A pseudomolecule assembly of the Rocky Mountain elk genome

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 success...

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Bibliographic Details
Published in:PloS one 2021-04, Vol.16 (4), p.e0249899-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: Article
Language:English
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
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Summary: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.
ISSN:1932-6203
1932-6203
DOI:10.1371/journal.pone.0249899