Computational reconstruction of ancestral genomic regions from evolutionarily conserved gene clusters

Reconstruction of ancestral genomic features can be considered on multiple evolutionary scopes and at different levels of biological sequence information. For instance, one could anticipate the reconstruction of genomic features for the last common ancestor of all species on Earth, last universal common ancestor or LUCA, whereas others would focus on reconstructing these features in the last common ancestor of vertebrates and/or arthropods. In an analogous manner, biological sequences themselves can be divided into subcategories as a function of their nature or their scale. It is possible to consider reconstructing ancestral genes, ancestral proteins, ancestral retro-elements, ancestral chromosomes, or even an ancestral genome. We present here our conceptual and computational approach for reconstructing gene clusters, with a particular emphasis on the major histocompatibility complex (MHC) region. We anticipate that our approach will be extended, and coincide with technological advancements allowing reconstructionists to synthesize ancient genomes in the laboratory.