High-quality genome assembly and comparative analysis reveal extensive genomic variation in Talaromyces marneffei

<i>Talaromyces marneffei</i> is a dimorphic fungus that transitions from a filamentous form at 25 °C to a pathogenic yeast form at 37 °C, demonstrating pathogenicity mostly in immunocompromised individuals, such as those with human immunodeficiency virus/AIDS. Though it is one of the most severe infectious fungi in Southeast Asia, the lack of comprehensive genomic analysis has hindered advancement in strain differentiation, diagnosis and treatment. In this study, we assembled a high-quality genome of <i>T. marneffei</i> ATCC 18224, resulting in a 28.9 Mb genome distributed across 11 contigs, using third-generation Oxford Nanopore Technologies sequencing reads. Notably, we identified a strain-specific 740-kb segmental duplication in strain ATCC 18224, potentially mediated by inserting a Ty1/<i>Copia</i> long terminal repeat (LTR) retrotransposon. This segmental duplication includes various functional genes, with 75 differentially expressed during its dimorphic transition. Comparative genomic analysis revealed large-scale rearrangements in strains PM1 and 11CN-20-091, which were inconsistent with the phylogenomic trees of six <i>T. marneffei</i> strains and required further investigation. Additionally, we observed substantial genetic structural variations in LTR retrotransposons, particularly within the Ty1/<i>Copia</i> family, including two significant recent expansions in strain ATCC 18224. In summary, the identification and characterization of these extensive genomic structural variations in <i>T. marneffei</i> contribute to a deep understanding of its genetic diversity and will facilitate improvements in genotyping, classification and genomic surveillance.