Sequences from higher primates orthologous to the human Xp/Yp telomere junction region reveal gross rearrangements and high levels of divergence

A high level of sequence polymorphism combined with linkage disequilibriumhas created a limited number of highly diverged haplotypes across the humanXp/Yp telomere junction region. To gain insight into the unusual geneticcharacteristics of this region, we have examined the orthologous sequencesin the common chimpanzee (Pan troglodytes ), the gorilla (Gorilla gorilla)and the orang-utan (Pongo pygmaeus). Divergence from the human Xp/Ypsequence is higher (average 2.6-fold) than that observed at other loci. Theposition of the human Xp/Yp telomere is unique, as additional sequences arepresent at this location in the other three species. These included anarray of subterminal satellite in the chimpanzee and, in the gorilla asmall interstitial array of telomere-like repeats followed by sequenceswith strong homology to the human 18p subterminal region. In theorang-utan, two alleles with different structures were identified. Thesediffer by the presence or absence of a short interspersed nuclear element(SINE) sequence just proximal to long arrays of telomere-like repeatsequences that probably represent the proximal end of the orang-utan Xp/Yptelomere. In addition, a high level of sequence divergence between the twoorang-utan structures was identified. This divergence is similar to thatobserved between the human Xp/Yp telomere-adjacent haplotypes. The highsequence divergence and evidence of gross rearrangements indicate that theXp/Yp telomeric region has evolved faster than the rest of the genome.