{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,28]],"date-time":"2026-04-28T02:53:16Z","timestamp":1777344796814,"version":"3.51.4"},"reference-count":90,"publisher":"Oxford University Press (OUP)","issue":"11","license":[{"start":{"date-parts":[[2024,8,20]],"date-time":"2024-08-20T00:00:00Z","timestamp":1724112000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Canada's Genomic Enterprise"},{"DOI":"10.13039\/100015454","name":"The Centre for Applied Genomics","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100015454","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,11,6]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Blastomyces dermatitidis and Blastomyces gilchristii are cryptic species of fungi that cause blastomycosis, an often severe disease involving pulmonary infection capable of systemic dissemination. While these species appear morphologically identical, differences exist in the genetic makeup, geographical range, and possibly the clinical presentation of infection. Here, we show genetic divergence between the cryptic species through both a Blastomyces species tree constructed from orthologous protein sequences and whole genome single-nucleotide variant phylogenomic analysis. Following linked-read sequencing and de novo genome assembly, we characterized and compared the genomes of 3 B. dermatitidis and 3 B. gilchristii isolates. The B. gilchristii genomes (73.25\u201375.4\u2005Mb) were \u223c8\u2005Mb larger than the B. dermatitidis genomes (64.88\u201366.61\u2005Mb). Average nucleotide identity was lower between genomes of different species than genomes of the same species, yet functional classification of genes suggested similar proteomes. The most striking difference involved long terminal repeat retrotransposons. Although the same retrotransposon elements were detected in the genomes, the quantity of elements differed between the 2 species. Gypsy retrotransposon content was significantly higher in B. gilchristii (38.04\u201339.26\u2005Mb) than in B. dermatitidis (30.85\u201332.40\u2005Mb), accounting for the majority of genome size difference between species. Age estimation and phylogenetic analysis of the reverse transcriptase domains suggested that these retrotransposons are relatively ancient, with genome insertion predating the speciation of B. dermatitidis and B. gilchristii. We postulate that different trajectories of genome contraction led to genetic incompatibility, reproductive isolation, and speciation, highlighting the role of transposable elements in fungal evolution.<\/jats:p>","DOI":"10.1093\/g3journal\/jkae194","type":"journal-article","created":{"date-parts":[[2024,8,21]],"date-time":"2024-08-21T22:39:53Z","timestamp":1724279993000},"source":"Crossref","is-referenced-by-count":4,"title":["Comparative genome analysis and the genome-shaping role of long terminal repeat retrotransposons in the evolutionary divergence of fungal pathogens <i>Blastomyces dermatitidis<\/i> and <i>Blastomyces gilchristii<\/i>"],"prefix":"10.1093","volume":"14","author":[{"ORCID":"https:\/\/orcid.org\/0009-0004-4073-3265","authenticated-orcid":false,"given":"Lisa R","family":"McTaggart","sequence":"first","affiliation":[{"name":"Microbiology and Laboratory Services, Public Health Ontario , 661 University Avenue, Toronto, ON M5G 1M1 ,","place":["Canada"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2452-3776","authenticated-orcid":false,"given":"Thomas W A","family":"Braukmann","sequence":"additional","affiliation":[{"name":"Microbiology and Laboratory Services, Public Health Ontario , 661 University Avenue, Toronto, ON M5G 1M1 ,","place":["Canada"]},{"name":"Department of Laboratory Medicine and Pathobiology, University of Toronto , 1 King's College Circle, Toronto, ON M5S 1A8 ,","place":["Canada"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6033-7244","authenticated-orcid":false,"given":"Julianne V","family":"Kus","sequence":"additional","affiliation":[{"name":"Microbiology and Laboratory Services, Public Health Ontario , 661 University Avenue, Toronto, ON M5G 1M1 ,","place":["Canada"]},{"name":"Department of Laboratory Medicine and Pathobiology, University of Toronto , 1 King's College Circle, Toronto, ON M5S 1A8 ,","place":["Canada"]}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2024,8,20]]},"reference":[{"issue":"6","key":"2024110622330731700_jkae194-B1","doi-asserted-by":"publisher","first-page":"1332","DOI":"10.1093\/molbev\/msy083","article-title":"Neutral theory, transposable elements, and eukaryotic genome evolution","volume":"35","author":"Arkhipova","year":"2018","journal-title":"Mol Biol Evol"},{"issue":"5","key":"2024110622330731700_jkae194-B2","doi-asserted-by":"publisher","first-page":"843","DOI":"10.1007\/s11046-020-00431-2","article-title":"Re-drawing the maps for endemic mycoses","volume":"185","author":"Ashraf","year":"2020","journal-title":"Mycopathologia"},{"issue":"9","key":"2024110622330731700_jkae194-B3","doi-asserted-by":"publisher","first-page":"1924","DOI":"10.3201\/eid2809.220392","article-title":"Molecular epidemiology of Blastomyces gilchristii clusters, Minnesota, 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