Comparative Assembly of Mammalian Genomes: Bovidae

Recent advances in DNA sequencing has democratized the field of genetics and genomics beyond a handful of model organisms. Creating a reference genome for every organism of economic interest is within reach. However, because of both the complexity of eukaryotic genomes and limitations of sequencing/assembly technologies, assembling genomes at chromosome level resolution, in the absence of extensive physical/genetic maps, remains a challenge. Here, we have attempted to generate near chromosome level resolution genome sequences for wild yak and water buffalo, from the respective draft assemblies available in the public repositories using high-resolution cattle genome by comparative assembly. We have been able to significantly improve the draft assembly of the genome of wild yak and water buffalo. For example, the L95 for yak is improved to 146 from 2536 and the N95 is increased to 30,88,584 from 1,80,302 with 5.1% Ns. For water buffalo, the L95 was improved to 970 from 2284 and N95 raised to 4,76,155 from 1,99,060 with 3.6% Ns. Using the high levels of synteny between these three species, we have been able to place the yak scaffolds on respective cattle chromosomes. We will be discussing the challenges in improving the buffalo assembly and will be presenting a highly annotated genome for wild yak and water buffalo to aid association between desirable traits and respective genotypes to guide translation efforts.