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Prado NA, Armstrong EE, Brown JL, Goldenberg SZ, Leimgruber P, Pearson VR, Maldonado JE, Campana MG. Genomic resources for Asian (Elephas maximus) and African savannah elephant (Loxodonta africana) conservation and health research. J Hered 2023; 114:529-538. [PMID: 37246890 DOI: 10.1093/jhered/esad034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 05/26/2023] [Indexed: 05/30/2023] Open
Abstract
We provide novel genomic resources to help understand the genomic traits involved in elephant health and to aid conservation efforts. We sequence 11 elephant genomes (5 African savannah, 6 Asian) from North American zoos, including 9 de novo assemblies. We estimate elephant germline mutation rates and reconstruct demographic histories. Finally, we provide an in-solution capture assay to genotype Asian elephants. This assay is suitable for analyzing degraded museum and noninvasive samples, such as feces and hair. The elephant genomic resources we present here should allow for more detailed and uniform studies in the future to aid elephant conservation efforts and disease research.
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Affiliation(s)
- Natalia A Prado
- Biology Department, College of Arts and Sciences, Adelphi University, Garden City, NY, United States
- Center for Conservation Genomics, Smithsonian's National Zoo and Conservation Biology Institute, Washington, DC, United States
- Endocrinology Research Laboratory, Center for Species Survival, Smithsonian's National Zoo and Conservation Biology Institute, Front Royal, VA, United States
| | - Ellie E Armstrong
- Department of Biology, Stanford University, Stanford, CA, United States
- School of Biological Sciences, Washington State University, Pullman, WA, United States
| | - Janine L Brown
- Endocrinology Research Laboratory, Center for Species Survival, Smithsonian's National Zoo and Conservation Biology Institute, Front Royal, VA, United States
| | - Shifra Z Goldenberg
- Conservation Ecology Center, Smithsonian's National Zoo and Conservation Biology Institute, Washington, DC, United States
- Conservation Science and Wildlife Health, San Diego Zoo Wildlife Alliance, Escondido, CA, United States
| | - Peter Leimgruber
- Conservation Ecology Center, Smithsonian's National Zoo and Conservation Biology Institute, Washington, DC, United States
| | - Virginia R Pearson
- Glenn Rall Laboratory, Fox Chase Cancer Center, Philadelphia, PA, United States
| | - Jesús E Maldonado
- Center for Conservation Genomics, Smithsonian's National Zoo and Conservation Biology Institute, Washington, DC, United States
| | - Michael G Campana
- Center for Conservation Genomics, Smithsonian's National Zoo and Conservation Biology Institute, Washington, DC, United States
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Pearson VR, Bosse JB, Koyuncu OO, Scherer J, Toruno C, Robinson R, Abegglen LM, Schiffman JD, Enquist LW, Rall GF. Identification of African Elephant Polyomavirus in wild elephants and the creation of a vector expressing its viral tumor antigens to transform elephant primary cells. PLoS One 2021; 16:e0244334. [PMID: 33544724 PMCID: PMC7864673 DOI: 10.1371/journal.pone.0244334] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Accepted: 12/07/2020] [Indexed: 11/29/2022] Open
Abstract
Wild elephant populations are declining rapidly due to rampant killing for ivory and body parts, range fragmentation, and human-elephant conflict. Wild and captive elephants are further impacted by viruses, including highly pathogenic elephant endotheliotropic herpesviruses. Moreover, while the rich genetic diversity of the ancient elephant lineage is disappearing, elephants, with their low incidence of cancer, have emerged as a surprising resource in human cancer research for understanding the intrinsic cellular response to DNA damage. However, studies on cellular resistance to transformation and herpesvirus reproduction have been severely limited, in part due to the lack of established elephant cell lines to enable in vitro experiments. This report describes creation of a recombinant plasmid, pAelPyV-1-Tag, derived from a wild isolate of African Elephant Polyomavirus (AelPyV-1), that can be used to create immortalized lines of elephant cells. This isolate was extracted from a trunk nodule biopsy isolated from a wild African elephant, Loxodonta africana, in Botswana. The AelPyV-1 genome contains open-reading frames encoding the canonical large (LTag) and small (STag) tumor antigens. We cloned the entire early region spanning the LTag and overlapping STag genes from this isolate into a high-copy vector to construct a recombinant plasmid, pAelPyV-1-Tag, which effectively transformed primary elephant endothelial cells. We expect that the potential of this reagent to transform elephant primary cells will, at a minimum, facilitate study of elephant-specific herpesviruses.
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Affiliation(s)
- Virginia R. Pearson
- Fox Chase Cancer Center, Program in Blood Cell Development and Function, Philadelphia, Pennsylvania, United States of America
- * E-mail:
| | - Jens B. Bosse
- RESIST Cluster of Excellence, Institute of Virology at Hannover Medical School, Center for Structural Systems Biology, Hamburg, Germany
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany
| | - Orkide O. Koyuncu
- Princeton University, Department of Molecular Biology, Princeton, New Jersey, United States of America
| | - Julian Scherer
- Princeton University, Department of Molecular Biology, Princeton, New Jersey, United States of America
| | - Cristhian Toruno
- Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah, United States of America
| | - Rosann Robinson
- Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah, United States of America
| | - Lisa M. Abegglen
- Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah, United States of America
| | - Joshua D. Schiffman
- Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah, United States of America
| | - Lynn W. Enquist
- Princeton University, Department of Molecular Biology, Princeton, New Jersey, United States of America
| | - Glenn F. Rall
- Fox Chase Cancer Center, Program in Blood Cell Development and Function, Philadelphia, Pennsylvania, United States of America
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