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The human fungal pathogen  Cryptococcus deuterogattii  is RNAi-deficient and lacks active transposons in its genome.  C. deuterogattii  has regional centromeres that contain only transposon relics. To investigate the impact of centromere loss on the  C. deuterogattii  genome, either centromere 9 or 10 was deleted. Deletion of either centromere resulted in neocentromere formation and interestingly, the genes covered by these neocentromeres maintained wild-type expression levels. In contrast to  cen9 ∆ mutants,  cen10 ∆ mutant strains exhibited growth defects and were aneuploid for chromosome 10. At an elevated growth temperature (37°C), the  cen10 ∆ chromosome was found to have undergone fusion with another native chromosome in some isolates and this fusion restored wild-type growth. Following chromosomal fusion, the neocentromere was inactivated, and the native centromere of the fused chromosome served as the active centromere. The neocentromere formation and chromosomal fusion events observed in this study in  C. deuterogattii  may be similar to events that triggered genomic changes within the  Cryptococcus / Kwoniella  species complex and may contribute to speciation throughout the eukaryotic domain.

Centromere deletion in Cryptococcus deuterogattii leads to neocentromere formation and chromosome fusions