Principles of 3D chromosome folding and evolutionary genome reshuffling in mammals

Studying the similarities and differences in genomic interactions between species provides fertile grounds for determining the evolutionary dynamics underpinning genome function and speciation. Here, we describe the principles of 3D genome folding in vertebrates and show how lineage-specific patterns of genome reshuffling can result in different chromatin configurations. We (1) identified different patterns of chromosome folding in across vertebrate species (centromere clustering versus chromosomal territories); (2) reconstructed ances-tral marsupial and afrotherian genomes analyzing whole-genome sequences of species representative of the major therian phylogroups; (3) detected lineage-specific chromosome rearrangements; and (4) identified the dynamics of the structural properties of genome reshuffling through therian evolution. We present evidence of chromatin configurational changes that result from ancestral inversions and fusions/fissions. We catalog the close interplay between chromatin higher-order organization and therian genome evolution and introduce an interpretative hypothesis that explains how chromatin folding influences evolutionary patterns of genome reshuffling.

Automated summary

This article describes the principles of studying the similarities and differences in genomic interactions between species and presents the patterns of 3D genome folding in vertebrates and lineage-specific patterns of genome reshuffling. By identifying different patterns of chromosome folding, reconstructing ancestral genomes, detecting lineage-specific chromosome rearrangements, and analyzing the dynamics of genome reshuffling, the article explores the interplay between chromatin higher-order organization and therian genome evolution, and proposes a hypothesis to explain the influence of chromatin folding on evolutionary patterns of genome reshuffling.