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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...
Autores principales: | , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Public Library of Science
2021
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8081196/ https://www.ncbi.nlm.nih.gov/pubmed/33909645 http://dx.doi.org/10.1371/journal.pone.0249899 |
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author | 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 |
author_facet | 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 |
author_sort | Masonbrink, Rick E. |
collection | PubMed |
description | 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. |
format | Online Article Text |
id | pubmed-8081196 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2021 |
publisher | Public Library of Science |
record_format | MEDLINE/PubMed |
spelling | pubmed-80811962021-05-06 A pseudomolecule assembly of the Rocky Mountain elk genome 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 PLoS One Research Article 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. Public Library of Science 2021-04-28 /pmc/articles/PMC8081196/ /pubmed/33909645 http://dx.doi.org/10.1371/journal.pone.0249899 Text en https://creativecommons.org/publicdomain/zero/1.0/This is an open access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the Creative Commons CC0 (https://creativecommons.org/publicdomain/zero/1.0/) public domain dedication. |
spellingShingle | Research Article 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 A pseudomolecule assembly of the Rocky Mountain elk genome |
title | A pseudomolecule assembly of the Rocky Mountain elk genome |
title_full | A pseudomolecule assembly of the Rocky Mountain elk genome |
title_fullStr | A pseudomolecule assembly of the Rocky Mountain elk genome |
title_full_unstemmed | A pseudomolecule assembly of the Rocky Mountain elk genome |
title_short | A pseudomolecule assembly of the Rocky Mountain elk genome |
title_sort | pseudomolecule assembly of the rocky mountain elk genome |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8081196/ https://www.ncbi.nlm.nih.gov/pubmed/33909645 http://dx.doi.org/10.1371/journal.pone.0249899 |
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