Artiodactyl Chromosome Evolution

The Artiodactyla (even-toed ungulate mammals) first appeared ~60 million years ago during the early Eocene. Today, there are >200 extant artiodactyl species found on every continent, except Antarctica. Their rapid diversification, unique adaptations, ecological importance, and economical significance have made artiodactyl species a prime target for genome sequencing and analysis. Recently, we demonstrated that genome rearrangements could have promoted adaptive changes in cattle and pigs, making them attractive targets for domestication. In this study we focused on analysis of chromosomal rearrangements that occurred in the ancestral artiodactyl and ruminant genomes ~60-35 Mya in order to: a) shed light on the evolution of economically important traits; and b) understand the mechanisms of lineage-specific adaptations. The genomes of ten artiodactyls, including eight ruminants, and eight outgroup species were compared. We detected 57 evolutionary breakpoint regions (EBRs; intervals flanking genome rearrangements) in the ancestral ruminant genome, 3 bovidae-specific EBRs, and 136 species-specific EBRs. To investigate the potential adaptive value of ancestral EBRs, we studied genes and gene networks affected by genome rearrangements in artiodactyls. We found that ruminant EBRs are significantly enriched for genes related to immunological function, e.g., they reorganize the MHC Class II cluster, which is involved in adaptive immunity and also reorganize the IgA pathway, involved in the rumen’s ability to maintain a wide range of symbiotic bacteria. Our research provides additional insights into chromosome evolution and lineage-specific biology of ruminants pointing out the genes and gene networks affected by structural reorganizations that occurred in the ancestral ruminant genome.