The size and sequence organization of the centromeric region of Arabidopsis thaliana chromosome 5

We have determined the size of the centromeric region of Arabidopsis thalia na chromosome 5, which corresponds to the genetically defined centromere by Copenhaver et al. (Science, 286, 2468-2474, 1999) on the basis of restrict ion analysis. As a large clone gap was present in the previously constructe d contig map of the centromeric region, the restriction map of this region was constructed using Ase I, Not I, Apa I and Pme I and genomic DNA from a hypomethylated strain. The size of the centromeric region finally estimated by combination with the sequence data of cloned regions at both sides was 4.35 megabases (Mb). This value is over 2 Mb longer than those estimated in our previous work and also by Copenhaver et al. Combing this centromeric r egion with the physical map previously constructed, the entire length of ch romosome 5 becomes 31 Mb. Although the internal moiety of the centromeric r egion has not been sequenced yet because of extremely high repetition, the result of sequence analysis from both sides toward the inside strongly sugg ests that the centromeric region is composed of the central 2.9-Mb domain c onsisting of mainly 180-bp repeats and Athila retrotransposons and flanking regions containing various types of transposons. On the basis of these obs ervations, a structural model for the centromeric region is discussed.