{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,30]],"date-time":"2026-09-30T08:37:40Z","timestamp":1790757460457,"version":"4.1.0"},"reference-count":120,"publisher":"Public Library of Science (PLoS)","issue":"1","license":[{"start":{"date-parts":[[2026,1,16]],"date-time":"2026-01-16T00:00:00Z","timestamp":1768521600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000057","name":"NIGMS","doi-asserted-by":"crossref","award":["R35GM118077"],"award-info":[{"award-number":["R35GM118077"]}],"id":[{"id":"10.13039\/100000057","id-type":"DOI","asserted-by":"crossref"}]},{"name":"NIH","award":["T32AI052080"],"award-info":[{"award-number":["T32AI052080"]}]},{"DOI":"10.13039\/100006492","name":"Division of Intramural Research, National Institute of Allergy and Infectious Diseases","doi-asserted-by":"publisher","award":["K99\/R00AI166094"],"award-info":[{"award-number":["K99\/R00AI166094"]}],"id":[{"id":"10.13039\/100006492","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100007631","name":"Canadian Institute for Advanced Research","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100007631","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100006510","name":"Duke University","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100006510","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000057","name":"NIGMS","doi-asserted-by":"crossref","award":["R35GM122550"],"award-info":[{"award-number":["R35GM122550"]}],"id":[{"id":"10.13039\/100000057","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/100006492","name":"Division of Intramural Research, National Institute of Allergy and Infectious Diseases","doi-asserted-by":"publisher","award":["AI-73896 and AI-93257"],"award-info":[{"award-number":["AI-73896 and AI-93257"]}],"id":[{"id":"10.13039\/100006492","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100006492","name":"Division of Intramural Research, National Institute of Allergy and Infectious Diseases","doi-asserted-by":"publisher","award":["R01AI133654"],"award-info":[{"award-number":["R01AI133654"]}],"id":[{"id":"10.13039\/100006492","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["www.plosgenetics.org"],"crossmark-restriction":false},"short-container-title":["PLoS Genet"],"abstract":"<jats:p>\n                    Transposable elements (TEs) are key agents of genome evolution across all domains of life. These mobile genetic elements can cause mutations through transposition or by promoting structural rearrangements. Stress conditions can amplify TE mobility, either by impairing TE suppression mechanisms or through stress-induced interactions between transcription factors and TE sequences, offering a route for rapid genetic change. As such, TEs represent an important source of adaptability within populations. To investigate the interplay between environmental stress and eukaryotic TE dynamics relevant to infectious disease, we examined how heat stress and host-mimicking medium (RPMI) affect TE mobility in the global human fungal pathogen\n                    <jats:italic>Cryptococcus neoformans<\/jats:italic>\n                    , using a collection of clinical and environmental isolates. Using a selection-based screen, we captured the mobilization of seven distinct mobile element families, encompassing diverse retrotransposons and DNA transposons, whose insertions conferred antifungal resistance. This includes a novel element, CNEST, which belongs to the CACTA, Mirage, Chapaev (CMC) supergroup. Heat stress at human body temperature (37\u00b0C) significantly increased the mobilization of a subset of these TEs, leading to higher rates of acquired antifungal resistance. Whole-genome assemblies revealed that, compared to retrotransposons, DNA transposons were hypomethylated and approximately uniformly distributed throughout the genome, features that may contribute to their frequent mobilization. We further assessed TE-driven genomic changes within hosts using serial isolates from patients with recurrent cryptococcal infections and from isolates passaged through mice. While we observed evidence of TE copy number changes near chromosome ends, we found no indication of TE-mediated alterations near gene-coding regions across any of the serial isolates. Finally, TE mobility was isolate- and strain-dependent, with significant variation even among clonally related strains collected from the same patient, emphasizing the role of genetic background in shaping TE activity. Together, these findings reveal a complex and dynamic relationship between environmental stress, genetic background, TE type-specific epigenetic regulation, and TE mobility, with important implications for adaptation and acquired antifungal resistance in\n                    <jats:italic>C. neoformans<\/jats:italic>\n                    .\n                  <\/jats:p>","DOI":"10.1371\/journal.pgen.1011979","type":"journal-article","created":{"date-parts":[[2026,1,16]],"date-time":"2026-01-16T18:33:49Z","timestamp":1768588429000},"page":"e1011979","update-policy":"https:\/\/doi.org\/10.1371\/journal.pgen.corrections_policy","source":"Crossref","is-referenced-by-count":3,"title":["Temperature and genetic background drive mobilization of diverse transposable elements in a global human fungal pathogen"],"prefix":"10.1371","volume":"22","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-9263-1659","authenticated-orcid":true,"given":"Anna I.","family":"Mackey","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0009-1454-5443","authenticated-orcid":true,"given":"Vesper","family":"Fraunfelter","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0006-3509-2277","authenticated-orcid":true,"given":"Samantha","family":"Shaltz","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"John","family":"McCormick","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0007-3824-1757","authenticated-orcid":true,"given":"Callan","family":"Schroeder","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"John R.","family":"Perfect","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Cedric","family":"Feschotte","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7659-2589","authenticated-orcid":true,"given":"Paul M.","family":"Magwene","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9915-1834","authenticated-orcid":true,"given":"Asiya","family":"Gusa","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2026,1,16]]},"reference":[{"issue":"2","key":"pgen.1011979.ref001","doi-asserted-by":"crossref","first-page":"775","DOI":"10.1093\/nar\/gks1185","article-title":"Transposon integration enhances expression of stress response genes","volume":"41","author":"G Feng","year":"2013","journal-title":"Nucleic Acids Res"},{"issue":"1","key":"pgen.1011979.ref002","doi-asserted-by":"crossref","first-page":"85","DOI":"10.1101\/gr.239699.118","article-title":"Transposable element insertions in fission yeast drive adaptation to environmental stress","volume":"29","author":"C Esnault","year":"2019","journal-title":"Genome Res"},{"issue":"5","key":"pgen.1011979.ref003","doi-asserted-by":"crossref","DOI":"10.1016\/j.cub.2021.12.048","article-title":"A large transposable element mediates metal resistance in the fungus Paecilomyces variotii","volume":"32","author":"AS Urquhart","year":"2022","journal-title":"Curr Biol"},{"issue":"5","key":"pgen.1011979.ref004","doi-asserted-by":"crossref","DOI":"10.1128\/mBio.01515-19","article-title":"Transposon-mediated horizontal transfer of the host-specific virulence protein toxA between three fungal wheat pathogens","volume":"10","author":"MC McDonald","year":"2019","journal-title":"MBio"},{"issue":"5","key":"pgen.1011979.ref005","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pgen.1010747","article-title":"Paths to adaptation under fluctuating nitrogen starvation: The spectrum of adaptive mutations in Saccharomyces cerevisiae is shaped by retrotransposons and microhomology-mediated recombination","volume":"19","author":"M Hays","year":"2023","journal-title":"PLoS Genet"},{"issue":"1","key":"pgen.1011979.ref006","doi-asserted-by":"crossref","first-page":"393","DOI":"10.1186\/s12864-021-07691-2","article-title":"Rapid sequence evolution driven by transposable elements at a virulence locus in a fungal wheat pathogen","volume":"22","author":"NK Singh","year":"2021","journal-title":"BMC Genomics"},{"issue":"2","key":"pgen.1011979.ref007","doi-asserted-by":"crossref","DOI":"10.1371\/journal.ppat.1011130","article-title":"Recent transposable element bursts are associated with the proximity to genes in a fungal plant pathogen","volume":"19","author":"U Oggenfuss","year":"2023","journal-title":"PLoS Pathog"},{"issue":"4","key":"pgen.1011979.ref008","doi-asserted-by":"crossref","DOI":"10.1093\/g3journal\/jkab068","article-title":"Dynamics of transposable elements in recently diverged fungal pathogens: lineage-specific transposable element content and efficiency of genome defenses","volume":"11","author":"C Lorrain","year":"2021","journal-title":"G3 (Bethesda)"},{"key":"pgen.1011979.ref009","article-title":"Recent reactivation of a pathogenicity-associated transposable element is associated with major chromosomal rearrangements in a fungal wheat pathogen","author":"T Badet","year":"2023","journal-title":"Nucleic Acids Research"},{"key":"pgen.1011979.ref010","doi-asserted-by":"crossref","DOI":"10.1146\/annurev-genet-040620-022145","article-title":"A field guide to eukaryotic transposable elements","volume":"54","author":"JN Wells","year":"2020","journal-title":"Annu Rev Genet"},{"issue":"1","key":"pgen.1011979.ref011","doi-asserted-by":"crossref","first-page":"199","DOI":"10.1186\/s13059-018-1577-z","article-title":"Ten things you should know about transposable elements","volume":"19","author":"G Bourque","year":"2018","journal-title":"Genome Biol"},{"issue":"5","key":"pgen.1011979.ref012","doi-asserted-by":"crossref","DOI":"10.1093\/molbev\/msac109","article-title":"Giant starship elements mobilize accessory genes in fungal genomes","volume":"39","author":"E Gluck-Thaler","year":"2022","journal-title":"Mol Biol Evol"},{"issue":"7","key":"pgen.1011979.ref013","doi-asserted-by":"crossref","DOI":"10.1111\/eva.13730","article-title":"The evolutionary consequences of interactions between the epigenome, the genome and the environment","volume":"17","author":"P Baduel","year":"2024","journal-title":"Evol Appl"},{"issue":"11","key":"pgen.1011979.ref014","doi-asserted-by":"crossref","first-page":"832","DOI":"10.1016\/j.tig.2017.08.007","article-title":"Revisiting the Relationship between Transposable Elements and the Eukaryotic Stress Response","volume":"33","author":"V Horv\u00e1th","year":"2017","journal-title":"Trends Genet"},{"issue":"1","key":"pgen.1011979.ref015","doi-asserted-by":"crossref","first-page":"221","DOI":"10.1093\/molbev\/msz216","article-title":"Stress-driven transposable element de-repression dynamics and virulence evolution in a fungal pathogen","volume":"37","author":"S Fouch\u00e9","year":"2020","journal-title":"Mol Biol Evol"},{"issue":"8","key":"pgen.1011979.ref016","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pgen.0030131","article-title":"SREBP controls oxygen-dependent mobilization of retrotransposons in fission yeast","volume":"3","author":"A Sehgal","year":"2007","journal-title":"PLoS Genet"},{"issue":"4670","key":"pgen.1011979.ref017","doi-asserted-by":"crossref","first-page":"53","DOI":"10.1126\/science.226.4670.53","article-title":"Temperature effects on the rate of ty transposition","volume":"226","author":"CE Paquin","year":"1984","journal-title":"Science"},{"issue":"12","key":"pgen.1011979.ref018","doi-asserted-by":"crossref","first-page":"5271","DOI":"10.1093\/nar\/gks166","article-title":"Tye7 regulates yeast Ty1 retrotransposon sense and antisense transcription in response to adenylic nucleotides stress","volume":"40","author":"G Servant","year":"2012","journal-title":"Nucleic Acids Res"},{"issue":"4","key":"pgen.1011979.ref019","doi-asserted-by":"crossref","first-page":"1449","DOI":"10.1093\/genetics\/159.4.1449","article-title":"Multiple regulators of Ty1 transposition in Saccharomyces cerevisiae have conserved roles in genome maintenance","volume":"159","author":"DT Scholes","year":"2001","journal-title":"Genetics"},{"key":"pgen.1011979.ref020","doi-asserted-by":"crossref","DOI":"10.7554\/eLife.89277.3","article-title":"The genomic landscape of transposable elements in yeast hybrids is shaped by structural variation and genotype-specific modulation of transposition rate","volume":"12","author":"M H\u00e9nault","year":"2024","journal-title":"Elife"},{"issue":"4","key":"pgen.1011979.ref021","doi-asserted-by":"crossref","first-page":"1845","DOI":"10.1534\/genetics.104.037317","article-title":"Ty1 copy number dynamics in Saccharomyces","volume":"169","author":"DJ Garfinkel","year":"2005","journal-title":"Genetics"},{"issue":"4","key":"pgen.1011979.ref022","doi-asserted-by":"crossref","DOI":"10.1128\/microbiolspec.MDNA3-0040-2014","article-title":"The Long Terminal Repeat Retrotransposons Tf1 and Tf2 of Schizosaccharomyces pombe","volume":"3","author":"C Esnault","year":"2015","journal-title":"Microbiol Spectr"},{"key":"pgen.1011979.ref023","doi-asserted-by":"crossref","first-page":"69","DOI":"10.1146\/annurev.micro.60.080805.142102","article-title":"The biology of the Cryptococcus neoformans species complex","volume":"60","author":"X Lin","year":"2006","journal-title":"Annu Rev Microbiol"},{"issue":"9","key":"pgen.1011979.ref024","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":"TJ Goodwin","year":"2001","journal-title":"Yeast"},{"key":"pgen.1011979.ref025","doi-asserted-by":"crossref","first-page":"3099","DOI":"10.1099\/mic.0.26529-0","article-title":"Cryptons: a group of tyrosine-recombinase-encoding DNA transposons from pathogenic fungi","volume":"149","author":"TJD Goodwin","year":"2003","journal-title":"Microbiology (Reading)"},{"issue":"8","key":"pgen.1011979.ref026","doi-asserted-by":"crossref","first-page":"873","DOI":"10.1016\/S1473-3099(17)30243-8","article-title":"Global burden of disease of HIV-associated cryptococcal meningitis: an updated analysis","volume":"17","author":"R Rajasingham","year":"2017","journal-title":"Lancet Infect Dis"},{"issue":"7","key":"pgen.1011979.ref027","doi-asserted-by":"crossref","DOI":"10.1016\/S1473-3099(23)00692-8","article-title":"Global incidence and mortality of severe fungal disease","volume":"24","author":"DW Denning","year":"2024","journal-title":"Lancet Infect Dis"},{"issue":"13","key":"pgen.1011979.ref028","doi-asserted-by":"crossref","first-page":"2089","DOI":"10.1097\/QAD.0b013e3283614a8d","article-title":"Clinical and mycological predictors of cryptococcosis-associated immune reconstitution inflammatory syndrome","volume":"27","author":"CC Chang","year":"2013","journal-title":"AIDS"},{"issue":"2","key":"pgen.1011979.ref029","doi-asserted-by":"crossref","DOI":"10.1128\/mBio.00166-17","article-title":"Microevolution of serial clinical isolates of Cryptococcus neoformans var. grubii and C. gattii","volume":"8","author":"Y Chen","year":"2017","journal-title":"MBio"},{"issue":"4","key":"pgen.1011979.ref030","doi-asserted-by":"crossref","first-page":"675","DOI":"10.1534\/g3.113.005660","article-title":"Comparative Genomics of Serial Isolates of Cryptococcus neoformans Reveals Gene Associated With Carbon Utilization and Virulence","volume":"3","author":"KL Ormerod","year":"2013","journal-title":"G3 (Bethesda)"},{"issue":"2","key":"pgen.1011979.ref031","doi-asserted-by":"crossref","DOI":"10.1073\/pnas.2217111120","article-title":"Similar evolutionary trajectories in an environmental Cryptococcus neoformans isolate after human and murine infection","volume":"120","author":"P Sephton-Clark","year":"2023","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"2","key":"pgen.1011979.ref032","article-title":"Microevolution during serial mouse passage demonstrates FRE3 as a virulence adaptation gene in Cryptococcus neoformans","volume":"5","author":"G Hu","year":"2014","journal-title":"MBio"},{"key":"pgen.1011979.ref033","doi-asserted-by":"crossref","first-page":"24","DOI":"10.1186\/s13100-015-0055-3","article-title":"Transposable element detection from whole genome sequence data","volume":"6","author":"AD Ewing","year":"2015","journal-title":"Mob DNA"},{"issue":"4","key":"pgen.1011979.ref034","doi-asserted-by":"crossref","first-page":"320","DOI":"10.1016\/j.mib.2007.05.014","article-title":"Cryptococcus neoformans, a fungus under stress","volume":"10","author":"SM Brown","year":"2007","journal-title":"Curr Opin Microbiol"},{"issue":"18","key":"pgen.1011979.ref035","doi-asserted-by":"crossref","first-page":"9973","DOI":"10.1073\/pnas.2001451117","article-title":"Transposon mobilization in the human fungal pathogen Cryptococcus is mutagenic during infection and promotes drug resistance in vitro","volume":"117","author":"A Gusa","year":"2020","journal-title":"Proc Natl Acad Sci USA"},{"issue":"4","key":"pgen.1011979.ref036","doi-asserted-by":"crossref","DOI":"10.1073\/pnas.2209831120","article-title":"Genome-wide analysis of heat stress-stimulated transposon mobility in the human fungal pathogen Cryptococcus deneoformans","volume":"120","author":"A Gusa","year":"2023","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"47","key":"pgen.1011979.ref037","doi-asserted-by":"crossref","DOI":"10.1073\/pnas.2416656121","article-title":"Distinct evolutionary trajectories following loss of RNA interference in Cryptococcus neoformans","volume":"121","author":"J Huang","year":"2024","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"8","key":"pgen.1011979.ref038","doi-asserted-by":"crossref","first-page":"1239","DOI":"10.1038\/s41564-022-01183-z","article-title":"Uncontrolled transposition following RNAi loss causes hypermutation and antifungal drug resistance in clinical isolates of Cryptococcus neoformans","volume":"7","author":"SJ Priest","year":"2022","journal-title":"Nat Microbiol"},{"issue":"1","key":"pgen.1011979.ref039","doi-asserted-by":"crossref","first-page":"179","DOI":"10.1016\/j.idc.2015.10.006","article-title":"Cryptococcosis","volume":"30","author":"EK Maziarz","year":"2016","journal-title":"Infect Dis Clin North Am"},{"issue":"12","key":"pgen.1011979.ref040","doi-asserted-by":"crossref","first-page":"973","DOI":"10.1038\/nrg2165","article-title":"A unified classification system for eukaryotic transposable elements","volume":"8","author":"T Wicker","year":"2007","journal-title":"Nat Rev Genet"},{"issue":"19","key":"pgen.1011979.ref041","doi-asserted-by":"crossref","first-page":"7884","DOI":"10.1073\/pnas.1104208108","article-title":"The catalytic domain of all eukaryotic cut-and-paste transposase superfamilies","volume":"108","author":"Y-W Yuan","year":"2011","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"12","key":"pgen.1011979.ref042","doi-asserted-by":"crossref","first-page":"3108","DOI":"10.1073\/pnas.1713725115","article-title":"RNAi is a critical determinant of centromere evolution in closely related fungi","volume":"115","author":"V Yadav","year":"2018","journal-title":"Proc Natl Acad Sci USA"},{"issue":"22","key":"pgen.1011979.ref043","doi-asserted-by":"crossref","first-page":"2566","DOI":"10.1101\/gad.1970910","article-title":"Sex-induced silencing defends the genome of Cryptococcus neoformans via RNAi","volume":"24","author":"X Wang","year":"2010","journal-title":"Genes Dev"},{"issue":"10","key":"pgen.1011979.ref044","doi-asserted-by":"crossref","first-page":"759","DOI":"10.1038\/s41580-025-00867-8","article-title":"Transcriptional and post-transcriptional regulation of transposable elements and their roles in development and disease","volume":"26","author":"\u0130A Il\u0131k","year":"2025","journal-title":"Nat Rev Mol Cell Biol"},{"key":"pgen.1011979.ref045","doi-asserted-by":"crossref","first-page":"43","DOI":"10.1146\/annurev.arplant.59.032607.092744","article-title":"Epigenetic regulation of transposable elements in plants","volume":"60","author":"D Lisch","year":"2009","journal-title":"Annu Rev Plant Biol"},{"issue":"1","key":"pgen.1011979.ref046","doi-asserted-by":"crossref","first-page":"141","DOI":"10.1186\/s12864-015-1347-1","article-title":"Whole genome comparative analysis of transposable elements provides new insight into mechanisms of their inactivation in fungal genomes","volume":"16","author":"J Amselem","year":"2015","journal-title":"BMC Genomics"},{"issue":"8","key":"pgen.1011979.ref047","doi-asserted-by":"crossref","first-page":"15348","DOI":"10.3390\/ijms140815348","article-title":"Functional diversity of RNAi-associated sRNAs in fungi","volume":"14","author":"FE Nicol\u00e1s","year":"2013","journal-title":"Int J Mol Sci"},{"issue":"5","key":"pgen.1011979.ref048","doi-asserted-by":"crossref","first-page":"957","DOI":"10.1016\/j.cell.2013.01.046","article-title":"Stalled spliceosomes are a signal for RNAi-mediated genome defense","volume":"152","author":"PA Dumesic","year":"2013","journal-title":"Cell"},{"issue":"7","key":"pgen.1011979.ref049","doi-asserted-by":"crossref","first-page":"2235","DOI":"10.1534\/g3.119.400330","article-title":"A Non-Dicer RNase III and Four Other Novel Factors Required for RNAi-Mediated Transposon Suppression in the Human Pathogenic Yeast Cryptococcus neoformans","volume":"9","author":"JE Burke","year":"2019","journal-title":"G3 (Bethesda)"},{"issue":"12","key":"pgen.1011979.ref050","doi-asserted-by":"crossref","first-page":"1070","DOI":"10.1016\/j.fgb.2010.10.005","article-title":"Characterizing the role of RNA silencing components in Cryptococcus neoformans","volume":"47","author":"G Janbon","year":"2010","journal-title":"Fungal Genet Biol"},{"issue":"8","key":"pgen.1011979.ref051","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pgen.1009743","article-title":"Epigenetic dynamics of centromeres and neocentromeres in Cryptococcus deuterogattii","volume":"17","author":"K Schotanus","year":"2021","journal-title":"PLoS Genet"},{"issue":"2","key":"pgen.1011979.ref052","doi-asserted-by":"crossref","DOI":"10.1016\/j.cell.2019.12.012","article-title":"Evolutionary Persistence of DNA Methylation for Millions of Years after Ancient Loss of a De Novo Methyltransferase","volume":"180","author":"S Catania","year":"2020","journal-title":"Cell"},{"key":"pgen.1011979.ref053","doi-asserted-by":"crossref","first-page":"204","DOI":"10.1016\/j.cell.2014.11.039","article-title":"Product binding enforces the genomic specificity of a yeast polycomb repressive complex","volume":"160","author":"PA Dumesic","year":"2015","journal-title":"Cell"},{"issue":"7","key":"pgen.1011979.ref054","doi-asserted-by":"crossref","first-page":"1207","DOI":"10.1101\/gr.218727.116","article-title":"Population genomics and the evolution of virulence in the fungal pathogen Cryptococcus neoformans","volume":"27","author":"CA Desjardins","year":"2017","journal-title":"Genome Res"},{"issue":"6","key":"pgen.1011979.ref055","doi-asserted-by":"crossref","first-page":"1921","DOI":"10.1128\/JCM.03177-13","article-title":"Multilocus sequence typing of serially collected isolates of Cryptococcus from HIV-infected patients in South Africa","volume":"52","author":"GERMS-SA","year":"2014","journal-title":"J Clin Microbiol"},{"issue":"4","key":"pgen.1011979.ref056","doi-asserted-by":"crossref","first-page":"400","DOI":"10.1016\/j.fgb.2007.12.004","article-title":"Six monophyletic lineages identified within Cryptococcus neoformans and Cryptococcus gattii by multi-locus sequence typing","volume":"45","author":"M Bovers","year":"2008","journal-title":"Fungal Genet Biol"},{"key":"pgen.1011979.ref057","article-title":"WHO fungal priority pathogens list to guide research, development and public health action","author":"Antimicrobial Resistance Division (AMR), Control of Neglected Tropical Diseases (NTD), Global Coordination and Partnership (GCP)","year":"2022"},{"issue":"6","key":"pgen.1011979.ref058","doi-asserted-by":"crossref","first-page":"4101","DOI":"10.1128\/MCB.19.6.4101","article-title":"Rapamycin antifungal action is mediated via conserved complexes with FKBP12 and TOR kinase homologs in Cryptococcus neoformans","volume":"19","author":"MC Cruz","year":"1999","journal-title":"Mol Cell Biol"},{"issue":"4","key":"pgen.1011979.ref059","first-page":"656","article-title":"BLAT--the BLAST-like alignment tool","volume":"12","author":"WJ Kent","year":"2002","journal-title":"Genome Res"},{"key":"pgen.1011979.ref060","doi-asserted-by":"crossref","first-page":"177","DOI":"10.1007\/978-1-62703-568-2_13","article-title":"Molecular genetics and epigenetics of CACTA elements","volume":"1057","author":"NV Fedoroff","year":"2013","journal-title":"Methods Mol Biol"},{"issue":"1","key":"pgen.1011979.ref061","doi-asserted-by":"crossref","first-page":"277","DOI":"10.1186\/s13059-019-1911-0","article-title":"SyRI: finding genomic rearrangements and local sequence differences from whole-genome assemblies","volume":"20","author":"M Goel","year":"2019","journal-title":"Genome Biol"},{"issue":"5","key":"pgen.1011979.ref062","doi-asserted-by":"crossref","first-page":"1676","DOI":"10.1073\/pnas.1321818111","article-title":"Lineage-specific expansions of TET\/JBP genes and a new class of DNA transposons shape fungal genomic and epigenetic landscapes","volume":"111","author":"LM Iyer","year":"2014","journal-title":"Proceedings of the National Academy of Sciences of the United States of America"},{"key":"pgen.1011979.ref063","unstructured":"Coffin JM, Hughes SH, Varmus HE. Structural classes of retroelements and replication strategies. 1997."},{"key":"pgen.1011979.ref064","doi-asserted-by":"crossref","first-page":"221","DOI":"10.1016\/j.virusres.2007.12.010","article-title":"The diversity of retrotransposons and the properties of their reverse transcriptases","volume":"134","author":"TH Eickbush","year":"2008","journal-title":"Virus Res"},{"issue":"21","key":"pgen.1011979.ref065","doi-asserted-by":"crossref","first-page":"5899","DOI":"10.1093\/emboj\/cdf592","article-title":"Human L1 element target-primed reverse transcription in vitro","volume":"21","author":"GJ Cost","year":"2002","journal-title":"EMBO J"},{"issue":"1","key":"pgen.1011979.ref066","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pgen.1008871","article-title":"Factors enforcing the species boundary between the human pathogens Cryptococcus neoformans and Cryptococcus deneoformans","volume":"17","author":"SJ Priest","year":"2021","journal-title":"PLoS Genet"},{"issue":"14","key":"pgen.1011979.ref067","doi-asserted-by":"crossref","first-page":"7847","DOI":"10.1073\/pnas.96.14.7847","article-title":"Identification of the endonuclease domain encoded by R2 and other site-specific, non-long terminal repeat retrotransposable elements","volume":"96","author":"J Yang","year":"1999","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"47","key":"pgen.1011979.ref068","doi-asserted-by":"crossref","first-page":"17602","DOI":"10.1073\/pnas.0605476103","article-title":"RNA from the 5\u2019 end of the R2 retrotransposon controls R2 protein binding to and cleavage of its DNA target site","volume":"103","author":"SM Christensen","year":"2006","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"2","key":"pgen.1011979.ref069","doi-asserted-by":"crossref","DOI":"10.1128\/microbiolspec.MDNA3-0001-2014","article-title":"Site-specific non-LTR retrotransposons","volume":"3","author":"H Fujiwara","year":"2015","journal-title":"Microbiol Spectr"},{"issue":"5","key":"pgen.1011979.ref070","doi-asserted-by":"crossref","first-page":"1872","DOI":"10.1073\/pnas.94.5.1872","article-title":"Sequence patterns indicate an enzymatic involvement in integration of mammalian retroposons","volume":"94","author":"J Jurka","year":"1997","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"2","key":"pgen.1011979.ref071","doi-asserted-by":"crossref","first-page":"389","DOI":"10.1534\/genetics.111.137950","article-title":"Telomere-targeted retrotransposons in the rice blast fungus Magnaporthe oryzae: agents of telomere instability","volume":"191","author":"JH Starnes","year":"2012","journal-title":"Genetics"},{"issue":"4","key":"pgen.1011979.ref072","doi-asserted-by":"crossref","DOI":"10.3390\/ijms22041555","article-title":"DNA demethylation in response to heat stress in Arabidopsis thaliana","volume":"22","author":"U Korotko","year":"2021","journal-title":"Int J Mol Sci"},{"issue":"6","key":"pgen.1011979.ref073","doi-asserted-by":"crossref","first-page":"655","DOI":"10.4161\/viru.32180","article-title":"The structure and retrotransposition mechanism of LTR-retrotransposons in the asexual yeast Candida albicans","volume":"5","author":"L Zhang","year":"2014","journal-title":"Virulence"},{"issue":"1","key":"pgen.1011979.ref074","doi-asserted-by":"crossref","first-page":"201","DOI":"10.1534\/genetics.116.190595","article-title":"Rewiring of Signaling Networks Modulating Thermotolerance in the Human Pathogen Cryptococcus neoformans","volume":"205","author":"DH Yang","year":"2017","journal-title":"Genetics"},{"issue":"1","key":"pgen.1011979.ref075","doi-asserted-by":"crossref","first-page":"5407","DOI":"10.1038\/s41467-022-33168-1","article-title":"Cryptococcal Hsf3 controls intramitochondrial ROS homeostasis by regulating the respiratory process","volume":"13","author":"X Gao","year":"2022","journal-title":"Nat Commun"},{"issue":"1","key":"pgen.1011979.ref076","first-page":"1","article-title":"Leveraging a new data resource to define the response of Cryptococcus neoformans to environmental signals","volume":"229","author":"YS Kang","year":"2025","journal-title":"Genetics"},{"issue":"3","key":"pgen.1011979.ref077","doi-asserted-by":"crossref","first-page":"205","DOI":"10.7326\/0003-4819-132-3-200002010-00006","article-title":"Evidence of zoonotic transmission of Cryptococcus neoformans from a pet cockatoo to an immunocompromised patient","volume":"132","author":"JD Nosanchuk","year":"2000","journal-title":"Ann Intern Med"},{"key":"pgen.1011979.ref078","doi-asserted-by":"crossref","first-page":"474","DOI":"10.1186\/1471-2105-7-474","article-title":"Annotation, submission and screening of repetitive elements in Repbase: RepbaseSubmitter and Censor","volume":"7","author":"O Kohany","year":"2006","journal-title":"BMC Bioinformatics"},{"issue":"4","key":"pgen.1011979.ref079","doi-asserted-by":"crossref","DOI":"10.1093\/molbev\/msae068","article-title":"Earl Grey: A Fully Automated User-Friendly Transposable Element Annotation and Analysis Pipeline","volume":"41","author":"T Baril","year":"2024","journal-title":"Mol Biol Evol"},{"issue":"5","key":"pgen.1011979.ref080","doi-asserted-by":"crossref","first-page":"464","DOI":"10.1101\/gr.8.5.464","article-title":"Transposable elements and genome organization: a comprehensive survey of retrotransposons revealed by the complete Saccharomyces cerevisiae genome sequence","volume":"8","author":"JM Kim","year":"1998","journal-title":"Genome Res"},{"issue":"12","key":"pgen.1011979.ref081","first-page":"6791","article-title":"Two related families of retrotransposons from Schizosaccharomyces pombe","volume":"10","author":"HL Levin","year":"1990","journal-title":"Mol Cell Biol"},{"issue":"2","key":"pgen.1011979.ref082","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1128\/microbiolspec.MDNA3-0053-2014","article-title":"The Ty1 LTR-retrotransposon of budding yeast, Saccharomyces cerevisiae","volume":"3","author":"MJ Curcio","year":"2015","journal-title":"Microbiol Spectr"},{"issue":"3","key":"pgen.1011979.ref083","doi-asserted-by":"crossref","first-page":"936","DOI":"10.1073\/pnas.88.3.936","article-title":"Single-step selection for Ty1 element retrotransposition","volume":"88","author":"MJ Curcio","year":"1991","journal-title":"Proc Natl Acad Sci USA"},{"issue":"23","key":"pgen.1011979.ref084","doi-asserted-by":"crossref","first-page":"4709","DOI":"10.1093\/nar\/28.23.4709","article-title":"Fission yeast retrotransposon Tf1 integration is targeted to 5\u2019 ends of open reading frames","volume":"28","author":"R Behrens","year":"2000","journal-title":"Nucleic Acids Res"},{"issue":"1","key":"pgen.1011979.ref085","doi-asserted-by":"crossref","first-page":"44","DOI":"10.1128\/EC.01.1.44-55.2002","article-title":"A long terminal repeat retrotransposon of fission yeast has strong preferences for specific sites of insertion","volume":"1","author":"TL Singleton","year":"2002","journal-title":"Eukaryot Cell"},{"issue":"8046","key":"pgen.1011979.ref086","doi-asserted-by":"crossref","first-page":"744","DOI":"10.1038\/s41586-024-08319-7","article-title":"Centrophilic retrotransposon integration via CENH3 chromatin in Arabidopsis","volume":"637","author":"S Tsukahara","year":"2025","journal-title":"Nature"},{"issue":"2","key":"pgen.1011979.ref087","doi-asserted-by":"crossref","first-page":"289","DOI":"10.1016\/j.molcel.2007.06.010","article-title":"Phosphorylation regulates integration of the yeast Ty5 retrotransposon into heterochromatin","volume":"27","author":"J Dai","year":"2007","journal-title":"Mol Cell"},{"issue":"10","key":"pgen.1011979.ref088","doi-asserted-by":"crossref","first-page":"691","DOI":"10.1038\/nrg2640","article-title":"The impact of retrotransposons on human genome evolution","volume":"10","author":"R Cordaux","year":"2009","journal-title":"Nat Rev Genet"},{"key":"pgen.1011979.ref089","doi-asserted-by":"crossref","first-page":"18","DOI":"10.1186\/1759-8753-5-18","article-title":"DINE-1, the highest copy number repeats in Drosophila melanogaster are non-autonomous endonuclease-encoding rolling-circle transposable elements (Helentrons)","volume":"5","author":"J Thomas","year":"2014","journal-title":"Mob DNA"},{"issue":"5","key":"pgen.1011979.ref090","doi-asserted-by":"crossref","first-page":"329","DOI":"10.1038\/nrg793","article-title":"Plant transposable elements: where genetics meets genomics","volume":"3","author":"C Feschotte","year":"2002","journal-title":"Nat Rev Genet"},{"issue":"1","key":"pgen.1011979.ref091","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pgen.1004115","article-title":"How a retrotransposon exploits the plant\u2019s heat stress response for its activation","volume":"10","author":"VV Cavrak","year":"2014","journal-title":"PLoS Genet"},{"issue":"1","key":"pgen.1011979.ref092","doi-asserted-by":"crossref","first-page":"209","DOI":"10.1186\/s13059-016-1072-3","article-title":"Recurrent evolution of heat-responsiveness in Brassicaceae COPIA elements","volume":"17","author":"B Pietzenuk","year":"2016","journal-title":"Genome Biol"},{"key":"pgen.1011979.ref093","doi-asserted-by":"crossref","DOI":"10.7554\/eLife.51139","article-title":"Diversification of the Caenorhabditis heat shock response by Helitron transposable elements","volume":"8","author":"JM Garrigues","year":"2019","journal-title":"Elife"},{"issue":"9","key":"pgen.1011979.ref094","doi-asserted-by":"crossref","first-page":"4233","DOI":"10.1128\/JVI.76.9.4233-4240.2002","article-title":"Ty1 defect in proteolysis at high temperature","volume":"76","author":"JF Lawler","year":"2002","journal-title":"J Virol"},{"issue":"36","key":"pgen.1011979.ref095","doi-asserted-by":"crossref","first-page":"17943","DOI":"10.1073\/pnas.1903936116","article-title":"The Hsp70 chaperone is a major player in stress-induced transposable element activation","volume":"116","author":"U Cappucci","year":"2019","journal-title":"Proc Natl Acad Sci USA"},{"key":"pgen.1011979.ref096","article-title":"Calcineurin contributes to RNAi-mediated transgene silencing and small interfering RNA production in the human fungal pathogen Cryptococcus neoformans","author":"V Yadav","year":"2024","journal-title":"Genetics"},{"issue":"6","key":"pgen.1011979.ref097","doi-asserted-by":"crossref","first-page":"115","DOI":"10.1007\/s11103-024-01509-x","article-title":"Heat stress causes chromatin accessibility and related gene expression changes in crown tissues of barley (Hordeum vulgare)","volume":"114","author":"A Kie\u0142bowicz-Matuk","year":"2024","journal-title":"Plant Mol Biol"},{"issue":"1","key":"pgen.1011979.ref098","doi-asserted-by":"crossref","first-page":"469","DOI":"10.1038\/s41467-023-36227-3","article-title":"HSFA1a modulates plant heat stress responses and alters the 3D chromatin organization of enhancer-promoter interactions","volume":"14","author":"Y Huang","year":"2023","journal-title":"Nat Commun"},{"issue":"12","key":"pgen.1011979.ref099","doi-asserted-by":"crossref","first-page":"1564","DOI":"10.1093\/bioinformatics\/btp253","article-title":"Fluctuation analysis CalculatOR: a web tool for the determination of mutation rate using Luria-Delbruck fluctuation analysis","volume":"25","author":"BM Hall","year":"2009","journal-title":"Bioinformatics"},{"key":"pgen.1011979.ref100","doi-asserted-by":"crossref","first-page":"5052","DOI":"10.1038\/srep05052","article-title":"PCR amplification of repetitive DNA: a limitation to genome editing technologies and many other applications","volume":"4","author":"CM Hommelsheim","year":"2014","journal-title":"Sci Rep"},{"key":"pgen.1011979.ref101","doi-asserted-by":"crossref","DOI":"10.1093\/nar\/gkae1082","article-title":"InterPro: the protein sequence classification resource in 2025","volume":"53","author":"M Blum","year":"2025","journal-title":"Nucleic Acids Research"},{"issue":"3","key":"pgen.1011979.ref102","article-title":"DNA strand-exchange patterns associated with double-strand break-induced and spontaneous mitotic crossovers in Saccharomyces cerevisiae","volume":"14","author":"YF Hum","year":"2018","journal-title":"PLoS Genet"},{"issue":"2","key":"pgen.1011979.ref103","doi-asserted-by":"crossref","first-page":"425","DOI":"10.1534\/genetics.118.300950","article-title":"Genetic Control of Genomic Alterations Induced in Yeast by Interstitial Telomeric Sequences","volume":"209","author":"A Moore","year":"2018","journal-title":"Genetics"},{"issue":"7","key":"pgen.1011979.ref104","doi-asserted-by":"crossref","first-page":"3022","DOI":"10.1093\/molbev\/msab120","article-title":"MEGA11: Molecular Evolutionary Genetics Analysis version 11","volume":"38","author":"K Tamura","year":"2021","journal-title":"Mol Biol Evol"},{"key":"pgen.1011979.ref105","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","author":"JW Pitkin","year":"1996","journal-title":"Microbiology (Reading)"},{"issue":"5","key":"pgen.1011979.ref106","doi-asserted-by":"crossref","first-page":"722","DOI":"10.1101\/gr.215087.116","article-title":"Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation","volume":"27","author":"S Koren","year":"2017","journal-title":"Genome Res"},{"issue":"5","key":"pgen.1011979.ref107","doi-asserted-by":"crossref","first-page":"540","DOI":"10.1038\/s41587-019-0072-8","article-title":"Assembly of long, error-prone reads using repeat graphs","volume":"37","author":"M Kolmogorov","year":"2019","journal-title":"Nat Biotechnol"},{"issue":"18","key":"pgen.1011979.ref108","doi-asserted-by":"crossref","first-page":"3094","DOI":"10.1093\/bioinformatics\/bty191","article-title":"Minimap2: pairwise alignment for nucleotide sequences","volume":"34","author":"H Li","year":"2018","journal-title":"Bioinformatics"},{"issue":"4","key":"pgen.1011979.ref109","doi-asserted-by":"crossref","first-page":"357","DOI":"10.1038\/nmeth.1923","article-title":"Fast gapped-read alignment with Bowtie 2","volume":"9","author":"B Langmead","year":"2012","journal-title":"Nat Methods"},{"issue":"11","key":"pgen.1011979.ref110","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0112963","article-title":"Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement","volume":"9","author":"BJ Walker","year":"2014","journal-title":"PLoS One"},{"issue":"1","key":"pgen.1011979.ref111","doi-asserted-by":"crossref","first-page":"24","DOI":"10.1038\/nbt.1754","article-title":"Integrative genomics viewer","volume":"29","author":"JT Robinson","year":"2011","journal-title":"Nat Biotechnol"},{"issue":"4","key":"pgen.1011979.ref112","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pgen.1004261","article-title":"Analysis of the genome and transcriptome of Cryptococcus neoformans var. grubii reveals complex RNA expression and microevolution leading to virulence attenuation","volume":"10","author":"G Janbon","year":"2014","journal-title":"PLoS Genet"},{"issue":"3","key":"pgen.1011979.ref113","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":"SF Altschul","year":"1990","journal-title":"J Mol Biol"},{"key":"pgen.1011979.ref114","doi-asserted-by":"crossref","first-page":"421","DOI":"10.1186\/1471-2105-10-421","article-title":"BLAST+: architecture and applications","volume":"10","author":"C Camacho","year":"2009","journal-title":"BMC Bioinformatics"},{"issue":"10","key":"pgen.1011979.ref115","doi-asserted-by":"crossref","first-page":"2922","DOI":"10.1093\/bioinformatics\/btac196","article-title":"plotsr: visualizing structural similarities and rearrangements between multiple genomes","volume":"38","author":"M Goel","year":"2022","journal-title":"Bioinformatics"},{"issue":"12","key":"pgen.1011979.ref116","doi-asserted-by":"crossref","first-page":"1639","DOI":"10.1093\/bioinformatics\/btaa1016","article-title":"Liftoff: accurate mapping of gene annotations","volume":"37","author":"A Shumate","year":"2021","journal-title":"Bioinformatics"},{"issue":"5","key":"pgen.1011979.ref117","doi-asserted-by":"crossref","first-page":"867","DOI":"10.1093\/bioinformatics\/btx699","article-title":"Mosdepth: quick coverage calculation for genomes and exomes","volume":"34","author":"BS Pedersen","year":"2018","journal-title":"Bioinformatics"},{"issue":"14","key":"pgen.1011979.ref118","doi-asserted-by":"crossref","first-page":"3059","DOI":"10.1093\/nar\/gkf436","article-title":"MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform","volume":"30","author":"K Katoh","year":"2002","journal-title":"Nucleic Acids Res"},{"issue":"4","key":"pgen.1011979.ref119","article-title":"SNP-sites: rapid efficient extraction of SNPs from multi-FASTA alignments","volume":"2","author":"AJ Page","year":"2016","journal-title":"Microb Genom"},{"issue":"2","key":"pgen.1011979.ref120","doi-asserted-by":"crossref","first-page":"80","DOI":"10.4161\/fly.19695","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":"P Cingolani","year":"2012","journal-title":"Fly (Austin)"}],"container-title":["PLOS Genetics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pgen.1011979","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,1,16]],"date-time":"2026-01-16T18:34:12Z","timestamp":1768588452000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pgen.1011979"}},"subtitle":[],"editor":[{"given":"Guilhem","family":"Janbon","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2026,1,16]]},"references-count":120,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2026,1,16]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pgen.1011979","relation":{},"ISSN":["1553-7404"],"issn-type":[{"value":"1553-7404","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,1,16]]}}}