A pseudomolecule assembly of the Rocky Mountain elk genome

• Published in: PloS one Vol. 16; no. 4; p. e0249899
• Main Authors: Masonbrink, Rick E, Alt, David, Bayles, Darrell O, Boggiatto, Paola, Edwards, William, Tatum, Fred, Williams, Jeffrey, Wilson-Welder, Jennifer, Zimin, Aleksey, Severin, Andrew, Olsen, Steven
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 28.04.2021; Public Library of Science (PLoS)
• Subjects: Agricultural research; Animal diseases; Annotations; Assembly; Bacterial diseases; Biology and Life Sciences; Cattle; Cervus elaphus; Chromosome rearrangements; Chromosomes; Conservation; Earth sciences; Elk; Genes; Genetic aspects; Genomes; Health aspects; Immune response; Immune response (cell-mediated); Immune system; Informatics; Livestock; Lymphatic system; Medicine and Health Sciences; Mountains; Populations; Protection and preservation; Research and analysis methods; Synteny; Vaccination; Vaccines; United States; Iowa; Chicago Illinois; Wyoming; United States > US
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0249899

Rocky Mountain elk (Cervus canadensis) populations have significant economic implications to the cattle industry, as they are a major reservoir for Brucella abortus in the Greater Yellowstone area. Vaccination attempts against intracellular bacterial diseases 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 does not induce protective immunity. To overcome this limitation, PacBio, Illumina, and Hi-C 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. We conclude by comparing cattle immune system-related genes to the elk genome, revealing eight putative gene losses in elk.