Isolated clusters of paired tandemly repeated sequences in the Xenopus laevis genome

There exist in the Xenopus laevis genome clusters of tandemly repeated DNA sequences, consisting of two types of 393-base-pair repeating unit. Each such cluster contains several units of one of these paired tandem repeats (PTR-1), followed by several units of the other repeat (PTR-2). The number of repeats of each type is variable from cluster to cluster and averages about seven of each type per cluster. Every cluster has ca. 1,000 base pairs of common left flanking sequence (adjacent to the PTR-1 repeats) and 1,000 base pairs of common right flanking sequence (adjacent to the PTR-2 repeats). Beyond these common flanks, the DNA sequences are different in the eight cloned genomic fragments we have studied. Thus, the hundreds of PTR clusters in the genome are dispersed at apparently unrelated sites. Nucleotide sequences of representative PTR-1 and PTR-2 repeats are 64% homologous. These sequences do not reveal an obvious function. However, the related species X. mulleri and X. borealis have sequences homologous to PTR-1 and PTR-2, which show the same repeat lengths and genomic organization. This evolutionary conservation suggests positive selection for the clusters. Maintenance of these sequences at dispersed sites imposes constraints on possible mechanisms of concerted evolution.