Holocentromeres in Rhynchospora are associated with genome-wide centromere-specific repeat arrays interspersed among euchromatin

Holocentric chromosomes are characterized by kinetochore activity along each sister chromatid. Although the kinetochore structure seems to be well conserved, as in monocentric organisms, the organization of holocentromeres is still elusive, and no centromeric repeat has been found associated with centromeric histone H3 variant-positive centromeric nucleosomes for any holocentric organism studied hitherto. We demonstrate that holocentrics of the sedge (Cyperaceae) Rhynchospora pubera possess different classes of centromere-specific repeats. Holocentromeres are composed of multiple centromeric units interspersing the gene-containing chromatin, and, as a functional adaption, a cell-cycle-dependent shuffling of centromeric units results in the formation of functional (poly)centromeres during cell division. The genome-wide distribution of centromeric repeat arrays interspersing the euchromatin provides a previously unidentified type of centromere organization.