Genomic insights into chromosomal fusion and its evolutionary implications for zokors

Chromosomal fusion and fission are widespread across species, yet the underlying genomic mechanisms and their evolutionary implications remain poorly understood. Here, we present high-quality chromosome-level genome assemblies for two closely related subterranean rodent species, Eospalax rufescens and E. rothschildi. Through comparative genomic and synteny analyses, we identified two species-specific chromosomal fusions in E. rothschildi, likely mediated by ectopic recombination through repetitive elements and by mutations affecting genome stability. Despite minimal changes in base-level genomic features, the fused chromosomes are associated with altered three-dimensional (3D) chromatin architecture, including increased chromatin entropy, topologically associating domain (TAD) rearrangement, and compartment switching. Reduced gene flow on the fused chromosomes suggests a role in reproductive isolation. Additionally, molecular signals of relaxed selection and adaptive evolution in pathways related to DNA repair, chromatin dynamics, and environmental sensing highlight the interplay between structural and ecological factors in shaping divergence. Together, our findings provide a mechanistic and evolutionary framework linking chromosomal fusions with genome architecture remodeling, epigenetic changes, and barriers to gene flow in mammals, offering a valuable resource for future evolutionary genomics studies.