{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,15]],"date-time":"2026-10-15T14:48:54Z","timestamp":1792075734390,"version":"4.4.0"},"reference-count":67,"publisher":"Oxford University Press (OUP)","issue":"4","license":[{"start":{"date-parts":[[2013,4,1]],"date-time":"2013-04-01T00:00:00Z","timestamp":1364774400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2013,4,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>The opportunistic fungal pathogen Cryptococcus neoformans is a leading cause of mortality among the human immunodeficiency virus\/acquired immunodeficiency syndrome population and is known for frequently causing life-threatening relapses. To investigate the potential contribution of in-host microevolution to persistence and relapse, we have analyzed two serial isolates obtained from a patient with acquired immunodeficiency syndrome who suffered an initial and relapse episode of cryptococcal meningoencephalitis. Despite being identical by multilocus sequence typing, the isolates differ phenotypically, exhibiting changes in key virulence factors, nutrient acquisition, metabolic profiles, and the ability to disseminate in an animal model. Whole-genome sequencing uncovered a clonal relationship, with only a few unique differences. Of these, two key changes are expected to explain the phenotypic differences observed in the relapse isolate: loss of a predicted AT-rich interaction domain protein and changes in copy number of the left and right arms of chromosome 12. Gene deletion of the predicted transcriptional regulator produced changes in melanin, capsule, carbon source use, and dissemination in the host, consistent with the phenotype of the relapse isolate. In addition, the deletion mutant displayed altered virulence in the murine model. The observed differences suggest the relapse isolate evolved subsequent to penetration of the central nervous system and may have gained dominance following the administration of antifungal therapy. These data reveal the first molecular insights into how the Cryptococcus neoformans genome changes during infection of humans and the manner in which microevolution progresses in this deadly fungal pathogen.<\/jats:p>","DOI":"10.1534\/g3.113.005660","type":"journal-article","created":{"date-parts":[[2013,3,28]],"date-time":"2013-03-28T17:36:03Z","timestamp":1364492163000},"page":"675-686","source":"Crossref","is-referenced-by-count":71,"title":["Comparative Genomics of Serial Isolates of <i>Cryptococcus neoformans<\/i> Reveals Gene Associated With Carbon Utilization and Virulence"],"prefix":"10.1093","volume":"3","author":[{"given":"Kate L","family":"Ormerod","sequence":"first","affiliation":[{"name":"Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, QLD 4072 Australia"},{"name":"School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, QLD 4072 Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Carl A","family":"Morrow","sequence":"additional","affiliation":[{"name":"Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, QLD 4072 Australia"},{"name":"School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, QLD 4072 Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Eve W L","family":"Chow","sequence":"additional","affiliation":[{"name":"Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, QLD 4072 Australia"},{"name":"School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, QLD 4072 Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"I Russel","family":"Lee","sequence":"additional","affiliation":[{"name":"Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, QLD 4072 Australia"},{"name":"School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, QLD 4072 Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Samantha D M","family":"Arras","sequence":"additional","affiliation":[{"name":"Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, QLD 4072 Australia"},{"name":"School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, QLD 4072 Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Horst Joachim","family":"Schirra","sequence":"additional","affiliation":[{"name":"School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, QLD 4072 Australia"},{"name":"Centre for Advanced Imaging, University of Queensland, Brisbane, QLD 4072 Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gary M","family":"Cox","sequence":"additional","affiliation":[{"name":"Department of Medicine, Mycology Research Unit, Duke University, Durham, North Carolina 27710"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bettina C","family":"Fries","sequence":"additional","affiliation":[{"name":"Department of Microbiology & Immunology, Albert Einstein College of Medicine, Bronx, New York 10461"},{"name":"Department of Medicine, Albert Einstein College of Medicine, Bronx, New York 10461"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"James A","family":"Fraser","sequence":"additional","affiliation":[{"name":"Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, QLD 4072 Australia"},{"name":"Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, QLD 4072 Australia"},{"name":"School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, QLD 4072 Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2013,4,1]]},"reference":[{"key":"2021041813050568000_bib1","doi-asserted-by":"crossref","first-page":"961","DOI":"10.1101\/gr.112326.110","article-title":"Dindel: Accurate indel calls from short-read data","volume":"21","author":"Albers","year":"2011","journal-title":"Genome Res."},{"key":"2021041813050568000_bib2","doi-asserted-by":"crossref","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":"2021041813050568000_bib3","doi-asserted-by":"crossref","first-page":"71","DOI":"10.1093\/genetics\/77.1.71","article-title":"Genetics of Caenorhabditis elegans","volume":"77","author":"Brenner","year":"1974","journal-title":"Genetics"},{"key":"2021041813050568000_bib4","doi-asserted-by":"crossref","first-page":"442","DOI":"10.1002\/(SICI)1522-2594(199909)42:3<442::AID-MRM6>3.0.CO;2-Q","article-title":"Heteronuclear NMR studies of metabolites produced by Cryptococcus neoformans in culture media: Identification of possible virulence factors","volume":"42","author":"Bubb","year":"1999","journal-title":"Magn. Reson. Med."},{"key":"2021041813050568000_bib5","doi-asserted-by":"crossref","first-page":"677","DOI":"10.1038\/nmeth.1363","article-title":"BreakDancer: an algorithm for high-resolution mapping of genomic structural variation","volume":"6","author":"Chen","year":"2009","journal-title":"Nat. Methods"},{"key":"2021041813050568000_bib6","doi-asserted-by":"crossref","first-page":"e1002177","DOI":"10.1371\/journal.ppat.1002177","article-title":"Unique evolution of the UPR pathway with a novel bZIP transcription factor, Hxl1, for controlling pathogenicity of Cryptococcus neoformans","volume":"7","author":"Cheon","year":"2011","journal-title":"PLoS Pathog."},{"key":"2021041813050568000_bib7","doi-asserted-by":"crossref","first-page":"323","DOI":"10.1186\/1471-2164-8-323","article-title":"Adaptive expression responses in the Pol-\u03b3 null strain of S. pombe depleted of mitochondrial genome","volume":"8","author":"Chu","year":"2007","journal-title":"BMC Genomics"},{"key":"2021041813050568000_bib8","doi-asserted-by":"crossref","first-page":"225","DOI":"10.1371\/journal.ppat.0030022","article-title":"A link between virulence and homeostatic responses to hypoxia during infection by the human fungal pathogen Cryptococcus neoformans","volume":"3","author":"Chun","year":"2007","journal-title":"PLoS Pathog."},{"key":"2021041813050568000_bib9","doi-asserted-by":"crossref","first-page":"2247","DOI":"10.1099\/mic.0.28798-0","article-title":"Cryptococcus neoformans var. grubii isolates recovered from persons with AIDS demonstrate a wide range of virulence during murine meningoencephalitis that correlates with the expression of certain virulence factors","volume":"152","author":"Clancy","year":"2006","journal-title":"Microbiology-Sgm"},{"key":"2021041813050568000_bib10","doi-asserted-by":"crossref","first-page":"443","DOI":"10.1128\/IAI.68.2.443-448.2000","article-title":"Urease as a virulence factor in experimental cryptococcosis","volume":"68","author":"Cox","year":"2000","journal-title":"Infect. Immun."},{"key":"2021041813050568000_bib11","doi-asserted-by":"crossref","first-page":"e00091","DOI":"10.1128\/mBio.00091-10","article-title":"Mixed infections and in vivo evolution in the human fungal pathogen Cryptococcus neoformans","volume":"1","author":"Desnos-Ollivier","year":"2010","journal-title":"Mbio"},{"key":"2021041813050568000_bib12","doi-asserted-by":"crossref","first-page":"16144","DOI":"10.1073\/pnas.242624799","article-title":"Characteristic genome rearrangements in experimental evolution of Saccharomyces cerevisiae","volume":"99","author":"Dunham","year":"2002","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"2021041813050568000_bib13","doi-asserted-by":"crossref","first-page":"e00129","DOI":"10.1128\/mBio.00129-11","article-title":"Stress alters rates and types of loss of heterozygosity in Candida albicans","volume":"2","author":"Forche","year":"2011","journal-title":"Mbio"},{"key":"2021041813050568000_bib14","doi-asserted-by":"crossref","first-page":"799","DOI":"10.1534\/genetics.109.103325","article-title":"Evolution in Candida albicans populations during a single passage through a mouse host","volume":"182","author":"Forche","year":"2009","journal-title":"Genetics"},{"key":"2021041813050568000_bib15","doi-asserted-by":"crossref","first-page":"20552","DOI":"10.1016\/S0021-9258(19)47098-1","article-title":"Cloning and sequencing of the nuclear gene MIP1 encoding the catalytic subunit of the yeast mitochondrial DNA polymerase","volume":"264","author":"Foury","year":"1989","journal-title":"J. Biol. Chem."},{"key":"2021041813050568000_bib16","doi-asserted-by":"crossref","first-page":"401","DOI":"10.1128\/EC.4.2.401-406.2005","article-title":"Chromosomal translocation and segmental duplication in Cryptococcus neoformans","volume":"4","author":"Fraser","year":"2005","journal-title":"Eukaryot. Cell"},{"key":"2021041813050568000_bib17","doi-asserted-by":"crossref","first-page":"1036","DOI":"10.1128\/EC.2.5.1036-1045.2003","article-title":"Recapitulation of the sexual cycle of the primary fungal pathogen Cryptococcus neoformans var. gattii: Implications for an outbreak on Vancouver Island, Canada","volume":"2","author":"Fraser","year":"2003","journal-title":"Eukaryot. Cell"},{"key":"2021041813050568000_bib18","doi-asserted-by":"crossref","first-page":"1531","DOI":"10.1128\/JCM.34.6.1531-1534.1996","article-title":"Karyotype instability in Cryptococcus neoformans infection","volume":"34","author":"Fries","year":"1996","journal-title":"J. Clin. Microbiol."},{"key":"2021041813050568000_bib19","doi-asserted-by":"crossref","first-page":"3204","DOI":"10.1128\/JCM.37.10.3204-3209.1999","article-title":"Epidemiological evidence for dormant Cryptococcus neoformans infection","volume":"37","author":"Garcia-Hermoso","year":"1999","journal-title":"J. Clin. Microbiol."},{"key":"2021041813050568000_bib20","doi-asserted-by":"crossref","first-page":"865","DOI":"10.1002\/yea.733","article-title":"The diversity of retrotransposons in the yeast Cryptococcus neoformans","volume":"18","author":"Goodwin","year":"2001","journal-title":"Yeast"},{"key":"2021041813050568000_bib21","doi-asserted-by":"crossref","first-page":"e1000303","DOI":"10.1371\/journal.pgen.1000303","article-title":"The repertoire and dynamics of evolutionary adaptations to controlled nutrient-limited environments in yeast","volume":"4","author":"Gresham","year":"2008","journal-title":"PLoS Genet."},{"key":"2021041813050568000_bib22","doi-asserted-by":"crossref","first-page":"122","DOI":"10.1148\/radiology.220.1.r01jl25122","article-title":"Cryptococcomas distinguished from gliomas with MR spectroscopy: An experimental rat and cell culture study","volume":"220","author":"Himmelreich","year":"2001","journal-title":"Radiology"},{"key":"2021041813050568000_bib23","doi-asserted-by":"crossref","first-page":"118","DOI":"10.1086\/599360","article-title":"Dynamics of adaptive microevolution of hypermutable Pseudomonas aeruginosa during chronic pulmonary infection in patients with cystic fibrosis","volume":"200","author":"Hoboth","year":"2009","journal-title":"J. Infect. Dis."},{"key":"2021041813050568000_bib24","doi-asserted-by":"crossref","first-page":"1456","DOI":"10.1111\/j.1365-2958.2008.06374.x","article-title":"Metabolic adaptation in Cryptococcus neoformans during early murine pulmonary infection","volume":"69","author":"Hu","year":"2008","journal-title":"Mol. Microbiol."},{"key":"2021041813050568000_bib25","doi-asserted-by":"crossref","first-page":"526","DOI":"10.1186\/1471-2164-12-526","article-title":"Variation in chromosome copy number influences the virulence of Cryptococcus neoformans and occurs in isolates from AIDS patients","volume":"12","author":"Hu","year":"2011","journal-title":"BMC Genomics"},{"key":"2021041813050568000_bib26","doi-asserted-by":"crossref","first-page":"5733","DOI":"10.1128\/JCM.43.11.5733-5742.2005","article-title":"Molecular epidemiology of clinical Cryptococcus neoformans strains from India","volume":"43","author":"Jain","year":"2005","journal-title":"J. Clin. Microbiol."},{"key":"2021041813050568000_bib27","doi-asserted-by":"crossref","first-page":"617","DOI":"10.1038\/nature02424","article-title":"Proof and evolutionary analysis of ancient genome duplication in the yeast Saccharomyces cerevisiae","volume":"428","author":"Kellis","year":"2004","journal-title":"Nature"},{"key":"2021041813050568000_bib28","doi-asserted-by":"crossref","first-page":"5033","DOI":"10.1073\/pnas.1018444108","article-title":"Helicobacter pylori genome evolution during human infection","volume":"108","author":"Kennemann","year":"2011","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"2021041813050568000_bib29","doi-asserted-by":"crossref","first-page":"294","DOI":"10.1016\/S0968-0004(00)01597-8","article-title":"ARID proteins come in from the desert","volume":"25","author":"Kortschak","year":"2000","journal-title":"Trends Biochem. Sci."},{"key":"2021041813050568000_bib30","doi-asserted-by":"crossref","first-page":"309","DOI":"10.1534\/genetics.111.128538","article-title":"Nitrogen metabolite repression of metabolism and virulence in the human fungal pathogen Cryptococcus neoformans","volume":"188","author":"Lee","year":"2011","journal-title":"Genetics"},{"key":"2021041813050568000_bib31","doi-asserted-by":"crossref","first-page":"14455","DOI":"10.1073\/pnas.97.26.14455","article-title":"Identification of the MATa mating-type locus of Cryptococcus neoformans reveals a serotype A MATa strain thought to have been extinct","volume":"97","author":"Lengeler","year":"2000","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"2021041813050568000_bib32","doi-asserted-by":"crossref","first-page":"2223","DOI":"10.1534\/genetics.105.046672","article-title":"Multilocus sequence typing reveals three genetic subpopulations of Cryptococcus neoformans var. grubii (Serotype A), including a unique population in Botswana","volume":"172","author":"Litvintseva","year":"2006","journal-title":"Genetics"},{"key":"2021041813050568000_bib33","doi-asserted-by":"crossref","first-page":"1321","DOI":"10.1126\/science.1103773","article-title":"The genome of the basidiomycetous yeast and human pathogen Cryptococcus neoformans","volume":"307","author":"Loftus","year":"2005","journal-title":"Science"},{"key":"2021041813050568000_bib34","doi-asserted-by":"crossref","first-page":"9272","DOI":"10.1073\/pnas.0803466105","article-title":"A genome-wide view of the spectrum of spontaneous mutations in yeast","volume":"105","author":"Lynch","year":"2008","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"2021041813050568000_bib35","doi-asserted-by":"crossref","first-page":"e1002936","DOI":"10.1371\/journal.ppat.1002936","article-title":"DNA mutations mediate microevolution between host-adapted forms of the pathogenic fungus Cryptococcus neoformans","volume":"8","author":"Magditch","year":"2012","journal-title":"PLoS Pathog."},{"key":"2021041813050568000_bib36","doi-asserted-by":"crossref","first-page":"151","DOI":"10.1080\/mmy.39.1.151.154","article-title":"A new dominant selectable marker for use in Cryptococcus neoformans","volume":"39","author":"McDade","year":"2001","journal-title":"Med. Mycol."},{"key":"2021041813050568000_bib37","doi-asserted-by":"crossref","first-page":"139","DOI":"10.1186\/1471-2164-12-139","article-title":"Widespread, focal copy number variations (CNV) and whole chromosome aneuploidies in Trypanosoma cruzi strains revealed by array comparative genomic hybridization","volume":"12","author":"Minning","year":"2011","journal-title":"BMC Genomics"},{"key":"2021041813050568000_bib38","doi-asserted-by":"crossref","first-page":"e00310","DOI":"10.1128\/mBio.00310-11","article-title":"A unique chromosomal rearrangement in the Cryptococcus neoformans var. grubii type strain enhances key phenotypes associated with virulence","volume":"3","author":"Morrow","year":"2012","journal-title":"mBio"},{"key":"2021041813050568000_bib39","doi-asserted-by":"crossref","first-page":"2243","DOI":"10.1128\/JCM.00213-11","article-title":"Aspergillus species and other molds in respiratory samples from patients with cystic fibrosis: a laboratory-based study with focus on Aspergillus fumigatus azole resistance","volume":"49","author":"Mortensen","year":"2011","journal-title":"J. Clin. Microbiol."},{"key":"2021041813050568000_bib40","doi-asserted-by":"crossref","first-page":"15675","DOI":"10.1073\/pnas.232568599","article-title":"Killing of Caenorhabditis elegans by Cryptococcus neoformans as a model of yeast pathogenesis","volume":"99","author":"Mylonakis","year":"2002","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"2021041813050568000_bib41","doi-asserted-by":"crossref","first-page":"1693","DOI":"10.1128\/IAI.72.3.1693-1699.2004","article-title":"CNLAC1 is required for extrapulmonary dissemination of Cryptococcus neoformans but not pulmonary persistence","volume":"72","author":"Noverr","year":"2004","journal-title":"Infect. Immun."},{"key":"2021041813050568000_bib42","doi-asserted-by":"crossref","DOI":"10.1007\/978-3-642-86659-3","volume-title":"Evolution by Gene Duplication","author":"Ohno","year":"1970"},{"key":"2021041813050568000_bib43","doi-asserted-by":"crossref","first-page":"525","DOI":"10.1097\/QAD.0b013e328322ffac","article-title":"Estimation of the current global burden of cryptococcal meningitis among persons living with HIV\/AIDS","volume":"23","author":"Park","year":"2009","journal-title":"AIDS"},{"key":"2021041813050568000_bib44","doi-asserted-by":"crossref","first-page":"66","DOI":"10.1093\/nar\/gki145","article-title":"DNA-binding properties of ARID family proteins","volume":"33","author":"Patsialou","year":"2005","journal-title":"Nucleic Acids Res."},{"key":"2021041813050568000_bib45","doi-asserted-by":"crossref","first-page":"321","DOI":"10.1038\/nature09529","article-title":"Aneuploidy confers quantitative proteome changes and phenotypic variation in budding yeast","volume":"468","author":"Pavelka","year":"2010","journal-title":"Nature"},{"key":"2021041813050568000_bib46","doi-asserted-by":"crossref","first-page":"563","DOI":"10.1099\/jmm.0.007716-0","article-title":"Evaluation of laccases and melanization in clinical and environmental Cryptococcus neoformans samples by non-denaturing PAGE","volume":"58","author":"Pereira","year":"2009","journal-title":"J. Med. Microbiol."},{"key":"2021041813050568000_bib47","first-page":"177","article-title":"Chronic cryptococcal meningitis: A new experimental model in rabbits","volume":"101","author":"Perfect","year":"1980","journal-title":"Am. J. Pathol."},{"key":"2021041813050568000_bib48","doi-asserted-by":"crossref","first-page":"5877","DOI":"10.1128\/IAI.00624-06","article-title":"Characterization and regulation of the trehalose synthesis pathway and its importance in the pathogenicity of Cryptococcus neoformans","volume":"74","author":"Petzold","year":"2006","journal-title":"Infect. Immun."},{"key":"2021041813050568000_bib49","doi-asserted-by":"crossref","first-page":"1557","DOI":"10.1099\/13500872-142-6-1557","article-title":"A putative cyclic peptide efflux pump encoded by the TOXA gene of the plant-pathogenic fungus Cochliobolus carbonum","volume":"142","author":"Pitkin","year":"1996","journal-title":"Microbiology-Uk"},{"key":"2021041813050568000_bib50","doi-asserted-by":"crossref","first-page":"2688","DOI":"10.1073\/pnas.0809793106","article-title":"Formation of new chromosomes as a virulence mechanism in yeast Candida glabrata","volume":"106","author":"Polakova","year":"2009","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"2021041813050568000_bib51","doi-asserted-by":"crossref","first-page":"367","DOI":"10.1126\/science.1128242","article-title":"Aneuploidy and isochromosome formation in drug-resistant Candida albicans","volume":"313","author":"Selmecki","year":"2006","journal-title":"Science"},{"key":"2021041813050568000_bib52","doi-asserted-by":"crossref","first-page":"991","DOI":"10.1128\/EC.00060-10","article-title":"Genomic plasticity of the human fungal pathogen Candida albicans","volume":"9","author":"Selmecki","year":"2010","journal-title":"Eukaryot. Cell"},{"key":"2021041813050568000_bib53","doi-asserted-by":"crossref","first-page":"e1000705","DOI":"10.1371\/journal.pgen.1000705","article-title":"Acquisition of aneuploidy provides increased fitness during the evolution of antifungal drug resistance","volume":"5","author":"Selmecki","year":"2009","journal-title":"PLoS Genet."},{"key":"2021041813050568000_bib54","doi-asserted-by":"crossref","first-page":"e1000848","DOI":"10.1371\/journal.ppat.1000848","article-title":"Cryptococcus neoformans overcomes stress of azole drugs by formation of disomy in specific multiple chromosomes","volume":"6","author":"Sionov","year":"2010","journal-title":"PLoS Pathog."},{"key":"2021041813050568000_bib55","doi-asserted-by":"crossref","first-page":"10136","DOI":"10.1073\/pnas.0914418107","article-title":"Multiple GAL pathway gene clusters evolved independently and by different mechanisms in fungi","volume":"107","author":"Slot","year":"2010","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"2021041813050568000_bib56","unstructured":"Smit, A. F. A., R. Hubley, and P. Green, 1996\u20132010\u2003RepeatMasker Open-3.0. Available at: http:\/\/www.repeatmasker.org\/."},{"key":"2021041813050568000_bib57","doi-asserted-by":"crossref","first-page":"8487","DOI":"10.1073\/pnas.0602138103","article-title":"Genetic adaptation by Pseudomonas aeruginosa to the airways of cystic fibrosis patients","volume":"103","author":"Smith","year":"2006","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"2021041813050568000_bib58","doi-asserted-by":"crossref","first-page":"518","DOI":"10.1038\/nprot.2006.73","article-title":"Southern blotting","volume":"1","author":"Southern","year":"2006","journal-title":"Nat. Protoc."},{"key":"2021041813050568000_bib59","doi-asserted-by":"crossref","first-page":"595","DOI":"10.1016\/0140-6736(93)90354-J","article-title":"Persistence of initial infection in recurrent Cryptococcus neoformans meningitis","volume":"341","author":"Spitzer","year":"1993","journal-title":"Lancet"},{"key":"2021041813050568000_bib60","doi-asserted-by":"crossref","first-page":"12","DOI":"10.1371\/journal.pgen.1001189","article-title":"Whole-genome and chromosome evolution associated with host adaptation and speciation of the wheat pathogen Mycosphaerella graminicola","volume":"6","author":"Stukenbrock","year":"2010","journal-title":"PLoS Genet."},{"key":"2021041813050568000_bib61","doi-asserted-by":"crossref","first-page":"345","DOI":"10.1016\/S0168-9525(00)02060-6","article-title":"The Swi\/Snf family: nucleosome-remodeling complexes and transcriptional control","volume":"16","author":"Sudarsanam","year":"2000","journal-title":"Trends Genet."},{"key":"2021041813050568000_bib62","doi-asserted-by":"crossref","first-page":"916","DOI":"10.1126\/science.1142210","article-title":"Effects of aneuploidy on cellular physiology and cell division in haploid yeast","volume":"317","author":"Torres","year":"2007","journal-title":"Science"},{"key":"2021041813050568000_bib63","doi-asserted-by":"crossref","first-page":"R115","DOI":"10.1186\/gb-2008-9-7-r115","article-title":"Modulation of gene expression in drug resistant Leishmania is associated with gene amplification, gene deletion and chromosome aneuploidy","volume":"9","author":"Ubeda","year":"2008","journal-title":"Genome Biol."},{"key":"2021041813050568000_bib64","doi-asserted-by":"crossref","first-page":"652","DOI":"10.1038\/nmeth.1628","article-title":"CREST maps somatic structural variation in cancer genomes with base-pair resolution","volume":"8","author":"Wang","year":"2011","journal-title":"Nat. Methods"},{"key":"2021041813050568000_bib65","doi-asserted-by":"crossref","first-page":"794","DOI":"10.1172\/JCI30006","article-title":"Role of a CUF1\/CTR4 copper regulatory axis in the virulence of Cryptococcus neoformans","volume":"117","author":"Waterman","year":"2007","journal-title":"J. Clin. Invest."},{"key":"2021041813050568000_bib66","doi-asserted-by":"crossref","first-page":"306","DOI":"10.1165\/ajrcmb.26.3.4479","article-title":"Complementation of a capsule deficient Cryptococcus neoformans with CAP64 restores virulence in a murine lung infection","volume":"26","author":"Wilder","year":"2002","journal-title":"Am. J. Respir. Cell Mol. Biol."},{"key":"2021041813050568000_bib67","doi-asserted-by":"crossref","first-page":"242","DOI":"10.1016\/j.ygeno.2005.03.013","article-title":"Nomenclature of the ARID family of DNA-binding proteins","volume":"86","author":"Wilsker","year":"2005","journal-title":"Genomics"}],"container-title":["G3 Genes|Genomes|Genetics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/g3journal\/article-pdf\/3\/4\/675\/37067900\/g3journal0675.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"http:\/\/academic.oup.com\/g3journal\/article-pdf\/3\/4\/675\/37067900\/g3journal0675.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,4,18]],"date-time":"2021-04-18T13:10:19Z","timestamp":1618751419000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/g3journal\/article\/3\/4\/675\/6026116"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2013,4,1]]},"references-count":67,"journal-issue":{"issue":"4","published-print":{"date-parts":[[2013,4,1]]}},"URL":"https:\/\/doi.org\/10.1534\/g3.113.005660","relation":{},"ISSN":["2160-1836"],"issn-type":[{"value":"2160-1836","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2013,4,1]]},"published":{"date-parts":[[2013,4,1]]}}}