TAD conservation in vertebrate genomes is driven by stabilising selection.

1. Mcool Matrices

The dataset includes 12 .mcool files, each representing a Hi-C contact matrix for a distinct species ('human;mouse;rhesus;rabbit;rat;pig;cow;sheep;dog;cat;chicken;zfish') . These matrices provide chromosome conformation data that enable the study of 3D genome organization.

2. Synteny Blocks

The .synteny files contain the output from Cyntenator, a tool used for identifying syntenic blocks across genomes. These files provide information about conserved genomic regions (syntenic blocks) for each clade. The mapping between clades and file names is encoded as follows:

Rodents (mr): (mouse and rat)

Primates (hr): Human - rhesus.

Glires (mrr): Mouse-rat-rabbit.

Eurarchontoglires (hrmrr): human;mouse;rhesus;rabbit;rat.

Cattle (cs): cow;sheep.

Carnivores (cd): cat;dog.

Ungulates (csp): pig;cow;sheep.

Laurasiatheria (cspcd): pig;cow;sheep;dog;cat.

Mammals (hrmrrcspcd): human;mouse;rhesus;rabbit;rat;pig;cow;sheep;dog;cat.

Tetrapods (hrmrrcspcdc): human;mouse;rhesus;rabbit;rat;pig;cow;sheep;dog;cat;chicken.

Vertebrates (hrmrrcspcdcz): human;mouse;rhesus;rabbit;rat;pig;cow;sheep;dog;cat;chicken;zfish.

3. TADs at 32k Resolution

The tad_32_k.zip archive contains Topologically Associating Domains (TADs) for each species. These TADs were identified at a resolution of 32 kb. Each file within the directory corresponds to a species-specific TAD dataset.

4. Intersection of TADs and Synteny Blocks

The sb_in_tad_3.zip archive includes data on the intersection of TADs and syntenic blocks.