Beyond inversions and deletions: the evolutionary and functional insights from translocations, fissions, and fusions in animal genomes.

Structural variants, such as deletions, insertions, and inversions, have been increasingly recognized as important drivers of genome evolution, in the era of high-throughput sequencing. However, large-scale chromosomal rearrangements involving multiple chromosomes, including translocations, chromosomal fusions, and fissions, remain relatively understudied, especially outside of clinical and model systems, due to challenges in their detection and analysis. While the earlier understanding of translocations came from human cancer genomics, how such mutations have shaped genome evolution across animal lineages remains insufficiently understood. Recent advances in long-read sequencing, chromosome-level assemblies, and 3D genome conformation techniques are now revealing the prevalence and evolutionary significance of these large genomic structural rearrangements. Translocations can relocate genes into new regulatory environments, chromosome fusions can suppress recombination, and chromosome fissions can restructure chromosomal architecture, modifying the spatial and regulatory context of genes, thereby shaping evolutionary potential. Transposable elements further complicate this landscape by both promoting chromosomal instability and serving as substrates for rearrangement. Together, these changes can drive adaptive evolution, shape karyotype evolution, and contribute to sex chromosome turnover.