Composition and Structure of Rice Centromeres and Telomeres

Complete or partial sequences of centromeres and telomeres of a number of rice chromosomes are now publicly available. In this chapter, we summarize the current findings on the DNA content and structure of these special regions. Core regions of rice centromeres consist of the satellite repeat CentO organized in tandem arrays and copies of the Ty3/gypsy-type retrotransposon CRR physically associated with the CentO arrays. The physical size of CentO arrays differs considerably among individual chromosomes. Unexpectedly, rice centromeres also contain active genes. Telomere satellite repeat arrays are highly conserved within the plant kingdom, but their length varies considerably among species and even among rice chromosomes. Frequent nucleotide substitutions and rearrangements of the satellite repeat sequences are detected mainly within the proximal telomere regions in rice. Subtelomere-associated repeats appear to be species-specific; at least 14 of its 24 chromosomal ends in the rice cultivar Nipponbare contain no TrsA sequences, that is, the telomere arrays are directly attached to gene-containing regions. Despite the conservation of functions, both centromeres and telomeres in rice reveal a considerable size variation and sequence divergence, thereby providing insights into the structural and evolutionary dynamics of these highly heterochromatic regions.