{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"institution":[{"name":"bioRxiv"}],"indexed":{"date-parts":[[2026,1,16]],"date-time":"2026-01-16T01:25:45Z","timestamp":1768526745970,"version":"3.49.0"},"posted":{"date-parts":[[2025,11,3]]},"group-title":"Microbiology","reference-count":0,"publisher":"openRxiv","license":[{"start":{"date-parts":[[2025,11,3]],"date-time":"2025-11-03T00:00:00Z","timestamp":1762128000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"accepted":{"date-parts":[[2025,10,30]]},"abstract":"<jats:p>\n                  <jats:italic>Paracoccidioides<\/jats:italic>\n                  is a genus of dimorphic fungal pathogens endemic to Latin America. We generated long-read de novo assemblies for 11 isolates representing four species of the\n                  <jats:italic>brasiliensis<\/jats:italic>\n                  complex (\n                  <jats:italic>P. brasiliensis, P. americana, P. restrepiensis, P. venezuelensis<\/jats:italic>\n                  ) and\n                  <jats:italic>P. lutzii<\/jats:italic>\n                  . These include the first complete telomere-to-telomere assemblies for\n                  <jats:italic>P. brasiliensis<\/jats:italic>\n                  (Pb18) and\n                  <jats:italic>P. americana<\/jats:italic>\n                  (Pb03), each with five chromosomes. Comparative analyses revealed chromosomal fusion and fission events distinguishing\n                  <jats:italic>P. brasiliensis<\/jats:italic>\n                  and\n                  <jats:italic>P. americana<\/jats:italic>\n                  , and a 90 kb tandem duplication in\n                  <jats:italic>P. americana<\/jats:italic>\n                  containing siderophore biosynthesis genes (\n                  <jats:italic>sid1, sid3, sid4<\/jats:italic>\n                  ), a cluster of putative virulence factors. Mitochondrial genomes showed conserved gene order but a phylogenetic topology inconsistent with the nuclear tree, suggesting mitochondrial introgression between\n                  <jats:italic>P. lutzii<\/jats:italic>\n                  and\n                  <jats:italic>P. venezuelensis<\/jats:italic>\n                  . RNA transposable elements were enriched near telomeres, correlated with genome size, and most abundant in\n                  <jats:italic>P. lutzii<\/jats:italic>\n                  . These assemblies provide key resources for understanding genome evolution and introgression in\n                  <jats:italic>Paracoccidioides<\/jats:italic>\n                  .\n                <\/jats:p>","DOI":"10.1101\/2025.10.30.685552","type":"posted-content","created":{"date-parts":[[2025,11,3]],"date-time":"2025-11-03T14:40:19Z","timestamp":1762180819000},"source":"Crossref","is-referenced-by-count":0,"title":["Telomeric assemblies of\n                  <i>Paracoccidioides<\/i>\n                  genomes"],"prefix":"10.64898","author":[{"given":"Dmitry","family":"Grinevich","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Oliver","family":"Kompathoum","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jingbaoyi (Janet)","family":"Li","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"David A","family":"Turissini","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Patrick","family":"Kelly","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"McKenna","family":"Sutherland","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Santiago","family":"Marin","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Oscar M.","family":"Gomez","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Gil","family":"Benard","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Maria Aparecida","family":"Shikanai-yasuda","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Tiago Alexandre","family":"Cocio","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Adriana Pardini","family":"Vicentini","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Zoilo","family":"Pires de Camargo","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Anderson","family":"Messias Rodrigues","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2686-8193","authenticated-orcid":false,"given":"Rosane","family":"Hahn","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Beatriz","family":"Mota","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Priscilla","family":"Marques de Macedo","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6639-6058","authenticated-orcid":false,"given":"Rodrigo","family":"Almeida-Paes","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Primavera","family":"Alvarado","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Rosely Maria","family":"Zancope-Oliveira","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8594-9087","authenticated-orcid":false,"given":"Juan G.","family":"McEwen","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2085-9667","authenticated-orcid":false,"given":"Victoria E","family":"Sep\u00falveda","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1763-3464","authenticated-orcid":false,"given":"Marcus de Melo","family":"Teixeira","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7597-602X","authenticated-orcid":false,"given":"Daniel R","family":"Matute","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"54368","container-title":[],"original-title":[],"link":[{"URL":"https:\/\/syndication.highwire.org\/content\/doi\/10.1101\/2025.10.30.685552","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,1,15]],"date-time":"2026-01-15T09:56:55Z","timestamp":1768471015000},"score":1,"resource":{"primary":{"URL":"http:\/\/biorxiv.org\/lookup\/doi\/10.1101\/2025.10.30.685552"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,11,3]]},"references-count":0,"URL":"https:\/\/doi.org\/10.1101\/2025.10.30.685552","relation":{},"subject":[],"published":{"date-parts":[[2025,11,3]]},"subtype":"preprint"}}