Sequential De Novo Centromere Formation and Inactivation on a Chromosomal Fragment in Maize

De novo centromere formation and centromere inactivation indicate significant epigenetic aspects controlling centromere assembly and function. In maize (Zea mays), misdivision of the B chromosome centromere on chromosome B-9 from reciprocal translocation between B chromosome and the short arm of chromosome 9 (TB-9Sb) can produce many variants with varying centromere sizes and centromeric DNA sequences. In such derivatives of TB-9Sb, we found a de novo centromere on chromosome derivative 3-3, which has no canonical centromeric repeat sequences. This centromere is derived from a 288-kb region on the short arm of chromosome 9, and is 19 megabases (Mb) removed from the translocation breakpoint of chromosome 9 in TB-9Sb. The functional B centromere in progenitor telo2-2 is deleted from derivative 3-3 but some B-repeat sequences remain. The de novo centromere of derivative 3-3 becomes inactive in three further derivatives with new centromeres being formed elsewhere on each chromosome. In derivative 3-3-11, the new centromere is only 200kb and located 3 Mb away from the translocation breakpoint of TB-9Sb. Our results suggest that de novo centromere initiation is quite common and can persist on chromosomal fragments without a canonical centromere, newly formed centromere on the acentric chromosomal fragment can take place of the former one by inactivation. However, we hypothesize that when de novo centromeres are initiated in opposition to a larger normal centromere, they are cleared from the chromosome by inactivation, thus maintaining karyotype integrity.