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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Published in | PloS one Vol. 16; no. 4; p. e0249899 |
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Main Authors | , , , , , , , , , , |
Format | Journal Article |
Language | English |
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28.04.2021
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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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AbstractList | 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. 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. |
Audience | Academic |
Author | Olsen, Steven Alt, David Bayles, Darrell O Boggiatto, Paola Tatum, Fred Severin, Andrew Wilson-Welder, Jennifer Edwards, William Masonbrink, Rick E Williams, Jeffrey Zimin, Aleksey |
AuthorAffiliation | 3 Wildlife Health Laboratory, Wyoming Game and Fish Department, Laramie, Wyoming, United States of America 1 Genome Informatics Facility, Department of Biotech, Iowa State University, Ames, Iowa, United States of America 2 Infectious Bacterial Diseases Research Unit, National Animal Disease Center, U.S. Department of Agriculture, Agricultural Research Service, Ames, Iowa, United States of America 5 Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland, United States of America Clemson University, UNITED STATES 4 Respiratory Diseases Research Unit, National Animal Disease Center, U.S. Department of Agriculture, Agricultural Research Service, Ames, Iowa, United States of America |
AuthorAffiliation_xml | – name: 2 Infectious Bacterial Diseases Research Unit, National Animal Disease Center, U.S. Department of Agriculture, Agricultural Research Service, Ames, Iowa, United States of America – name: 4 Respiratory Diseases Research Unit, National Animal Disease Center, U.S. Department of Agriculture, Agricultural Research Service, Ames, Iowa, United States of America – name: 5 Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland, United States of America – name: Clemson University, UNITED STATES – name: 1 Genome Informatics Facility, Department of Biotech, Iowa State University, Ames, Iowa, United States of America – name: 3 Wildlife Health Laboratory, Wyoming Game and Fish Department, Laramie, Wyoming, United States of America |
Author_xml | – sequence: 1 givenname: Rick E orcidid: 0000-0002-6848-2144 surname: Masonbrink fullname: Masonbrink, Rick E organization: Genome Informatics Facility, Department of Biotech, Iowa State University, Ames, Iowa, United States of America – sequence: 2 givenname: David surname: Alt fullname: Alt, David organization: Infectious Bacterial Diseases Research Unit, National Animal Disease Center, U.S. Department of Agriculture, Agricultural Research Service, Ames, Iowa, United States of America – sequence: 3 givenname: Darrell O orcidid: 0000-0003-1898-977X surname: Bayles fullname: Bayles, Darrell O organization: Infectious Bacterial Diseases Research Unit, National Animal Disease Center, U.S. Department of Agriculture, Agricultural Research Service, Ames, Iowa, United States of America – sequence: 4 givenname: Paola surname: Boggiatto fullname: Boggiatto, Paola organization: Infectious Bacterial Diseases Research Unit, National Animal Disease Center, U.S. Department of Agriculture, Agricultural Research Service, Ames, Iowa, United States of America – sequence: 5 givenname: William surname: Edwards fullname: Edwards, William organization: Wildlife Health Laboratory, Wyoming Game and Fish Department, Laramie, Wyoming, United States of America – sequence: 6 givenname: Fred surname: Tatum fullname: Tatum, Fred organization: Respiratory Diseases Research Unit, National Animal Disease Center, U.S. Department of Agriculture, Agricultural Research Service, Ames, Iowa, United States of America – sequence: 7 givenname: Jeffrey surname: Williams fullname: Williams, Jeffrey organization: Infectious Bacterial Diseases Research Unit, National Animal Disease Center, U.S. Department of Agriculture, Agricultural Research Service, Ames, Iowa, United States of America – sequence: 8 givenname: Jennifer surname: Wilson-Welder fullname: Wilson-Welder, Jennifer organization: Infectious Bacterial Diseases Research Unit, National Animal Disease Center, U.S. Department of Agriculture, Agricultural Research Service, Ames, Iowa, United States of America – sequence: 9 givenname: Aleksey surname: Zimin fullname: Zimin, Aleksey organization: Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland, United States of America – sequence: 10 givenname: Andrew surname: Severin fullname: Severin, Andrew organization: Genome Informatics Facility, Department of Biotech, Iowa State University, Ames, Iowa, United States of America – sequence: 11 givenname: Steven surname: Olsen fullname: Olsen, Steven organization: Infectious Bacterial Diseases Research Unit, National Animal Disease Center, U.S. Department of Agriculture, Agricultural Research Service, Ames, Iowa, United States of America |
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Snippet | Rocky Mountain elk (Cervus canadensis) populations have significant economic implications to the cattle industry, as they are a major reservoir for Brucella... Rocky Mountain elk ( Cervus canadensis ) populations have significant economic implications to the cattle industry, as they are a major reservoir for Brucella... Rocky Mountain elk ( Cervus canadensis ) populations have significant economic implications to the cattle industry, as they are a major reservoir for Brucella... |
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SubjectTerms | 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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Title | A pseudomolecule assembly of the Rocky Mountain elk genome |
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