At anaphase onset, the protease separase triggers chromosome segregation by 
cleaving the chromosomal cohesin complex. Here, we show that cohesin destruction 
in metaphase is sufficient for segregation of much of the budding yeast genome, 
but not of the long arm of chromosome XII that contains the rDNA repeats. rDNA 
in metaphase, unlike most other sequences, remains in an undercondensed and 
topologically entangled state. Separase, concomitantly with cleaving cohesin, 
activates the phosphatase Cdc14. We find that Cdc14 exerts two effects on rDNA, 
both mediated by the condensin complex. Lengthwise condensation of rDNA shortens 
the chromosome XII arm sufficiently for segregation. This condensation depends 
on the aurora B kinase complex. Independently of condensation, Cdc14 induces 
condensin-dependent resolution of cohesin-independent rDNA linkage. 
Cdc14-dependent sister chromatid resolution at the rDNA could introduce a 
temporal order to chromosome segregation.