The mule deer (Odocoileus hemionus) is a species of Cervidae native to Western North America. They occupy a variety of habitats, from high mountain ecosystems to sagebrush deserts. Because their habitat is vast, their herbivorous diet consists of a large variety of plants. Mule deer are an iconic species of the Western United States and are important to the survival of many other species in the ecosystems in which they reside, as they are a primary food source for many of North America’s large predator species, such as pumas, coyotes, bears, and wolves.[i]
Mule deer are well-known for their striking antlers, the bony protrusions that rise out of the top of the skulls of males. Their antlers are one of their more definitive features and differ in branching pattern from the closely related whitetail deer. Mule deer antlers grow in an annual cycle, starting in the late spring when the antlers begin to form, and ending in the early fall when increased levels of testosterone hardens the antlers. After mating, reduced testosterone levels cause the antlers to fall off. Antlers are important for a variety of reasons, including defense, and acquisition of mating opportunities.[ii]
We are excited today to present a de novo chromosome-length genome assembly of the mule deer with chromosome-length scaffolding. A research team from two labs at Brigham Young University (Sydney Lamb, Tabitha Hughes, Randy Larsen, and Brock McMillan https://pws.byu.edu/wildlife-ecology and Adam Taylor and Paul Frandsen https://frandsen.byu.edu) generated the de novo draft genome assembly using high coverage PacBio and Illumina sequencing while DNA Zoo completed a Hi-C experiment to provide chromosome-level information. The genome was assembled using RedBean, followed by two rounds of polishing with Racon (PacBio reads) and Pilon (Illumina reads, fix-indels only), and finally 3D-DNA and Juicebox Assembly Tools for the Hi-C part (see dnazoo.org/methods). Check out the chromosomes below!
A paper describing genome assembly and annotation description is in the process of being written and will be made available as a preprint soon, but we wanted to make the genome assembly available as soon as possible for use in the community. In some areas, mule deer populations are in decline. Possible reasons for the decline include habitat loss, collisions with vehicles, predation, and the rising spread of Chronic Wasting Disease (CWD)[iii]. We hope this reference genome will provide genomic resources that will help in monitoring and management efforts across the species range. We express our gratitude to the Utah Division of Wildlife Resources for providing the tissue of the specimen that was used for this project.
Blog post by: Adam M. Taylor, Sydney Lamb, & Tabitha Hughes
[i] DeVivo, M. T. et al. Endemic chronic wasting disease causes mule deer population decline in Wyoming. PLoS One 12, (2017).
[ii] Wang, Y. et al. Genetic basis of ruminant headgear and rapid antler regeneration. Science 364, (2019).
[iii] Madson, Icon of the American West: Science Reference Center. National Wildlife (World Edition) 53, 26–29 (2014).