Gene density homogeneity is disrupted by repetitive DNA Expansion

The democratization of sequencing has led to a wealth of high-quality genome assemblies from across the Tree of Life. One pattern that has emerged is that chromosomes within a genome can vary drastically in their gene density (e.g., human chromosomes 13 and 19, with gene densities of 17.5 and 60.5 genes per megabase, respectively). To our knowledge, the cause of this variation in gene density has not been explored. In this study, we leveraged genome assemblies of 262 vertebrate species to examine the range of within-genome variation in gene density. We combined gene density data with repeat landscape analyses in each species. We predicted that genomes with more recently expanded repeat families should show greater variation in gene density, because repetitive elements accumulate unevenly across the genome, while chromosomal rearrangements such as fusions, fissions, insertions, deletions, and inversions homogenize gene density over time. Our empirical analysis reveals a significant yet variable effect of repeat expansions, with additional processes likely contributing to variation in gene density.