A pseudomolecule assembly of the Rocky Mountain elk genome

Date
2021-04-28
Authors
Masonbrink, Rick
Alt, David
Bayles, Darrell
Severin, Andrew
Boggiatto, Paola
Edwards, William
Tatum, Fred
Williams, Jeffrey
Wilson-Welder, Jennifer
Zimin, Aleksey
Severin, Andrew
Olsen, Steven
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Office of Biotechnology
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Genome Informatics Facility
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Office of BiotechnologyGenome Informatics Facility
Abstract

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.

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This article is published as Masonbrink RE, Alt D, Bayles DO, Boggiatto P, Edwards W, Tatum F, et al. (2021) A pseudomolecule assembly of the Rocky Mountain elk genome. PLoS ONE 16(4): e0249899. doi:10.1371/journal.pone.0249899.

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