Robust 3D modeling reveals spatiosyntenic properties of animal genomes

Animal genomes are organized into chromosomes that are remarkably conserved in their gene content, forming distinct evolutionary units (synteny). Using versa-tile chromosomal modeling, we infer three-dimensional topology of genomes from representative clades spanning the earliest animal diversification. We apply a partitioning approach using interaction spheres to compensate for varying qual-ity of topological data. Using comparative genomics approaches, we test whether syntenic signal at gene pair, local, and whole chromosomal scale is re-flected in the reconstructed spatial organization. We identify evolutionarily conserved three-dimensional networks at all syntenic scales revealing novel evolutionarily maintained interactors associated with known conserved local gene linkages (such as hox). We thus present evidence for evolutionary con-straints that are associated with three-, rather than just two-, dimensional animal genome organization, which we term spatiosynteny. As more accurate topolog-ical data become available, together with validation approaches, spatiosynteny may become relevant in understanding the functionality behind the observed conservation of animal chromosomes.

Automated summary

Animal genomes are organized into conserved chromosomes that form distinct evolutionary units. By using chromosomal modeling, researchers have inferred the three-dimensional topology of animal genomes. They have identified evolutionarily conserved three-dimensional networks and novel interactors associated with known gene linkages. This evidence suggests that the spatial organization of animal genomes, termed spatiosynteny, plays a role in understanding the conservation of chromosomes.