Differential k-mer distributions enable identification of tetrapod subterminal heterochromatin

Abstract

Subterminal heterochromatin are dynamic regions of the genome that are repeat rich and vary in structure between individuals of the same species. With advances in genome sequencing technology, these regions are being assembled for the first time in many groups such as Xenopus. We develop a k-mer based algorithm capable of identifying previously characterized subterminal satellites, as well as lower density satellites in diploid primates and X. tropicalis. When applying our algorithm to the allotetraploid genome of Xenopus laevis, we find that the subterminal heterochromatin regions include ancient subgenome-specific repeats that originated while the X. laevis progenitors were distinct species. This pattern challenges the model proposed in primates of ectopic recombination driving non-homologous chromosomes to share repeat sequences.