Characterization of Chromosomal Ends on the Basis of Chromosome-Specific Telomere Variants and Subtelomeric Repeats in Rice ( Oryza sativa L.)

The telomeric sequences in rice are composed of the plant canonical telomeric sequence TTTAGGG and blocks of at least six variants in a chromosome-specific manner. Variants are more common in the proximal region than in the distal region, suggesting that the telomeres in the proximal region have rarely been reconstructed by the action of telomerase on an evolutionary timescale. The chromosome-specific distribution of telomeric variants suggests that they have arisen from the rapid expansion of a single mutation rather than from the gradual accumulation of random mutations. TrsA—a subtelomeric repetitive sequence of rice—is arrayed in tandem on the ends of 5L, 6S, 8L, 9L, and 12L. Rice subtelomeres are composed of discrete clusters of a TrsA-rich region and a gene-rich region with high transcriptional activity. Intra-chromosomal duplications have resulted in a striking degree of variation in the number and distribution of TrsAs, suggesting that the areas near the ends of the chromosomes are dynamic and variable.