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Genomic rearrangements associated with speciation often result in variation in chromosome number among closely related species.  Malassezia  species show variable karyotypes ranging between six and nine chromosomes. Here, we experimentally identified all eight centromeres in  M. sympodialis  as 3–5-kb long kinetochore-bound regions that span an AT-rich core and are depleted of the canonical histone H3. Centromeres of similar sequence features were identified as CENP-A-rich regions in  Malassezia furfur , which has seven chromosomes, and histone H3 depleted regions in  Malassezia slooffiae  and  Malassezia globosa  with nine chromosomes each. Analysis of synteny conservation across centromeres with newly generated chromosome-level genome assemblies suggests two distinct mechanisms of chromosome number reduction from an inferred nine-chromosome ancestral state: (a) chromosome breakage followed by loss of centromere DNA and (b) centromere inactivation accompanied by changes in DNA sequence following chromosome–chromosome fusion. We propose that AT-rich centromeres drive karyotype diversity in the  Malassezia  species complex through breakage and inactivation.

Loss of centromere function drives karyotype evolution in closely related Malassezia species