Evolution of chromosomes and nuclear architectures of amniotes

Chromosomes of mammals and reptiles have diverged extensively in sequence and three-dimensional (3D) nuclear organization since their last common amniote ancestor. The fine-scale evolutionary patterns and mechanisms underlying this divergence and the relationship between chromosome rearrangements and 3D genome architecture remain unclear. Here we reconstruct ancestral linkage groups (ALGs) of the amniote ancestor and its descendent nodes using chromosome-level assemblies from 36 species, including two newly generated genomes. We infer that most microchromosomes originated in the jawed vertebrate ancestor were retained as distinct ALGs across all ancestral amniote nodes. They were mainly involved in fusions with each other in reptiles, but underwent frequent translocations with the larger ALGs (macro-ALGs) during the mammalian evolution. Despite extensive rearrangements, sequences derived from micro-ALGs consistently occupy nuclear interior positions in both reptiles and mammals, likely enriched near nuclear speckles, supported by published lamina-positioning data and our lamin-B1 ChIP-seq data. In contrast, mammals independently evolved interchromosomal interactions associated with lineage specific transposable elements, reflecting local innovations in nuclear architecture. Together, these results reveal contrasting rearrangement regimes in mammals and reptiles, yet a conserved higher-order nuclear organization linked to ancient micro- versus macro-ALG chromatin segregation, suggesting deep constraints on chromosome evolution.