Subfamilies and nearest-neighbour dendrogram for the LTRs of human endogenous retroviruses HERV-K mapped on human chromosome 19: physical neighbourhood does not correlate with identity level

Abstract

Sequences of 45 long terminal repeats (LTRs) of the human endogenous retroviruses HERV-K family, precisely mapped by us earlier on human chromosome 19, were determined and a nearest-neighbour dendrogram was constructed. No correlation was observed between the degree of identity of the LTR pairs and their relative positions on the chromosome. Thus, sequences of distantly located LTRs, even positioned on different chromosome arms, could be highly similar to each other, whereas those of closely located LTRs could differ significantly. We conclude that the LTRs have randomly transposed across the chromosome in the course of evolution. The alignment of the LTR sequences allowed us to assign most of the LTRs to two major subfamilies. The LTRs belonging to the first subfamily (LTR-I) are characterised by higher intrasubfamily sequence divergence than those of the second subfamily (LTR-II). The two subfamilies are easily distinguished by the presence of characteristic deletions/insertions in the LTR sequences. The higher divergence of the first subfamily members suggests that their propagation started at earlier stages of evolution, probably soon after the insertion of their ancestral sequence into the primate genome. In turn, each of the subfamilies includes several distinct branches with various degrees of intragroup divergence and with characteristic diagnostic features, suggesting that the members of the branches represent amplified copies of particular master genes which had appeared at different periods of evolution. The sequences of the LTRs demonstrate a characteristic distribution of conservative and variable regions, indicating that the LTRs might have some sequence-dependent functions in the primate genome.