Amniotes exhibit a great interspecific diversity of chromosome number and syntenic order during their 310 million years’ evolution. Previous efforts of reconstructing the ancestral karyotypes to infer the amniote chromosome evolution process suffered from using mostly scaffold-level fragmented genomes or the lack of key species at certain lineages. Here, we used 11 amniote and three outgroup species to reconstruct the 32 ancestral linkage groups (ALGs) of mammalian ancestor, and infer a total of 42 and 43 ALGs of reptile and amniote ancestors. Comparison of the reconstructed ancestral chromosomes to the extant species uncovered that the ancestor of mammals exhibit much more intra- and inter-chromosome rearrangements than that of reptiles, with a constant pattern characterized by the fission of macrochromosomes and the fusion of microchromosomes across the amniote species. Unlike the dominant interchromosomal changes occurring among microchromosomes in reptiles, extensive rearrangements had occurred between ancestral macro- and micro-chromosomes. The dramatic changes in mammals had reshuffled the chromosomal syntenic orders, as well as the spatial architectures compared to the ancestors. Despite that, human and mouse have largely retained a ‘bird-like’ spatial nuclear organization that the majority of ancestral microchromosome-originated sequences remained to be closer to the nuclear interior and have significant interchromosomal interactions. This architecture could have been strengthened by the lineage-specific repeat elements. Our results provide novel insights into the sequence and spatial evolution of amniote chromosomes.


 

羊膜动物，哺乳动物，祖先染色体，染色体构象