Telomeric assemblies of Paracoccidioides genomes

Paracoccidioides 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 brasiliensis complex ( P. brasiliensis, P. americana, P. restrepiensis, P. venezuelensis ) and P. lutzii . These include the first complete telomere-to-telomere assemblies for P. brasiliensis (Pb18) and P. americana (Pb03), each with five chromosomes. Comparative analyses revealed chromosomal fusion and fission events distinguishing P. brasiliensis and P. americana , and a 90 kb tandem duplication in P. americana containing siderophore biosynthesis genes ( sid1, sid3, sid4 ), 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 P. lutzii and P. venezuelensis . RNA transposable elements were enriched near telomeres, correlated with genome size, and most abundant in P. lutzii . These assemblies provide key resources for understanding genome evolution and introgression in Paracoccidioides .