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Despite the increasing clinical significance, genomic data for M. clavatus remain limited. In this study, we report the first chromosomal-level genome assembly of M. clavatus using hybrid sequencing with Illumina and Oxford Nanopore Technologies. Three clinical isolates obtained from ICU patients in Verona (Italy) were sequenced and analyzed. The M. clavatus genome was resolved into 4 nuclear chromosomes and 1 circular mitochondrial genome, with a total length of 17.6\u2005Mb and with 4,065 predicted protein-coding genes. Comparative analyses revealed structural differences from its closely related species M. capitatus. Phylogenetic analysis of 40 strains assembled on the resolved genome identified a novel clade (D), distinct from the previously described clades A, B, and C. All isolates exhibited intrinsic resistance to echinocandins and fluconazole. Genetic analysis identified conserved mutations in the FKS1 hotspot region encoding 1,3-\u03b2-glucan synthase, mirroring resistance-associated substitutions in M. capitatus. Additionally, a putative cyp51 homolog was identified as a likely contributor to azole resistance, suggesting conserved resistance mechanisms across Magnusiomyces species. This study discloses a new chromosomal-level assembly for M. clavatus, providing a significant genomic framework. This resource could enhance the accuracy of diagnostic methods, enabling comparative genomics with closely related fungi and facilitating a deeper investigation into the mechanisms of antifungal resistance and pathogenicity of this rare but increasingly reported pathogen.<\/jats:p>","DOI":"10.1093\/g3journal\/jkaf201","type":"journal-article","created":{"date-parts":[[2025,9,3]],"date-time":"2025-09-03T19:13:21Z","timestamp":1756926801000},"source":"Crossref","is-referenced-by-count":2,"title":["Chromosomal-level assembly of\n                    <i>Magnusiomyces clavatus<\/i>\n                    : novel genetic insights on an emerging fungal pathogen"],"prefix":"10.1093","volume":"15","author":[{"given":"Emil","family":"Tonon","sequence":"first","affiliation":[{"name":"Department of Diagnostic and Public Health, Division of Microbiology, University of Verona , Verona 37134 ,","place":["Italy"]},{"name":"UOC Microbiology, AOUI Verona , Verona 37134 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