Topological Approaches in Animal Comparative Genomics

The surge in chromosome-scale genome sequences from across the tree of life, as well as new comparative methods, has made it possible to study the impact of genomic changes on macroevolution. In this review, we discuss the state of animal comparative genomics. We outline developments in genomic taxonomic sampling and technological advancements in sequencing as well as emerging 3D genomics and provide a perspective on outstanding problems in biodiversity-driven comparative genomics. We discuss the importance of studying genomes holistically and propose the recently introduced evolutionary genome topology framework for topological, multi-scale comparisons across distantly related clades. We highlight how this approach is crucial to understanding the interlinked evolution of subchromosomal and chromosomal changes and their functional implications (e.g., via regulatory entanglement). Lastly, we provide a vision for future areas of research in these approaches and make predictions about the future potential of animal genome evolution.