| dc.description.abstract | Complex and highly repetitive regions are absent from nearly all genome assemblies and are often referred to as genomic “dark matter”. Many of these regions also harbor large copy number repeats and/or other structural differences within and between species, further confounding their assembly from a diploid genome, and eluding our understanding of their biological properties. We identified and characterized one such region, the macrosatellite DXZ4, as a candidate hybrid-sterility locus in a cat interspecific hybrid cross. Previous investigations of DXZ4 have been limited to female somatic cells, where it plays a role in structural organization of the inactive X chromosome. We demonstrate that DXZ4 is transcriptionally active in germ cells undergoing meiotic sex chromosome inactivation and reveal that divergence across this macrosatellite results in perturbed methylation and ncRNA expression in testes of male interspecific hybrids. Due to its structurally complex nature, DXZ4 was incomplete in the human reference genome and nearly all other mammalian genomes, limiting insights into its structure and functional evolution. Trio binning was developed to sort and independently assemble the divergent parental haplotypes of an F1 hybrid using a combination of short-read and long-read sequence data from the parents and hybrid. Here we applied this method to three feline F1 hybrids to generate six ultra-continuous single-haplotype genome assemblies from five species: domestic cat, Asian leopard cat, Geoffroy’s cat, tiger, and lion. For the first time, we were able to fully resolve X-linked macrosatellites in other mammal species and thereby discovered the feline DXZ4 satellite is composed of a compound tandem repeat with two distinct and highly divergent repeat arrays (A and B). Interestingly, the presence and organization of the two felid DXZ4 repeat arrays have diverged rapidly across mammalian orders, revealing a far greater scope of complexity and divergence than previously appreciated, especially for a locus involved in a conserved developmental process like X-chromosome inactivation (XCI). As ultracontinuous genomes become available for a wider variety of organisms, “dark matter” regions previously missing from genomes might hold the key to answering pervasive questions in disease biology, genome organization, gene regulation, and speciation. | en |
