{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,29]],"date-time":"2026-05-29T14:50:26Z","timestamp":1780066226052,"version":"3.54.0"},"reference-count":105,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2020,5,12]],"date-time":"2020-05-12T00:00:00Z","timestamp":1589241600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Genet."],"DOI":"10.3389\/fgene.2020.00459","type":"journal-article","created":{"date-parts":[[2020,5,12]],"date-time":"2020-05-12T07:52:56Z","timestamp":1589269976000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":62,"title":["Genomic and Phenotypic Heterogeneity of Clinical Isolates of the Human Pathogens Aspergillus fumigatus, Aspergillus lentulus, and Aspergillus fumigatiaffinis"],"prefix":"10.3389","volume":"11","author":[{"given":"Renato A. C.","family":"dos Santos","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jacob L.","family":"Steenwyk","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Olga","family":"Rivero-Menendez","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Matthew E.","family":"Mead","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lilian P.","family":"Silva","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rafael W.","family":"Bastos","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ana","family":"Alastruey-Izquierdo","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gustavo H.","family":"Goldman","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Antonis","family":"Rokas","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2020,5,12]]},"reference":[{"key":"B1","doi-asserted-by":"publisher","first-page":"155","DOI":"10.1016\/j.riam.2010.10.003","article-title":"What makes Aspergillus fumigatus a successful pathogen? Genes and molecules involved in invasive aspergillosis.","volume":"27","author":"Abad","year":"2010","journal-title":"Rev. Iberoam. Micol."},{"key":"B2","doi-asserted-by":"publisher","DOI":"10.1128\/mBio.00536-15","article-title":"Genomic context of azole resistance mutations in Aspergillus fumigatus determined using whole-genome sequencing.","volume":"6","author":"Abdolrasouli","year":"2015","journal-title":"mBio"},{"key":"B3","doi-asserted-by":"publisher","first-page":"850","DOI":"10.1111\/cea.12141","article-title":"Allergic bronchopulmonary aspergillosis: review of literature and proposal of new diagnostic and classification criteria.","volume":"43","author":"Agarwal","year":"2013","journal-title":"Clin. Exp. Allergy"},{"key":"B4","doi-asserted-by":"publisher","first-page":"427","DOI":"10.1007\/s11046-014-9775-z","article-title":"Antifungal susceptibility profile of cryptic species of aspergillus.","volume":"178","author":"Alastruey-Izquierdo","year":"2014","journal-title":"Mycopathologia"},{"key":"B5","doi-asserted-by":"publisher","first-page":"403","DOI":"10.1016\/S0022-2836(05)80360-2","article-title":"Basic local alignment search tool.","volume":"215","author":"Altschul","year":"1990","journal-title":"J. Mol. Biol."},{"key":"B6","article-title":"Subcommittee on Antifungal Susceptibility Testing of the Escmid European Committee for Antimicrobial Susceptibility Testing","author":"Arendrup","year":"2020","journal-title":"EUCAST DEFINITIVE DOCUMENT E.DEF 9.3.1: Method for the Determination of Broth Dilution Minimum Inhibitory Concentrations of Antifungal Agents for Conidia Forming Moulds."},{"key":"B7","doi-asserted-by":"publisher","first-page":"625","DOI":"10.1128\/EC.4.3.625-632.2005","article-title":"Aspergillus lentulus sp. nov., a new sibling species of A. fumigatus.","volume":"4","author":"Balajee","year":"2005","journal-title":"Eukaryot. Cell"},{"key":"B8","doi-asserted-by":"publisher","first-page":"3138","DOI":"10.1128\/JCM.01070-09","article-title":"Molecular identification of Aspergillus species collected for the transplant-associated infection surveillance network.","volume":"47","author":"Balajee","year":"2009","journal-title":"J. Clin. Microbiol."},{"key":"B9","doi-asserted-by":"publisher","first-page":"1197","DOI":"10.1128\/AAC.48.4.1197-1203.2004","article-title":"Aspergillus fumigatus variant with decreased susceptibility to multiple antifungals.","volume":"48","author":"Balajee","year":"2004","journal-title":"Antimicrob. Agents Chemother."},{"key":"B10","doi-asserted-by":"publisher","first-page":"455","DOI":"10.1089\/cmb.2012.0021","article-title":"SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing.","volume":"19","author":"Bankevich","year":"2012","journal-title":"J. Comput. Biol."},{"key":"B11","doi-asserted-by":"publisher","DOI":"10.3390\/jof4010039","article-title":"FungiDB: an integrated bioinformatic resource for fungi and oomycetes.","volume":"4","author":"Basenko","year":"2018","journal-title":"J. Fungi"},{"key":"B12","doi-asserted-by":"crossref","DOI":"10.1128\/mSphere.00153-20","article-title":"Functional characterization of clinical isolates of the opportunistic fungal pathogen Aspergillus nidulans.","volume":"5","author":"Bastos","year":"2020","journal-title":"mSphere"},{"key":"B13","doi-asserted-by":"publisher","first-page":"1175","DOI":"10.2217\/fmb-2018-0059","article-title":"Responding to the emergence of antifungal drug resistance: perspectives from the bench and the bedside.","volume":"13","author":"Beardsley","year":"2018","journal-title":"Fut. Microbiol."},{"key":"B14","doi-asserted-by":"publisher","DOI":"10.1038\/s41579-019-0322-2","article-title":"Drug resistance and tolerance in fungi.","volume":"18","author":"Berman","year":"2020","journal-title":"Nat. Rev. Microbiol."},{"key":"B15","doi-asserted-by":"publisher","first-page":"2114","DOI":"10.1093\/bioinformatics\/btu170","article-title":"Trimmomatic: a flexible trimmer for Illumina sequence data.","volume":"30","author":"Bolger","year":"2014","journal-title":"Bioinformatics"},{"key":"B16","doi-asserted-by":"publisher","DOI":"10.1126\/scitranslmed.3004404","article-title":"Hidden killers: human fungal infections.","volume":"4","author":"Brown","year":"2012","journal-title":"Sci. Transl. Med."},{"key":"B17","doi-asserted-by":"publisher","first-page":"1972","DOI":"10.1093\/bioinformatics\/btp348","article-title":"trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses.","volume":"25","author":"Capella-Gutierrez","year":"2009","journal-title":"Bioinformatics"},{"key":"B18","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2019.03127","article-title":"Uncovering new mutations conferring azole resistance in the Aspergillus fumigatus cyp51A Gene.","volume":"10","author":"Chen","year":"2020","journal-title":"Front. Microbiol."},{"key":"B19","doi-asserted-by":"publisher","first-page":"80","DOI":"10.1016\/S1877-1203(13)70353-7","article-title":"A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3.","volume":"6","author":"Cingolani","year":"2013","journal-title":"Fly (Austin)"},{"key":"B20","doi-asserted-by":"publisher","first-page":"1422","DOI":"10.1093\/bioinformatics\/btp163","article-title":"Biopython: freely available Python tools for computational molecular biology and bioinformatics.","volume":"25","author":"Cock","year":"2009","journal-title":"Bioinformatics"},{"key":"B21","doi-asserted-by":"publisher","first-page":"1034","DOI":"10.1002\/ps.3263","article-title":"Overexpression of the sterol 14\u03b1\u2212demethylase gene (MgCYP51) in Mycosphaerella graminicola isolates confers a novel azole fungicide sensitivity phenotype.","volume":"68","author":"Cools, Hans","year":"2012","journal-title":"Pest. Manag. Sci."},{"key":"B22","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-017-1151-0","article-title":"Comparative genomics reveals high biological diversity and specific adaptations in the industrially and medically important fungal genus Aspergillus.","volume":"18","author":"de Vries","year":"2017","journal-title":"Genome Biol."},{"key":"B23","doi-asserted-by":"publisher","first-page":"45","DOI":"10.1183\/13993003.00583-2015","article-title":"Chronic pulmonary aspergillosis: rationale and clinical guidelines for diagnosis and management.","volume":"47","author":"Denning","year":"2016","journal-title":"Eur. Respir. J."},{"key":"B24","doi-asserted-by":"publisher","first-page":"491","DOI":"10.1038\/ng.806","article-title":"A framework for variation discovery and genotyping using next-generation DNA sequencing data.","volume":"43","author":"Depristo","year":"2011","journal-title":"Nat. Genet."},{"key":"B25","doi-asserted-by":"publisher","first-page":"3092","DOI":"10.1128\/aac.00088-08","article-title":"Mutations in the fks1 gene in Candida albicans, C. tropicalis, and C. krusei correlate with elevated caspofungin MICs uncovered in AM3 medium using the method of the European committee on antibiotic susceptibility testing.","volume":"52","author":"Desnos-Ollivier","year":"2008","journal-title":"Antimicrob. Agents Chemother."},{"key":"B26","doi-asserted-by":"publisher","first-page":"1065","DOI":"10.1128\/CMR.00095-16","article-title":"Molecular tools for the detection and deduction of azole antifungal drug resistance phenotypes in Aspergillus species.","volume":"30","author":"Dudakova","year":"2017","journal-title":"Clin. Microbiol. Rev."},{"key":"B27","doi-asserted-by":"crossref","DOI":"10.1186\/s13059-019-1832-y","article-title":"OrthoFinder: phylogenetic orthology inference for comparative genomics.","volume":"20","author":"Emms","year":"2019","journal-title":"Genome Biol."},{"key":"B28","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pgen.1000046","article-title":"Genomic islands in the pathogenic filamentous fungus Aspergillus fumigatus.","volume":"4","author":"Fedorova","year":"2008","journal-title":"PLoS Genet."},{"key":"B29","doi-asserted-by":"publisher","first-page":"739","DOI":"10.1126\/science.aap7999","article-title":"Worldwide emergence of resistance to antifungal drugs challenges human health and food security.","volume":"360","author":"Fisher","year":"2018","journal-title":"Science"},{"key":"B30","doi-asserted-by":"publisher","first-page":"475","DOI":"10.4161\/viru.1.6.12985","article-title":"Methods for using Galleria mellonella as a model host to study fungal pathogenesis.","volume":"1","author":"Fuchs","year":"2010","journal-title":"Virulence"},{"key":"B31","doi-asserted-by":"publisher","DOI":"10.1128\/mBio.01517-16","article-title":"Aspergillus fumigatus photobiology illuminates the marked heterogeneity between isolates.","volume":"7","author":"Fuller","year":"2016","journal-title":"mBio"},{"key":"B32","doi-asserted-by":"publisher","first-page":"2305","DOI":"10.1128\/aac.00262-08","article-title":"A naturally occurring proline-to-alanine amino acid change in Fks1p in Candida parapsilosis, Candida orthopsilosis, and Candida metapsilosis accounts for reduced echinocandin susceptibility.","volume":"52","author":"Garcia-Effron","year":"2008","journal-title":"Antimicrob. Agents Chemother."},{"key":"B33","doi-asserted-by":"publisher","DOI":"10.1128\/AAC.00241-18","article-title":"Insight into the significance of Aspergillus fumigatus cyp51A polymorphisms.","volume":"62","author":"Garcia-Rubio","year":"2018","journal-title":"Antimicrob. Agents Chemother."},{"key":"B34","doi-asserted-by":"publisher","first-page":"599","DOI":"10.1007\/s40265-017-0714-4","article-title":"Triazole resistance in Aspergillus species: an emerging problem.","volume":"77","author":"Garcia-Rubio","year":"2017","journal-title":"Drugs"},{"key":"B35","doi-asserted-by":"publisher","first-page":"535","DOI":"10.1016\/j.eimc.2018.03.018","article-title":"Executive summary of clinical practice guideline for the management of invasive diseases caused by Aspergillus: 2018 update by the GEMICOMED-SEIMC\/REIPI.","volume":"37","author":"Garcia-Vidal","year":"2019","journal-title":"Enferm. Infecc. Microbiol. Clin."},{"key":"B36","doi-asserted-by":"publisher","first-page":"198","DOI":"10.1111\/myc.12469","article-title":"Epidemiology and molecular mechanisms of antifungal resistance in Candida and Aspergillus.","volume":"59","author":"Gon\u00e7alves","year":"2016","journal-title":"Mycoses"},{"key":"B37","doi-asserted-by":"publisher","first-page":"1072","DOI":"10.1093\/bioinformatics\/btt086","article-title":"QUAST: quality assessment tool for genome assemblies.","volume":"29","author":"Gurevich","year":"2013","journal-title":"Bioinformatics"},{"key":"B38","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2016.01382","article-title":"Epidemiological and genomic landscape of azole resistance mechanisms in Aspergillus fungi.","volume":"7","author":"Hagiwara","year":"2016","journal-title":"Front. Microbiol."},{"key":"B39","doi-asserted-by":"publisher","first-page":"135","DOI":"10.1111\/brv.12440","article-title":"The evolutionary origins of pesticide resistance.","volume":"94","author":"Hawkins","year":"2019","journal-title":"Biol. Rev."},{"key":"B40","doi-asserted-by":"publisher","first-page":"1793","DOI":"10.1093\/molbev\/msu134","article-title":"Paralog re-emergence: a novel, historically contingent mechanism in the evolution of antimicrobial resistance.","volume":"31","author":"Hawkins","year":"2014","journal-title":"Mol. Biol. Evol."},{"key":"B41","doi-asserted-by":"publisher","first-page":"413","DOI":"10.1101\/gr.174623.114","article-title":"Genetic and phenotypic intra-species variation in Candida albicans.","volume":"25","author":"Hirakawa","year":"2015","journal-title":"Genome Res."},{"key":"B42","doi-asserted-by":"publisher","first-page":"518","DOI":"10.1093\/molbev\/msx281","article-title":"UFBoot2: improving the ultrafast bootstrap approximation.","volume":"35","author":"Hoang","year":"2018","journal-title":"Mol. Biol. Evol."},{"key":"B43","first-page":"3","article-title":"DNA mini prep method for Aspergillus fumigatus (and other filamentous fungi)","author":"Holden","year":"1994","journal-title":"Molecular Biology of Pathogenic Fungi, a Laboratory Manual"},{"key":"B44","doi-asserted-by":"publisher","first-page":"1316","DOI":"10.3852\/mycologia.97.6.1316","article-title":"Polyphasic taxonomy of Aspergillus fumigatus and related species.","volume":"97","author":"Hong","year":"2005","journal-title":"Mycologia"},{"key":"B45","doi-asserted-by":"publisher","DOI":"10.1371\/journal.ppat.0030024","article-title":"Essential gene identification and drug target prioritization in Aspergillus fumigatus.","volume":"3","author":"Hu","year":"2007","journal-title":"PLoS Pathog."},{"key":"B46","doi-asserted-by":"publisher","first-page":"465","DOI":"10.1016\/b978-0-12-407863-5.00021-6","article-title":"Microbial community analysis using MEGAN.","volume":"531","author":"Huson","year":"2013","journal-title":"Methods Enzymol."},{"key":"B47","doi-asserted-by":"publisher","DOI":"10.1128\/AAC.01277-17","article-title":"Emergence of echinocandin resistance due to a point mutation in the fks1 gene of Aspergillus fumigatus in a patient with chronic pulmonary aspergillosis.","volume":"61","author":"Jim\u00e9nez-Ortigosa","year":"2017","journal-title":"Antimicrob. Agents Chemother."},{"key":"B48","doi-asserted-by":"publisher","first-page":"1236","DOI":"10.1093\/bioinformatics\/btu031","article-title":"InterProScan 5: genome-scale protein function classification.","volume":"30","author":"Jones","year":"2014","journal-title":"Bioinformatics"},{"key":"B49","doi-asserted-by":"publisher","first-page":"772","DOI":"10.1093\/molbev\/mst010","article-title":"MAFFT multiple sequence alignment software version 7: improvements in performance and usability.","volume":"30","author":"Katoh","year":"2013","journal-title":"Mol. Biol. Evol."},{"key":"B50","doi-asserted-by":"publisher","first-page":"551","DOI":"10.1128\/JCM.43.2.551-555.2005","article-title":"Multiple genetically distinct groups revealed among clinical isolates identified as atypical Aspergillus fumigatus.","volume":"43","author":"Katz","year":"2005","journal-title":"J. Clin. Microbiol."},{"key":"B51","doi-asserted-by":"publisher","DOI":"10.1128\/mBio.00135-17","article-title":"Heterogeneity confounds establishment of \u201ca\u201d model microbial strain.","volume":"8","author":"Keller","year":"2017","journal-title":"mBio"},{"key":"B52","doi-asserted-by":"publisher","first-page":"E753","DOI":"10.1073\/pnas.1715954115","article-title":"Linking secondary metabolites to gene clusters through genome sequencing of six diverse Aspergillus species.","volume":"115","author":"Kj\u00e6rb\u00f8lling","year":"2018","journal-title":"Proc. Natl. Acad. Sci. U.S.A."},{"key":"B53","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-018-28948-z","article-title":"GOATOOLS: a python library for gene ontology analyses.","volume":"8","author":"Klopfenstein","year":"2018","journal-title":"Sci. Rep."},{"key":"B54","doi-asserted-by":"publisher","DOI":"10.1128\/mBio.01515-16","article-title":"Heterogeneity among isolates reveals that fitness in low oxygen correlates with Aspergillus fumigatus virulence.","volume":"7","author":"Kowalski","year":"2016","journal-title":"mBio"},{"key":"B55","doi-asserted-by":"publisher","first-page":"2430","DOI":"10.1038\/s41564-019-0558-7","article-title":"Fungal biofilm morphology impacts hypoxia fitness and disease progression.","volume":"4","author":"Kowalski","year":"2019","journal-title":"Nat. Microbiol."},{"key":"B56","doi-asserted-by":"publisher","DOI":"10.1128\/genomeA.01568-15","article-title":"Draft genome sequence of the pathogenic filamentous fungus Aspergillus lentulus IFM 54703T.","volume":"4","author":"Kusuya","year":"2016","journal-title":"Genome Announc."},{"key":"B57","doi-asserted-by":"publisher","DOI":"10.1128\/genomeA.00834-15","article-title":"Draft genome sequence of the pathogenic filamentous fungus Aspergillus udagawae strain IFM 46973T.","volume":"3","author":"Kusuya","year":"2015","journal-title":"Genome Announc."},{"key":"B58","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2016.00683","article-title":"Aspergillus fumigatus-related species in clinical practice.","volume":"7","author":"Lamoth","year":"2016","journal-title":"Front. Microbiol."},{"key":"B59","doi-asserted-by":"publisher","DOI":"10.1128\/CMR.00140-18","article-title":"Aspergillus fumigatus and aspergillosis in 2019.","volume":"33","author":"Latg\u00e9","year":"2020","journal-title":"Clin. Microbiol. Rev."},{"key":"B60","doi-asserted-by":"publisher","first-page":"1","DOI":"10.18637\/jss.v025.i01","article-title":"FactoMineR: an R package for multivariate analysis.","volume":"25","author":"L\u00ea","year":"2008","journal-title":"J. Stat. Softw."},{"key":"B61","doi-asserted-by":"publisher","first-page":"1754","DOI":"10.1093\/bioinformatics\/btp324","article-title":"Fast and accurate short read alignment with Burrows-Wheeler transform.","volume":"25","author":"Li","year":"2009","journal-title":"Bioinformatics"},{"key":"B62","doi-asserted-by":"publisher","first-page":"2078","DOI":"10.1093\/bioinformatics\/btp352","article-title":"The sequence alignment\/map format and SAMtools.","volume":"25","author":"Li","year":"2009","journal-title":"Bioinformatics"},{"key":"B63","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pbio.2003583","article-title":"Drivers of genetic diversity in secondary metabolic gene clusters within a fungal species.","volume":"15","author":"Lind","year":"2017","journal-title":"PLoS Biol."},{"key":"B64","doi-asserted-by":"publisher","first-page":"2598","DOI":"10.1128\/AAC.05477-11","article-title":"The T788G mutation in the cyp51C gene confers voriconazole resistance in Aspergillus flavus causing aspergillosis.","volume":"56","author":"Liu","year":"2012","journal-title":"Antimicrob. Agents Chemother."},{"key":"B65","doi-asserted-by":"publisher","first-page":"1297","DOI":"10.1101\/gr.107524.110","article-title":"The genome analysis toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data.","volume":"20","author":"McKenna","year":"2010","journal-title":"Genome Res."},{"key":"B66","doi-asserted-by":"crossref","DOI":"10.1128\/mSphere.00018-19","article-title":"Characterizing the pathogenic, genomic, and chemical traits of Aspergillus fischeri, a close relative of the major human fungal pathogen Aspergillus fumigatus.","volume":"4","author":"Mead","year":"2019","journal-title":"mSphere"},{"key":"B67","doi-asserted-by":"publisher","first-page":"186","DOI":"10.1099\/00222615-45-3-186","article-title":"Variation in virulence of Aspergillus fumigatus strains in a murine model of invasive pulmonary aspergillosis.","volume":"45","author":"Mondon","year":"1996","journal-title":"J. Med. Microbiol."},{"key":"B68","doi-asserted-by":"publisher","first-page":"603","DOI":"10.1016\/S0960-9822(98)70232-5","article-title":"The lissencephaly gene product Lis1, a protein involved in neuronal migration, interacts with a nuclear movement protein, NudC.","volume":"8","author":"Morris","year":"1998","journal-title":"Curr. Biol."},{"key":"B69","doi-asserted-by":"publisher","first-page":"3633","DOI":"10.1128\/JCM.01582-14","article-title":"Cryptic and rare Aspergillus species in Brazil: prevalence in clinical samples and in Vitro susceptibility to Triazoles.","volume":"52","author":"Negri","year":"2014","journal-title":"J. Clin. Microbiol."},{"key":"B70","doi-asserted-by":"publisher","first-page":"268","DOI":"10.1093\/molbev\/msu300","article-title":"IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies.","volume":"32","author":"Nguyen","year":"2015","journal-title":"Mol. Biol. Evol."},{"key":"B71","doi-asserted-by":"publisher","first-page":"1151","DOI":"10.1038\/nature04332","article-title":"Genomic sequence of the pathogenic and allergenic filamentous fungus Aspergillus fumigatus.","volume":"438","author":"Nierman","year":"2005","journal-title":"Nature"},{"key":"B72","doi-asserted-by":"publisher","first-page":"143","DOI":"10.1007\/s12154-014-0121-1","article-title":"Resistance to antifungals that target CYP51.","volume":"7","author":"Parker","year":"2014","journal-title":"J. Chem. Biol."},{"key":"B73","doi-asserted-by":"publisher","first-page":"e1","DOI":"10.1093\/cid\/ciw326","article-title":"Practice guidelines for the diagnosis and management of aspergillosis: 2016 update by the infectious diseases society of America.","volume":"63","author":"Patterson","year":"2016","journal-title":"Clin. Infect. Dis."},{"key":"B74","doi-asserted-by":"publisher","DOI":"10.1016\/j.ijantimicag.2019.09.011","article-title":"Azole resistance mechanisms in Aspergillus: update and recent advances.","volume":"55","author":"Perez-Cantero","year":"2020","journal-title":"Int. J. Antimicrob. Agents"},{"key":"B75","doi-asserted-by":"publisher","first-page":"73","DOI":"10.1093\/mmy\/myx119","article-title":"Aspergillus terreus: novel lessons learned on amphotericin B resistance.","volume":"56","author":"Posch","year":"2018","journal-title":"Med. Mycol."},{"key":"B76","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2019.01970","article-title":"Revealing the virulence potential of clinical and environmental Aspergillus fumigatus isolates using whole-genome sequencing.","volume":"10","author":"Pu\u00e9rtolas-Balint","year":"2019","journal-title":"Front. Microbiol."},{"key":"B77","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2019.00854","article-title":"Nutritional heterogeneity among Aspergillus fumigatus strains has consequences for virulence in a strain- and host-dependent manner.","volume":"10","author":"Ries","year":"2019","journal-title":"Front. Microbiol."},{"key":"B78","doi-asserted-by":"publisher","first-page":"1586","DOI":"10.1093\/jac\/dkz078","article-title":"In vitro activity of olorofim (F901318) against clinical isolates of cryptic species of Aspergillus by EUCAST and CLSI methodologies.","volume":"74","author":"Rivero-Menendez","year":"2019","journal-title":"J. Antimicrob. Chemother."},{"key":"B79","doi-asserted-by":"publisher","first-page":"753","DOI":"10.1146\/annurev-micro-030117-020345","article-title":"Molecular evolution of antifungal drug resistance.","volume":"71","author":"Robbins","year":"2017","journal-title":"Annu. Rev. Microbiol."},{"key":"B80","doi-asserted-by":"publisher","DOI":"10.1371\/journal.ppat.1008315","article-title":"Evolving moldy murderers: Aspergillus section Fumigati as a model for studying the repeated evolution of fungal pathogenicity.","volume":"16","author":"Rokas","year":"2020","journal-title":"PLoS Pathog."},{"key":"B81","doi-asserted-by":"publisher","first-page":"607","DOI":"10.1016\/j.ijantimicag.2017.06.018","article-title":"Molecular bases of antifungal resistance in filamentous fungi.","volume":"50","author":"Sharma","year":"2017","journal-title":"Int. J. Antimicrob. Agents"},{"key":"B82","doi-asserted-by":"publisher","DOI":"10.1128\/AAC.01928-17","article-title":"Investigation of multiple resistance mechanisms in voriconazole-resistant Aspergillus flavus clinical isolates from a chest hospital surveillance in Delhi, India.","volume":"62","author":"Sharma","year":"2018","journal-title":"Antimicrob. Agents Chemother."},{"key":"B83","doi-asserted-by":"publisher","first-page":"3210","DOI":"10.1093\/bioinformatics\/btv351","article-title":"BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs.","volume":"31","author":"Sim\u00e3o","year":"2015","journal-title":"Bioinformatics"},{"key":"B84","doi-asserted-by":"crossref","first-page":"S107","DOI":"10.3109\/13693786.2010.523852","article-title":"Pathogenicity of Aspergillus fumigatus mutants assessed in Galleria mellonella matches that in mice.","volume":"49","author":"Slater","year":"2011","journal-title":"Med. Mycol."},{"key":"B85","doi-asserted-by":"publisher","first-page":"4992","DOI":"10.1128\/aac.00774-10","article-title":"Differential Aspergillus lentulus echinocandin susceptibilities are Fksp independent.","volume":"54","author":"Staab","year":"2010","journal-title":"Antimicrob. Agents Chemother."},{"key":"B86","doi-asserted-by":"crossref","first-page":"W309","DOI":"10.1093\/nar\/gkh379","article-title":"AUGUSTUS: a web server for gene finding in eukaryotes.","volume":"32","author":"Stanke","year":"2004","journal-title":"Nucleic Acids Res."},{"key":"B87","doi-asserted-by":"crossref","DOI":"10.1128\/mBio.00925-19","article-title":"Robust phylogenomic time tree for biotechnologically and medically important fungi in the genera Aspergillus and Penicillium.","volume":"10","author":"Steenwyk","year":"2019","journal-title":"mBio"},{"key":"B88","doi-asserted-by":"publisher","first-page":"3707","DOI":"10.1128\/JCM.01704-14","article-title":"Genetic relatedness versus biological compatibility between Aspergillus fumigatus and related species.","volume":"52","author":"Sugui","year":"2014","journal-title":"J. Clin. Microbiol."},{"key":"B89","doi-asserted-by":"publisher","first-page":"439","DOI":"10.1139\/cjm-2017-0749","article-title":"The pathogenicity of Aspergillus fumigatus, drug resistance, and nanoparticle delivery.","volume":"64","author":"Szalewski","year":"2018","journal-title":"Can. J. Microbiol."},{"key":"B90","doi-asserted-by":"publisher","first-page":"353","DOI":"10.1093\/mmy\/myv003","article-title":"Genome sequence comparison of Aspergillus fumigatus strains isolated from patients with pulmonary aspergilloma and chronic necrotizing pulmonary aspergillosis.","volume":"53","author":"Takahashi-Nakaguchi","year":"2015","journal-title":"Med. Mycol."},{"key":"B91","first-page":"57","article-title":"Some probabilistic and statistical problems in the analysis of DNA sequences.","volume":"17","author":"Tavar\u00e9","year":"1986","journal-title":"Lect. Math. Life Sci."},{"key":"B92","doi-asserted-by":"publisher","first-page":"21","DOI":"10.1006\/fgbi.2000.1228","article-title":"Phylogenetic species recognition and species concepts in fungi.","volume":"31","author":"Taylor","year":"2000","journal-title":"Fungal Genet. Biol."},{"key":"B93","author":"Therneau","year":"2020","journal-title":"A Package for Survival Analysis in S. R Package Version 2.37-7."},{"key":"B94","doi-asserted-by":"publisher","first-page":"3031","DOI":"10.1128\/jb.180.12.3031-3038.1998","article-title":"The developmentally regulated alb1 gene of Aspergillus fumigatus: its role in modulation of conidial morphology and virulence.","volume":"180","author":"Tsai","year":"1998","journal-title":"J. Bacteriol."},{"key":"B95","doi-asserted-by":"publisher","DOI":"10.1088\/1751-8113\/44\/8\/085201","article-title":"A \u2018missing\u2019 family of classical orthogonal polynomials.","volume":"44","author":"Vinet","year":"2011","journal-title":"J. Phys. A Math. Theor."},{"key":"B96","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0112963","article-title":"Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement.","volume":"9","author":"Walker","year":"2014","journal-title":"PLoS One"},{"key":"B97","doi-asserted-by":"publisher","first-page":"1189","DOI":"10.1093\/bioinformatics\/btp033","article-title":"Jalview version 2-A multiple sequence alignment editor and analysis workbench.","volume":"25","author":"Waterhouse","year":"2009","journal-title":"Bioinformatics"},{"key":"B98","doi-asserted-by":"crossref","first-page":"D358","DOI":"10.1093\/nar\/gks1116","article-title":"OrthoDB: a hierarchical catalog of animal, fungal and bacterial orthologs.","volume":"41","author":"Waterhouse","year":"2013","journal-title":"Nucleic Acids Res."},{"key":"B99","doi-asserted-by":"publisher","first-page":"91","DOI":"10.1007\/s12275-015-5014-7","article-title":"The molecular mechanism of azole resistance in Aspergillus fumigatus: from bedside to bench and back.","volume":"53","author":"Wei","year":"2015","journal-title":"J. Microbiol."},{"key":"B100","doi-asserted-by":"publisher","first-page":"D459","DOI":"10.1093\/nar\/gkj047","article-title":"PHI-base: a new database for pathogen host interactions.","volume":"34","author":"Winnenburg","year":"2006","journal-title":"Nucleic Acids Res."},{"key":"B101","doi-asserted-by":"publisher","first-page":"306","DOI":"10.1007\/bf00160154","article-title":"Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: approximate methods.","volume":"39","author":"Yang","year":"1994","journal-title":"J. Mol. Evol."},{"key":"B102","doi-asserted-by":"publisher","first-page":"367","DOI":"10.1016\/0169-5347(96)10041-0","article-title":"Among-site rate variation and its impact on phylogenetic analyses.","volume":"11","author":"Yang","year":"1996","journal-title":"Trends Ecol. Evol."},{"key":"B103","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1016\/j.jiph.2019.08.007","article-title":"Recent trends in the epidemiology, diagnosis, treatment, and mechanisms of resistance in clinical Aspergillus species: a general review with a special focus on the Middle Eastern and North African region.","volume":"13","author":"Zakaria","year":"2020","journal-title":"J. Infect. Public Health"},{"key":"B104","doi-asserted-by":"publisher","first-page":"E60","DOI":"10.1111\/j.1399-3062.2012.00779.x","article-title":"Fatal outcome after heart transplantation caused by Aspergillus lentulus.","volume":"14","author":"Zbinden","year":"2012","journal-title":"Transpl. Infect. Dis."},{"key":"B105","doi-asserted-by":"publisher","first-page":"396","DOI":"10.1002\/ps.5127","article-title":"Paralogous Cyp51s mediate the differential sensitivity of Fusarium oxysporum to sterol demethylation inhibitors.","volume":"75","author":"Zheng","year":"2019","journal-title":"Pest Manag. Sci."}],"container-title":["Frontiers in Genetics"],"original-title":[],"link":[{"URL":"https:\/\/www.frontiersin.org\/article\/10.3389\/fgene.2020.00459\/full","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2020,5,12]],"date-time":"2020-05-12T07:53:05Z","timestamp":1589269985000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.frontiersin.org\/article\/10.3389\/fgene.2020.00459\/full"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2020,5,12]]},"references-count":105,"alternative-id":["10.3389\/fgene.2020.00459"],"URL":"https:\/\/doi.org\/10.3389\/fgene.2020.00459","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/2020.02.28.970384","asserted-by":"object"}]},"ISSN":["1664-8021"],"issn-type":[{"value":"1664-8021","type":"electronic"}],"subject":[],"published":{"date-parts":[[2020,5,12]]},"article-number":"459"}}