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ARS Home » Midwest Area » Ames, Iowa » National Animal Disease Center » Infectious Bacterial Diseases Research » Research » Publications at this Location » Publication #377890

Research Project: Pathogenesis and Development of Improved Diagnostic and Control Strategies for Brucellosis in Livestock and Wildlife

Location: Infectious Bacterial Diseases Research

Title: A pseudomolecule assembly of the Rocky Mountain elk genome

item MASONBRINK, RICK - Iowa State University
item Alt, David
item Bayles, Darrell
item Boggiatto, Paola
item EDWARDS, HANK - Wyoming Department Of Game & Fish
item Tatum, Fred
item Williams, Jeffery
item Wilson-Welder, Jennifer
item WOOD, MARY - Colorado Parks And Wildlife
item ZIMIN, ALEKSEY - University Of Maryland
item SEVERIN, ANDREW - Iowa State University
item Olsen, Steven

Submitted to: PLOS ONE
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/28/2021
Publication Date: 4/28/2021
Citation: Masonbrink, R.E., Alt, D.P., Bayles, D.O., Boggiatto, P.M., Edwards, H., Tatum, F.M., Williams, J.E., Wilson-Welder, J.H., Wood, M., Zimin, A., Severin, A., Olsen, S.C. 2021. A pseudomolecule assembly of the Rocky Mountain elk genome. PLoS ONE. 16(4).

Interpretive Summary: Brucellosis is a zoonotic disease that currently has natural reservoirs in elk and bison in the United States. Having an annotated and complete genome of a species allows understanding of gene regulation associated with disease pathogenesis. In the current study, ARS scientists and academic partners completed and annotated the genome of the Rocky Mountain elk down to the chromosome level. This highly polisher genome is now available to understand molecular patterns associated with disease and to allow comparisons to the genomic structure and molecular patterns of other species. This work will be of interest to anyone interested in elk and/or elk diseases and will also allow comparative immunology studies to characterize why elk immune responses differ from other species.

Technical Abstract: Rocky Mountain elk (Cervus canadensis) is a major reservoir for Brucella abortus which has significant economic implications to the cattle industry. Vaccination attempts in Elk populations have not been successful due to a negligible adaptive cellular immune response. A lack of genomic resources has impeded attempts to better understand why vaccination has not been successful. To overcome this limitation, PacBio, Illumina, and HiC sequencing with a total of 686-fold coverage was used to assemble the Elk genome into 35 pseudomolecules. A robust gene annotation was generated resulting in 18,013 gene models and 33,422 mRNAs. The accuracy of the assembly was assessed using synteny to the red deer and cattle genomes identifying several chromosomal rearrangements, fusions and fissions. Because this genome assembly and annotation provide a foundation for genome-enabled exploration of Cervus species, we demonstrate its utility by exploring the conservation of immune system-related genes. Here we show that nine putative immune system genes have been lost in elk, when compared to cattle. We conclude by comparing cattle immune system-related genes to genes in our elk, revealing nine putative gene losses in elk.