparthi VS (1994) Developmental decisions in Aspergillus nidulans are modulated by Ras activity. Mol Cell Biol 14:5333–5348. https://doi.org/10.1128/mcb.14.8.5333-5348.1994

CAS  Article  PubMed  PubMed Ce