Centromeres in budding yeasts are conserved in chromosomal location but not in structure

The budding yeast Saccharomyces cerevisiae has 'point' centromeres, which are much smaller and simpler than centromeres of most other eukaryotes and have a defined DNA sequence. Other yeast taxa have different and highly diverse centromere structures, but a clear picture of how yeast centromeres have evolved is lacking. Here, we investigated nine yeast species in two taxonomic orders that are close outgroups to S. cerevisiae. We find that they have a wide diversity of centromere structures, indicating that multiple transitions of structure have occurred within the last 200 Myr. Some species have centromeres with defined sequence motifs (17 - 200 bp), others consist of Inverted Repeats (IRs), and others have Ty5-like retroelement clusters. Strikingly, the chromosomal locations of centromeres have largely been conserved across taxonomic orders, even as their structures have changed, which suggests that structure replacement occurs in situ. In some Barnettozyma species we find that a single genome can contain chromosomes with different centromere structures - some with IRs and some without - which suggests that a structural transition is underway in this genus. We identified only one example of a centromere moving by a long distance: a new centromere formed recently at the MAT locus of Barnettozyma californica, 250 kb from the previous centromere on that chromosome.