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Rice centromeres are comprised of centromeric retrotransposons, named CRR, and a 155-bp satellite repeats, called CentO. Analysis of CentO repeat arrays from rice chromosomes 1 and 8 revealed higher order structures and local homogenization of the CentO repeats. Sequence variability analysis of centromeric CentO repeats revealed a single variable domain within the repeat. Transcripts derived from both strands of the CentO repeats were also detected in rice. The CentO transcripts are processed into siRNA, suggesting a potential role of this satellite repeat family in epigenetic chromatin modification. Interestingly, several wild Oryza species lack the CentO repeat. Using ChIP-cloning, I identified three new repeats (CentO-C1, CentO-C2 and CentO-F) from the functional centromeric regions of O. rhizomatis and O. branchyantha. CentO-C1 has sequence homology within an 80-bp region on both CentO and the centromere repeats of maize and millet. CentO-C2 is mainly located in the centromere. However, CentO-F is entirely unique in sequence. Thus, centromeric satellite repeats have been shown to evolve rapidly in closely related rice species. In A. thaliana, centromeres are composed of megabase-sized arrays of a 178-bp satellite repeat, which is the key functional DNA element for centromeres. We analyzed the 178-bp satellite repeat arrays in the centromere of Arabidopsis chromosome 5 and identified higher order structures in centromere 5 (CEN5). Sequence variability analysis of the 178-bp satellite repeats revealed either conserved or variable domains within the 178-bp repeat from different chromosomal domains. Additionally, centromeric 178-bp repeats are hypomethylated compared with pericentromeric 178-bp repeats. This differential methylation may result from a distinct distribution pattern of the DNA methylation sites on these repeats. Finally, we characterized an A. thaliana transgenic line that accumulates satellite transcripts of the 178-bp centromeric repeat. While
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