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Neurotropic dissemination caused by this fungus has been reported in immunocompromised, but also immunocompetent individuals. If untreated, the infection is fatal. Outside of humans, the environmental niche of R. mackenziei is unknown, and the fungus has been only cultured from brain biopsies. In this paper, we describe the whole-genome resequencing of two R. mackenziei strains from patients in Saudi Arabia and Qatar. We assessed intraspecies variation and genetic signatures to uncover the genomic basis of the pathogenesis, and potential niche adaptations. We found that the duplicated genes (paralogs) are more susceptible to accumulating significant mutations. Comparative genomics with other filamentous ascomycetes revealed a diverse arsenal of genes likely engaged in pathogenicity, such as the degradation of aromatic compounds and iron acquisition. In addition, intracellular accumulation of trehalose and choline suggests possible adaptations to the conditions of an arid climate region. Specifically, protein family contractions were found, including short-chain dehydrogenase\/reductase SDR, the cytochrome P450 (CYP) (E-class), and the G-protein \u03b2 WD-40 repeat. Gene composition and metabolic potential indicate extremotolerance and hydrocarbon assimilation, suggesting a possible environmental habitat of oil-polluted desert soil.<\/jats:p>","DOI":"10.1534\/g3.117.300421","type":"journal-article","created":{"date-parts":[[2018,1,12]],"date-time":"2018-01-12T02:00:16Z","timestamp":1515722416000},"page":"909-922","source":"Crossref","is-referenced-by-count":26,"title":["Genomic Understanding of an Infectious Brain Disease from the Desert"],"prefix":"10.1093","volume":"8","author":[{"given":"Leandro F","family":"Moreno","sequence":"first","affiliation":[{"name":"Westerdijk Fungal Biodiversity Institute, 3584 CT Utrecht, The Netherlands"},{"name":"Institute of Biodiversity and Ecosystem Dynamics, University of Amsterdam, 1090 GE, The Netherlands"},{"name":"Department of Basic Pathology, Federal University of Paran\u00e1 State, Curitiba, PR, Brazil"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Abdalla A O","family":"Ahmed","sequence":"additional","affiliation":[{"name":"Department of Microbiology, College of Medicine, Umm Al-Qura University, 24381 Makkah, Saudi Arabia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bal\u00e1zs","family":"Brankovics","sequence":"additional","affiliation":[{"name":"Westerdijk Fungal Biodiversity Institute, 3584 CT Utrecht, The Netherlands"},{"name":"Institute of Biodiversity and Ecosystem Dynamics, University of Amsterdam, 1090 GE, The Netherlands"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Christina A","family":"Cuomo","sequence":"additional","affiliation":[{"name":"Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts 02142"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Steph B J","family":"Menken","sequence":"additional","affiliation":[{"name":"Institute of Biodiversity and Ecosystem Dynamics, University of Amsterdam, 1090 GE, The Netherlands"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Saad J","family":"Taj-Aldeen","sequence":"additional","affiliation":[{"name":"Microbiology Division, Department of Laboratory Medicine and Pathology, Hamad Medical Corporation, Box 3050, Doha, Qatar"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hani","family":"Faidah","sequence":"additional","affiliation":[{"name":"Department of Microbiology, College of Medicine, Umm Al-Qura University, 24381 Makkah, Saudi Arabia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"J Benjamin","family":"Stielow","sequence":"additional","affiliation":[{"name":"Westerdijk Fungal Biodiversity Institute, 3584 CT Utrecht, The Netherlands"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Marcus de M","family":"Teixeira","sequence":"additional","affiliation":[{"name":"Division of Pathogen Genomics, Translational Genomics Research Institute, Flagstaff, Arizona 86005"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Francesc X","family":"Prenafeta-Bold\u00fa","sequence":"additional","affiliation":[{"name":"GIRO Joint Research Unit IRTA-UPC, Torre Marimon, Caldes de Montbui, E-08140, Barcelona, Catalonia, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Vania A","family":"Vicente","sequence":"additional","affiliation":[{"name":"Department of Basic Pathology, Federal University of Paran\u00e1 State, Curitiba, PR, Brazil"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sybren","family":"de Hoog","sequence":"additional","affiliation":[{"name":"Westerdijk Fungal Biodiversity Institute, 3584 CT Utrecht, The Netherlands"},{"name":"Institute of Biodiversity and Ecosystem Dynamics, University of Amsterdam, 1090 GE, The Netherlands"},{"name":"Department of Basic Pathology, Federal University of Paran\u00e1 State, Curitiba, PR, Brazil"},{"name":"Center of Expertise in Mycology of Radboudumc\/CWZ, Nijmegen, 6525 GA, The Netherlands"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2018,3,1]]},"reference":[{"key":"2021042013301262000_bib1","doi-asserted-by":"crossref","first-page":"57","DOI":"10.3114\/sim.2007.58.03","article-title":"Phylogenetic and morphotaxonomic revision of Ramichloridium and allied genera.","volume":"58","author":"Arzanlou","year":"2007","journal-title":"Stud. 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