Genomes From 117 Vertebrate Species Reveal Rapidly Evolving Segmental-Duplication Landscapes

Segmental duplications are major drivers of evolutionary innovation; yet, their dynamics across vertebrates remain poorly understood. Here, we identify segmental duplications from long-read-sequenced genomes of 117 vertebrates and one starfish, generating the largest multispecies dataset of its kind. We find that vertebrate genomes show a higher propensity for tandem duplications than for interspersed duplications. However, when focusing only on subtelomeric regions, avian and mammalian genomes show the opposite propensity toward interspersed duplications. We also observe that, across vertebrates, tandem duplications tend to be larger than interspersed duplications. Next, we construct a segmental-duplication network for each species and use network-derived metrics to quantify the duplication landscape for that species. We then compute interspecies distances for each metric and find that these distances show at most weak correlations with phylogenetic distance, indicating that segmental-duplication landscapes evolve rapidly. Functional-enrichment analysis of hyperduplicated genes reveals a strong enrichment in platypus for pheromone response, driven by the expansion of the vomeronasal pheromone receptor V1R gene family. Overall, our results uncover the general properties of vertebrate segmental duplications, demonstrate the lability of segmental-duplication landscapes, and highlight the utility of network-based approaches for studying genome evolution.