Ruminant Genomics

Today, there are ~150 extant ruminant species, including three major livestock animals (cattle, sheep and goat). Their ecological importance and economic significance have made ruminant species a prime target for genome sequencing and selective breeding. In this study we focused on the genomic changes that occurred in the ancestral ruminant genome ~35 Mya to unravel the origin and evolution of adaptive traits. We compared the genomes of 9 ruminant and 11 outgroup species, four of which also belong to the order Cetartiodactyla. We detected evolutionary breakpoint regions (EBRs) that occurred in these genomes and estimated a rearrangement rate of 3.56 EBRs/My in the ancestral ruminant karyotype. Moreover we detected multi-species conserved synteny blocks across all ruminant genomes, covering 82.61% of the cattle genome. We found that 43 gene families were expanded in the ancestor of all ruminants, including genes related to innate immune system and placentation. Moreover, 42 genes were found under positive selection in the ruminant ancestor, e.g. the BSCL2 gene involved in the morphology of lipid droplets in cells. By excluding the conserved non-coding elements (CNEs) found in all cetartiodactyl genomes, we detected the CNEs that were formed in the ruminant ancestor (0.95% of the cattle genome). Interestingly, 54.68% of these ruminant-specific CNEs overlap with transposable elements, suggesting that transposable elements could have influenced regulation of genes in the ruminant ancestor. Our research provides significant insights into the organization of the ancestral ruminant genome that will facilitate ruminant breeding and genome evolution studies.