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Yet, the genetic mechanisms driving strain-to-strain variation remain poorly understood. Here, we determined the extent to which\n                      <jats:italic toggle=\"yes\">Starships<\/jats:italic>\n                      \u2014giant transposons capable of mobilizing numerous fungal genes\u2014generate genetic and phenotypic variability in the opportunistic human pathogen\n                      <jats:italic toggle=\"yes\">Aspergillus fumigatus<\/jats:italic>\n                      . We analyzed 519 diverse strains, including 11 newly sequenced with long-read technology and multiple isolates of the same reference strain, to reveal 20 distinct\n                      <jats:italic toggle=\"yes\">Starships<\/jats:italic>\n                      that are generating genomic heterogeneity over timescales relevant for experimental reproducibility.\n                      <jats:italic toggle=\"yes\">Starship<\/jats:italic>\n                      -mobilized genes encode diverse functions, including known biofilm-related virulence factors and biosynthetic gene clusters, and many are differentially expressed during infection and antifungal exposure in a strain-specific manner. These findings support a new model of fungal evolution wherein\n                      <jats:italic toggle=\"yes\">Starships<\/jats:italic>\n                      help generate variation in genome structure, gene content, and expression among fungal strains. Together, our results demonstrate that\n                      <jats:italic toggle=\"yes\">Starships<\/jats:italic>\n                      are a previously hidden mechanism generating genotypic and, in turn, phenotypic heterogeneity in a major human fungal pathogen.\n                    <\/jats:p>\n                    <jats:sec>\n                      <jats:title>IMPORTANCE<\/jats:title>\n                      <jats:p>\n                        No \u201cone size fits all\u201d option exists for treating fungal infections in large part due to genetic and phenotypic variability among strains. Accounting for strain heterogeneity is thus fundamental for developing efficacious treatments and strategies for safeguarding human health. Here, we report significant progress toward achieving this goal by uncovering a previously hidden mechanism generating heterogeneity in the human fungal pathogen\n                        <jats:italic toggle=\"yes\">Aspergillus fumigatus<\/jats:italic>\n                        : giant transposons, called\n                        <jats:italic toggle=\"yes\">Starships<\/jats:italic>\n                        , that span dozens of kilobases and mobilize fungal genes as cargo. By conducting a systematic investigation of these unusual transposons in a single fungal species, we demonstrate their contributions to population-level variation at the genome, pangenome, and transcriptome levels. The\n                        <jats:italic toggle=\"yes\">Starship<\/jats:italic>\n                        compendium we develop will not only help predict variation introduced by these elements in laboratory experiments but will serve as a foundational resource for determining how\n                        <jats:italic toggle=\"yes\">Starships<\/jats:italic>\n                        impact clinically relevant phenotypes, such as antifungal resistance and pathogenicity.\n                      <\/jats:p>\n                    <\/jats:sec>\n                  <\/jats:sec>","DOI":"10.1128\/mbio.01092-25","type":"journal-article","created":{"date-parts":[[2025,5,12]],"date-time":"2025-05-12T09:00:22Z","timestamp":1747040422000},"update-policy":"https:\/\/doi.org\/10.1128\/asmj-crossmark-policy-page","source":"Crossref","is-referenced-by-count":21,"title":["Giant transposons promote strain heterogeneity in a major fungal pathogen"],"prefix":"10.1128","volume":"16","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-0438-7495","authenticated-orcid":false,"given":"Emile","family":"Gluck-Thaler","sequence":"first","affiliation":[{"id":[{"id":"https:\/\/ror.org\/00vasag41","id-type":"ROR","asserted-by":"publisher"}],"name":"Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuch\u00e2tel","place":["Neuch\u00e2tel, Switzerland"]},{"id":[{"id":"https:\/\/ror.org\/01y2jtd41","id-type":"ROR","asserted-by":"publisher"}],"name":"Department of Plant Pathology, University of Wisconsin-Madison","place":["Madison, USA"]},{"id":[{"id":"https:\/\/ror.org\/05gbven85","id-type":"ROR","asserted-by":"publisher"}],"name":"Wisconsin Institute for Discovery","place":["Madison, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1966-9946","authenticated-orcid":false,"given":"Adrian","family":"Forsythe","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/048a87296","id-type":"ROR","asserted-by":"publisher"}],"name":"Systematic Biology, Department of Organismal Biology, Uppsala University","place":["Uppsala, Sweden"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4402-0295","authenticated-orcid":true,"given":"Charles","family":"Puerner","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/049s0rh22","id-type":"ROR","asserted-by":"publisher"}],"name":"Department of Microbiology and Immunology, Geisel School of Medicine, Dartmouth College","place":["Hanover, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9808-0701","authenticated-orcid":true,"given":"Cecilia","family":"Gutierrez-Perez","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/049s0rh22","id-type":"ROR","asserted-by":"publisher"}],"name":"Department of Microbiology and Immunology, Geisel School of Medicine, Dartmouth College","place":["Hanover, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7591-0020","authenticated-orcid":true,"given":"Jason E.","family":"Stajich","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/03nawhv43","id-type":"ROR","asserted-by":"publisher"}],"name":"Department of Microbiology and Plant Pathology, University of California-Riverside","place":["Riverside, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2072-380X","authenticated-orcid":true,"given":"Daniel","family":"Croll","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/00vasag41","id-type":"ROR","asserted-by":"publisher"}],"name":"Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuch\u00e2tel","place":["Neuch\u00e2tel, Switzerland"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5503-5006","authenticated-orcid":true,"given":"Robert A.","family":"Cramer","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/049s0rh22","id-type":"ROR","asserted-by":"publisher"}],"name":"Department of Microbiology and Immunology, Geisel School of Medicine, Dartmouth College","place":["Hanover, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2013-7445","authenticated-orcid":true,"given":"Aaron A.","family":"Vogan","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/048a87296","id-type":"ROR","asserted-by":"publisher"}],"name":"Systematic Biology, Department of Organismal Biology, Uppsala University","place":["Uppsala, Sweden"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"235","reference":[{"key":"e_1_3_4_2_2","volume-title":"WHO fungal priority pathogens list to guide research, development and public health action","author":"World Health Organization","year":"2022","unstructured":"World Health Organization. 2022. 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