Concerted evolution and unorthodox recombination of human subtelomeres

Authors

Guarracino, A., Gyamfi, A., Human Pangenome Reference Consortium,, Garrison, E.

Abstract

Human subtelomeres contain duplicated sequence that is shared among the ends of non-homologous chromosomes and provides a substrate for ectopic exchange. However, incomplete reference assemblies and chromosome-by-chromosome analyses have prevented a population-scale view of the extent and organization of subtelomeric exchange. Here we apply a reference-free pangenome approach to 465 near-complete human assemblies, comparing every chromosome end against every other, and find that high-identity pseudo-homolog regions occur on 41 of 48 chromosome arms. These regions form structured sequence communities in which previously described exchange systems appear as local peaks within a broader continuum. Human and mouse chromosome-contact maps show preferential proximity between subtelomeres with similar sequences. In mouse meiosis this proximity is strongest at the zygotene bouquet, when telomeres cluster at the nuclear envelope; in human data it persists even in adjacent flanks that lack the shared sequence used to define each pair. In a three-generation telomere-to-telomere pedigree, whole-genome comparison identifies putative recombination between subtelomeric regions on non-homologous chromosomes that matches this community organization, while recovering the obligate Xp/Yp PAR1 recombination in the male germline. These results generalize known subtelomeric exchange systems into a near-ubiquitous architecture and support recurrent ectopic exchange as a genome-wide force in the concerted evolution of human chromosome ends.

Preprint server: bioRxiv
The authors list and abstract were imported from bioRxiv on 11 Jul 2026.

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