"Horses have played a critical role in human societies, warfare and facilitating the exploration of novel territories. Moreover, the rich fossil record of the horse family is one of the most widely known examples of macroevolutionary change. Hence, horses offer a unique paradigm to understand the processes of domestication, lineage divergence and speciation. However, horses have become almost extinct in the wild precluding direct comparison of domestic and wild horse genomes. Here, we aim at using state-of-the-art ancient DNA methods in combination with 2nd and 3rd generation sequencing technologies to characterize the complete genomes of two Pleistocene horses conserved in permafrost soils, dating back to 13 KYBP and 700 KYBP respectively, together with the genomes of 4 modern domesticated breeds, the Przewalski horse and the domesticated donkey. The 13 KY-old genome will deliver the sequence of all horse genes before humans started breed selection and comparative genomics against modern breeds will reveal the genetic changes that occurred in the course of the domestication process. The 700 KY-old genome will illustrate genetic changes that occurred at deeper periods of horse evolutionary history. In addition, this multidisciplinary project will provide insights into the mysterious evolutionary history of the highly endangered Przewalski horse. Significantly, characterizing the complete genome of a 700KY-old individual will crack the time line for ancient DNA preservation by at least one order of magnitude. This will be achieved thanks to major methodological breakthrough as explored in this proposal, including ancient DNA repair and true Single Molecule Sequencing. As such, the EquusPaleoGenomics project will pave the way for the next-generation of paleogenomes by opening access to a brand new repertoire of fossils, that are so far still beyond the range of analysis."
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