1
|
Supple MA, Escalona M, Adkins J, Buchalski MR, Alexandre N, Sahasrabudhe RM, Nguyen O, Sacco S, Fairbairn C, Beraut E, Seligmann W, Green RE, Meredith E, Shapiro B. A genome assembly of the American black bear, Ursus americanus, from California. J Hered 2024; 115:498-506. [PMID: 39008331 PMCID: PMC11334205 DOI: 10.1093/jhered/esae037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2024] [Accepted: 07/09/2024] [Indexed: 07/16/2024] Open
Abstract
The American black bear, Ursus americanus, is a widespread and ecologically important species in North America. In California, the black bear plays an important role in a variety of ecosystems and serves as an important species for recreational hunting. While research suggests that the populations in California are currently healthy, continued monitoring is critical, with genomic analyses providing an important surveillance tool. Here we report a high-quality, near chromosome-level genome assembly from a U. americanus sample from California. The primary assembly has a total length of 2.5 Gb contained in 316 scaffolds, a contig N50 of 58.9 Mb, a scaffold N50 of 67.6 Mb, and a BUSCO completeness score of 96%. This U. americanus genome assembly will provide an important resource for the targeted management of black bear populations in California, with the goal of achieving an appropriate balance between the recreational value of black bears and the maintenance of viable populations. The high quality of this genome assembly will also make it a valuable resource for comparative genomic analyses among black bear populations and among bear species.
Collapse
Affiliation(s)
- Megan A Supple
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA, United States
- Howard Hughes Medical Institute, University of California, Santa Cruz, CA, United States
| | - Merly Escalona
- Department of Biomolecular Engineering, University of California, Santa Cruz, CA, United States
| | - Jillian Adkins
- Wildlife Forensic Lab, Law Enforcement Division, California Department of Fish and Wildlife, Sacramento, CA, United States
| | - Michael R Buchalski
- Wildlife Genetics Research Unit, Wildlife Health Laboratory, California Department of Fish and Wildlife, Sacramento, CA, United States
| | - Nicolas Alexandre
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA, United States
- Howard Hughes Medical Institute, University of California, Santa Cruz, CA, United States
| | - Ruta M Sahasrabudhe
- DNA Technologies and Expression Analysis Core Laboratory, Genome Center, University of California, Davis, CA, United States
| | - Oanh Nguyen
- DNA Technologies and Expression Analysis Core Laboratory, Genome Center, University of California, Davis, CA, United States
| | - Samuel Sacco
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA, United States
| | - Colin Fairbairn
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA, United States
| | - Eric Beraut
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA, United States
| | - William Seligmann
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA, United States
| | - Richard E Green
- Department of Biomolecular Engineering, University of California, Santa Cruz, CA, United States
| | - Erin Meredith
- Wildlife Forensic Lab, Law Enforcement Division, California Department of Fish and Wildlife, Sacramento, CA, United States
| | - Beth Shapiro
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA, United States
- Howard Hughes Medical Institute, University of California, Santa Cruz, CA, United States
| |
Collapse
|
2
|
Xu S, Wang J, Sun K, Meng L, Qin C, Feng R, Tian Y, Zhai Y, Liang D, Zhang R, Tian H, Liu H, Chen Y, Fu Y, Chen P, Zhu Q, Teng J, Wang X. Cognitive Impairment in Chronic Kidney Disease Is Associated with Glymphatic System Dysfunction. KIDNEY DISEASES (BASEL, SWITZERLAND) 2023; 9:384-397. [PMID: 37901711 PMCID: PMC10601941 DOI: 10.1159/000530635] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 04/01/2023] [Indexed: 10/31/2023]
Abstract
Introduction This study was designed to explore the associations between impaired cognition in chronic kidney disease (CKD) patients and the dysfunction of the glymphatic system. Method Data were obtained from 77 CKD patients and 50 age-matched healthy control individuals from the First Affiliated Hospital of Zhengzhou University. CKD patients were stratified into with and without impaired cognitive function. T2-weighted magnetic resonance imaging results were used to assess area ratios for the perivascular space and ventricles in participants, while the Montreal Cognitive Assessment and the Mini-Mental State Examination were employed to measure cognitive function. Correlations between the perivascular space or ventricle area ratios and cognitive impairment were assessed in CKD patients. Results Significant increases in the burden of enlarged perivascular spaces in the frontal cortex and basal ganglia were observed in CKD patients with cognitive impairment relative to those without such impairment, with a concomitant increase in analyzed ventricle area ratios. Enlarged perivascular spaces in the frontal cortex, basal ganglia and increased area ratios of lateral ventricles and 4th ventricle exhibited relatively high sensitivity and specificity as means of differing between the CKD patients with and without cognitive impairment. Conclusion These results indicate that the burden of enlarged perivascular spaces in the frontal cortex and basal ganglia and increases in ventricle area ratio values may offer utility as biomarkers that can aid in detection of even mild cognitive decline in individuals with CKD. The dysfunction of the glymphatic system may play a key role in the pathogenesis of CKD-related cognitive impairment.
Collapse
Affiliation(s)
- Shuqin Xu
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Institute of Parkinson and Movement Disorder, Zhengzhou University, Zhengzhou, China
| | - Jiuqi Wang
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Institute of Parkinson and Movement Disorder, Zhengzhou University, Zhengzhou, China
| | - Kedi Sun
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Institute of Parkinson and Movement Disorder, Zhengzhou University, Zhengzhou, China
| | - Lin Meng
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Institute of Parkinson and Movement Disorder, Zhengzhou University, Zhengzhou, China
| | - Chi Qin
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Institute of Parkinson and Movement Disorder, Zhengzhou University, Zhengzhou, China
| | - Renyi Feng
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Institute of Parkinson and Movement Disorder, Zhengzhou University, Zhengzhou, China
| | - Yiming Tian
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Institute of Parkinson and Movement Disorder, Zhengzhou University, Zhengzhou, China
| | - Yanping Zhai
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Institute of Parkinson and Movement Disorder, Zhengzhou University, Zhengzhou, China
| | - Dongxiao Liang
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Institute of Parkinson and Movement Disorder, Zhengzhou University, Zhengzhou, China
| | - Rui Zhang
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Institute of Parkinson and Movement Disorder, Zhengzhou University, Zhengzhou, China
| | - Haiyan Tian
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Institute of Parkinson and Movement Disorder, Zhengzhou University, Zhengzhou, China
| | - Han Liu
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Institute of Parkinson and Movement Disorder, Zhengzhou University, Zhengzhou, China
| | - Yongkang Chen
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Institute of Parkinson and Movement Disorder, Zhengzhou University, Zhengzhou, China
| | - Yu Fu
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Institute of Parkinson and Movement Disorder, Zhengzhou University, Zhengzhou, China
| | - Pei Chen
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Institute of Parkinson and Movement Disorder, Zhengzhou University, Zhengzhou, China
| | - Qingyong Zhu
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Institute of Parkinson and Movement Disorder, Zhengzhou University, Zhengzhou, China
| | - Junfang Teng
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Institute of Parkinson and Movement Disorder, Zhengzhou University, Zhengzhou, China
| | - Xuejing Wang
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Institute of Parkinson and Movement Disorder, Zhengzhou University, Zhengzhou, China
| |
Collapse
|
3
|
da Silva Coelho FA, Gill S, Tomlin CM, Papavassiliou M, Farley SD, Cook JA, Sonsthagen SA, Sage GK, Heaton TH, Talbot SL, Lindqvist C. Ancient bears provide insights into Pleistocene ice age refugia in Southeast Alaska. Mol Ecol 2023. [PMID: 37096383 DOI: 10.1111/mec.16960] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 03/28/2023] [Accepted: 04/12/2023] [Indexed: 04/26/2023]
Abstract
During the Late Pleistocene, major parts of North America were periodically covered by ice sheets. However, there are still questions about whether ice-free refugia were present in the Alexander Archipelago along the Southeast (SE) Alaska coast during the last glacial maximum (LGM). Numerous subfossils have been recovered from caves in SE Alaska, including American black (Ursus americanus) and brown (U. arctos) bears, which today are found in the Alexander Archipelago but are genetically distinct from mainland bear populations. Hence, these bear species offer an ideal system to investigate long-term occupation, potential refugial survival and lineage turnover. Here, we present genetic analyses based on 99 new complete mitochondrial genomes from ancient and modern brown and black bears spanning the last ~45,000 years. Black bears form two SE Alaskan subclades, one preglacial and another postglacial, that diverged >100,000 years ago. All postglacial ancient brown bears are closely related to modern brown bears in the archipelago, while a single preglacial brown bear is found in a distantly related clade. A hiatus in the bear subfossil record around the LGM and the deep split of their pre- and postglacial subclades fail to support a hypothesis of continuous occupancy in SE Alaska throughout the LGM for either species. Our results are consistent with an absence of refugia along the SE Alaska coast, but indicate that vegetation quickly expanded after deglaciation, allowing bears to recolonize the area after a short-lived LGM peak.
Collapse
Affiliation(s)
| | - Stephanie Gill
- Department of Biological Sciences, University at Buffalo, Buffalo, New York, USA
| | - Crystal M Tomlin
- Department of Biological Sciences, University at Buffalo, Buffalo, New York, USA
| | | | - Sean D Farley
- Alaska Department of Fish and Game, Anchorage, Alaska, USA
| | - Joseph A Cook
- Museum of Southwestern Biology and Department of Biology, University of New Mexico, Albuquerque, New Mexico, USA
| | - Sarah A Sonsthagen
- U.S. Geological Survey, Nebraska Cooperative Fish and Wildlife Research Unit, University of Nebraska-Lincoln, School of Natural Resources, Lincoln, Nebraska, USA
| | - George K Sage
- Far Northwestern Institute of Art and Science, Anchorage, Alaska, USA
| | - Timothy H Heaton
- Department of Earth Sciences, University of South Dakota, Vermillion, South Dakota, USA
| | - Sandra L Talbot
- Far Northwestern Institute of Art and Science, Anchorage, Alaska, USA
| | - Charlotte Lindqvist
- Department of Biological Sciences, University at Buffalo, Buffalo, New York, USA
| |
Collapse
|
4
|
Puckett EE, Davis IS, Harper DC, Wakamatsu K, Battu G, Belant JL, Beyer DE, Carpenter C, Crupi AP, Davidson M, DePerno CS, Forman N, Fowler NL, Garshelis DL, Gould N, Gunther K, Haroldson M, Ito S, Kocka D, Lackey C, Leahy R, Lee-Roney C, Lewis T, Lutto A, McGowan K, Olfenbuttel C, Orlando M, Platt A, Pollard MD, Ramaker M, Reich H, Sajecki JL, Sell SK, Strules J, Thompson S, van Manen F, Whitman C, Williamson R, Winslow F, Kaelin CB, Marks MS, Barsh GS. Genetic architecture and evolution of color variation in American black bears. Curr Biol 2023; 33:86-97.e10. [PMID: 36528024 PMCID: PMC10039708 DOI: 10.1016/j.cub.2022.11.042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 11/08/2022] [Accepted: 11/18/2022] [Indexed: 12/23/2022]
Abstract
Color variation is a frequent evolutionary substrate for camouflage in small mammals, but the underlying genetics and evolutionary forces that drive color variation in natural populations of large mammals are mostly unexplained. The American black bear, Ursus americanus (U. americanus), exhibits a range of colors including the cinnamon morph, which has a similar color to the brown bear, U. arctos, and is found at high frequency in the American southwest. Reflectance and chemical melanin measurements showed little distinction between U. arctos and cinnamon U. americanus individuals. We used a genome-wide association for hair color as a quantitative trait in 151 U. americanus individuals and identified a single major locus (p < 10-13). Additional genomic and functional studies identified a missense alteration (R153C) in Tyrosinase-related protein 1 (TYRP1) that likely affects binding of the zinc cofactor, impairs protein localization, and results in decreased pigment production. Population genetic analyses and demographic modeling indicated that the R153C variant arose 9.36 kya in a southwestern population where it likely provided a selective advantage, spreading both northwards and eastwards by gene flow. A different TYRP1 allele, R114C, contributes to the characteristic brown color of U. arctos but is not fixed across the range.
Collapse
Affiliation(s)
- Emily E Puckett
- Department of Biological Sciences, University of Memphis, Memphis, TN 38152, USA.
| | - Isis S Davis
- Department of Biological Sciences, University of Memphis, Memphis, TN 38152, USA
| | - Dawn C Harper
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Kazumasa Wakamatsu
- Institute for Melanin Chemistry, Fujita Health University, Toyoake, Japan
| | - Gopal Battu
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Jerrold L Belant
- Department of Fisheries and Wildlife, Michigan State University, East Lansing, MI 48824, USA
| | - Dean E Beyer
- Department of Fisheries and Wildlife, Michigan State University, East Lansing, MI 48824, USA
| | - Colin Carpenter
- West Virginia Division of Natural Resources, Beckley, WV 25801, USA
| | - Anthony P Crupi
- Division of Wildlife Conservation, Alaska Department of Fish and Game, Douglas, Juneau, AK 99824, USA
| | - Maria Davidson
- The Louisiana Department of Wildlife and Fisheries, Baton Rouge, LA 70898, USA
| | - Christopher S DePerno
- Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC 27695-7646, USA
| | - Nicholas Forman
- New Mexico Department of Game and Fish, Santa Fe, NM 87507, USA
| | - Nicholas L Fowler
- Division of Wildlife Conservation, Alaska Department of Fish and Game, Douglas, Juneau, AK 99824, USA
| | - David L Garshelis
- Minnesota Department of Natural Resources, Grand Rapids, MN 55744, USA; IUCN SSC Bear Specialist Group
| | - Nicholas Gould
- Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC 27695-7646, USA
| | - Kerry Gunther
- National Park Service, Yellowstone National Park, WY 82190-0168, USA
| | - Mark Haroldson
- U.S. Geological Survey, Northern Rocky Mountain Science Center, Interagency Grizzly Bear Study Team, Bozeman, MT 59715, USA
| | - Shosuke Ito
- Institute for Melanin Chemistry, Fujita Health University, Toyoake, Japan
| | - David Kocka
- Virginia Department of Wildlife Resources, Verona, VA 24482, USA
| | - Carl Lackey
- Nevada Department of Wildlife, Reno, NV 89512, USA
| | - Ryan Leahy
- National Park Service, Yosemite National Park Wildlife Management, Yosemite, CA 95389, USA
| | - Caitlin Lee-Roney
- National Park Service, Yosemite National Park Wildlife Management, Yosemite, CA 95389, USA
| | - Tania Lewis
- National Park Service, Glacier Bay National Park, Gustavus, AK 99826, USA
| | - Ashley Lutto
- U.S. Fish and Wildlife Service, Kenai National Wildlife Refuge, Soldotna, AK 99669, USA
| | - Kelly McGowan
- Department of Genetics, School of Medicine, Stanford University, Stanford, CA 94305, USA
| | | | - Mike Orlando
- Florida Fish and Wildlife Conservation Commission, Tallahassee, FL 32399, USA
| | - Alexander Platt
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Matthew D Pollard
- Department of Biological Sciences, University of Memphis, Memphis, TN 38152, USA
| | - Megan Ramaker
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | | | - Jaime L Sajecki
- Virginia Department of Wildlife Resources, Verona, VA 24482, USA
| | - Stephanie K Sell
- Division of Wildlife Conservation, Alaska Department of Fish and Game, Douglas, Juneau, AK 99824, USA
| | - Jennifer Strules
- Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC 27695-7646, USA
| | - Seth Thompson
- Virginia Department of Wildlife Resources, Verona, VA 24482, USA
| | - Frank van Manen
- U.S. Geological Survey, Northern Rocky Mountain Science Center, Interagency Grizzly Bear Study Team, Bozeman, MT 59715, USA
| | - Craig Whitman
- U.S. Geological Survey, Northern Rocky Mountain Science Center, Interagency Grizzly Bear Study Team, Bozeman, MT 59715, USA
| | - Ryan Williamson
- National Park Service, Great Smoky Mountains National Park, Gatlinburg, TN 37738, USA
| | | | - Christopher B Kaelin
- Department of Genetics, School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Michael S Marks
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Departments of Pathology and Laboratory Medicine and of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Gregory S Barsh
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA; Department of Genetics, School of Medicine, Stanford University, Stanford, CA 94305, USA
| |
Collapse
|
5
|
Willey C, Korstanje R. Sequencing and assembling bear genomes: the bare necessities. Front Zool 2022; 19:30. [PMID: 36451195 PMCID: PMC9710173 DOI: 10.1186/s12983-022-00475-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 11/08/2022] [Indexed: 12/12/2022] Open
Abstract
Unique genetic adaptations are present in bears of every species across the world. From (nearly) shutting down important organs during hibernation to preventing harm from lifestyles that could easily cause metabolic diseases in humans, bears may hold the answer to various human ailments. However, only a few of these unique traits are currently being investigated at the molecular level, partly because of the lack of necessary tools. One of these tools is well-annotated genome assemblies from the different, extant bear species. These reference genomes are needed to allow us to identify differences in genetic variants, isoforms, gene expression, and genomic features such as transposons and identify those that are associated with biomedical-relevant traits. In this review we assess the current state of the genome assemblies of the eight different bear species, discuss current gaps, and the future benefits these reference genomes may have in informing human biomedical applications, while at the same time improving bear conservation efforts.
Collapse
|
6
|
Armstrong EE, Perry BW, Huang Y, Garimella KV, Jansen HT, Robbins CT, Tucker NR, Kelley JL. A beary good genome: Haplotype-resolved, chromosome-level assembly of the brown bear (Ursus arctos). Genome Biol Evol 2022; 14:6656105. [PMID: 35929770 PMCID: PMC9447482 DOI: 10.1093/gbe/evac125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/20/2022] [Indexed: 11/30/2022] Open
Abstract
The brown bear (Ursus arctos) is the second largest and most widespread extant terrestrial carnivore on Earth and has recently emerged as a medical model for human metabolic diseases. Here, we report a fully phased chromosome-level assembly of a male North American brown bear built by combining Pacific Biosciences (PacBio) HiFi data and publicly available Hi-C data. The final genome size is 2.47 Gigabases (Gb) with a scaffold and contig N50 length of 70.08 and 43.94 Megabases (Mb), respectively. Benchmarking Universal Single-Copy Ortholog (BUSCO) analysis revealed that 94.5% of single copy orthologs from Mammalia were present in the genome (the highest of any ursid genome to date). Repetitive elements accounted for 44.48% of the genome and a total of 20,480 protein coding genes were identified. Based on whole genome alignment to the polar bear, the brown bear is highly syntenic with the polar bear, and our phylogenetic analysis of 7,246 single-copy orthologs supports the currently proposed species tree for Ursidae. This highly contiguous genome assembly will support future research on both the evolutionary history of the bear family and the physiological mechanisms behind hibernation, the latter of which has broad medical implications.
Collapse
Affiliation(s)
- Ellie E Armstrong
- School of Biological Sciences, Washington State University, Pullman, WA, 99164, USA
| | - Blair W Perry
- School of Biological Sciences, Washington State University, Pullman, WA, 99164, USA
| | - Yongqing Huang
- Data Sciences Platform, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Kiran V Garimella
- Data Sciences Platform, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Heiko T Jansen
- Integrative Physiology and Neuroscience, Washington State University, Pullman, WA, 99164, USA
| | - Charles T Robbins
- School of Biological Sciences, Washington State University, Pullman, WA, 99164, USA.,School of the Environment, Washington State University, Pullman, WA, 99164, USA
| | - Nathan R Tucker
- Masonic Medical Research Institute, 2150 Bleecker St, Utica, NY, 13501, USA.,Cardiovascular Disease Initiative, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Joanna L Kelley
- School of Biological Sciences, Washington State University, Pullman, WA, 99164, USA
| |
Collapse
|
7
|
Uncovering the enigmatic evolution of bears in greater depth: The hybrid origin of the Asiatic black bear. Proc Natl Acad Sci U S A 2022; 119:e2120307119. [PMID: 35858381 PMCID: PMC9351369 DOI: 10.1073/pnas.2120307119] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Bears are fascinating mammals because of their complex pattern of speciation and rapid evolution of distinct phenotypes. Interspecific hybridization has been common and has shaped the complex evolutionary history of bears. In this study, based on the largest population-level genomic dataset to date involving all Ursinae species and recently developed methods for detecting hybrid speciation, we provide explicit evidence for the hybrid origin of Asiatic black bears, which arose through historical hybridization between the ancestor of polar bear/brown bear/American black bears and the ancestor of sun bear/sloth bears. This was inferred to have occurred soon after the divergence of the two parental lineages in Eurasia due to climate-driven population expansion and dispersal. In addition, we found that the intermediate body size of this hybrid species arose from its combination of relevant genes derived from two parental lineages of contrasting sizes. This and alternate fixation of numerous other loci that had diverged between parental lineages may have initiated the reproductive isolation of the Asiatic black bear from its two parents. Our study sheds further light on the evolutionary history of bears and documents the importance of hybridization in new species formation and phenotypic evolution in mammals.
Collapse
|
8
|
Huang Y, Chu X, Zhang Y, Yang S, Shi Y, Chen Q. Transformation of Mitochondrial Architecture and Dynamics in the Chinese Soft-Shelled Turtle ( Pelodiscus sinensis) During Hibernation. MICROSCOPY AND MICROANALYSIS : THE OFFICIAL JOURNAL OF MICROSCOPY SOCIETY OF AMERICA, MICROBEAM ANALYSIS SOCIETY, MICROSCOPICAL SOCIETY OF CANADA 2022; 28:1-11. [PMID: 35317875 DOI: 10.1017/s1431927622000484] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Hibernation is a biological status during which hibernating animals acclimatize themselves to reduced energy consumption through extreme but governed decline in self-metabolism. The role of mitochondria (Mt) in metabolic suppression during hibernation has already been elaborated in different organs and species. Nonetheless, the concretely changing process of mitochondrial architecture and the mechanism underlying this transformation during hibernation remains unclear. Herein, the present study was aimed at clarifying the detailed alteration of mitochondrial morphology and its potential role in the Chinese soft-shelled turtle (Pelodiscus sinensis) during different stages of hibernation. Compared with the nonhibernation period, the mitochondrial architecture was changing from round to crescent, and lipid droplet (LD)/Mt interaction was enhanced during hibernation, as observed by transmission electron microscopy (TEM). Further ultrastructural analysis uncovered that mitochondrial fusion was promptly accelerated in the early stage of hibernation, followed by mitochondrial fission in the middle stage, and mitophagy was boosted in the late stage. Moreover, gene and protein expression related to mitochondrial fusion, fission, and mitophagy accorded closely with the mitochondrial ultrastructural changes in different stages of hibernation. Taken together, our results clarified that the transformation of mitochondrial architecture and mitochondrial dynamics are of vital importance in maintaining internal environment homeostasis of Pelodiscus sinensis.
Collapse
Affiliation(s)
- Yufei Huang
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, Jiangsu Province210095, P.R. China
- Institute of Comparative Medicine, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu Province225009, P.R. China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, Jiangsu Province 225009, P.R. China
| | - Xiaoya Chu
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, Jiangsu Province210095, P.R. China
| | - Yafei Zhang
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, Jiangsu Province210095, P.R. China
| | - Sheng Yang
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, Jiangsu Province210095, P.R. China
| | - Yonghong Shi
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, Jiangsu Province210095, P.R. China
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai200241, P.R. China
| | - Qiusheng Chen
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, Jiangsu Province210095, P.R. China
| |
Collapse
|
9
|
Tseng E, Underwood JG, Evans Hutzenbiler BD, Trojahn S, Kingham B, Shevchenko O, Bernberg E, Vierra M, Robbins CT, Jansen HT, Kelley JL. Long-read isoform sequencing reveals tissue-specific isoform expression between active and hibernating brown bears (Ursus arctos). G3 (BETHESDA, MD.) 2022; 12:6472356. [PMID: 35100340 PMCID: PMC9210309 DOI: 10.1093/g3journal/jkab422] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 11/17/2021] [Indexed: 11/13/2022]
Abstract
Understanding hibernation in brown bears (Ursus arctos) can provide insight into some human diseases. During hibernation, brown bears experience periods of insulin resistance, physical inactivity, extreme bradycardia, obesity, and the absence of urine production. These states closely mimic aspects of human diseases such as type 2 diabetes, muscle atrophy, as well as renal and heart failure. The reversibility of these states from hibernation to active season enables the identification of mediators with possible therapeutic value for humans. Recent studies have identified genes and pathways that are differentially expressed between active and hibernation seasons in bears. However, little is known about the role of differential expression of gene isoforms on hibernation physiology. To identify both distinct and novel mRNA isoforms, full-length RNA-sequencing (Iso-Seq) was performed on adipose, skeletal muscle, and liver from three individual bears sampled during both active and hibernation seasons. The existing reference genome annotation was improved by combining it with the Iso-Seq data. Short-read RNA-sequencing data from six individuals were mapped to the new reference annotation to quantify differential isoform usage (DIU) between tissues and seasons. We identified differentially expressed isoforms in all three tissues, to varying degrees. Adipose had a high level of DIU with isoform switching, regardless of whether the genes were differentially expressed. Our analyses revealed that DIU, even in the absence of differential gene expression, is an important mechanism for modulating genes during hibernation. These findings demonstrate the value of isoform expression studies and will serve as the basis for deeper exploration into hibernation biology.
Collapse
Affiliation(s)
| | | | - Brandon D Evans Hutzenbiler
- Department of Integrative Physiology and Neuroscience, Washington State University, Pullman, WA 99164, USA.,School of the Environment, Washington State University, Pullman, WA 99164, USA
| | - Shawn Trojahn
- School of Biological Sciences, Washington State University, Pullman, WA 99164, USA
| | - Brewster Kingham
- Sequencing & Genotyping Center, Delaware Biotechnology Institute, University of Delaware, Newark, DE 19711, USA
| | - Olga Shevchenko
- Sequencing & Genotyping Center, Delaware Biotechnology Institute, University of Delaware, Newark, DE 19711, USA
| | - Erin Bernberg
- Sequencing & Genotyping Center, Delaware Biotechnology Institute, University of Delaware, Newark, DE 19711, USA
| | | | - Charles T Robbins
- School of the Environment, Washington State University, Pullman, WA 99164, USA.,School of Biological Sciences, Washington State University, Pullman, WA 99164, USA
| | - Heiko T Jansen
- Department of Integrative Physiology and Neuroscience, Washington State University, Pullman, WA 99164, USA
| | - Joanna L Kelley
- School of Biological Sciences, Washington State University, Pullman, WA 99164, USA
| |
Collapse
|
10
|
Abstract
We found the three-dimensional (3D) structure of chromatin at the chromosome level to be highly conserved for more than 50 million y of carnivore evolution. Intrachromosomal contacts were maintained even after chromosome rearrangements within carnivore lineages, demonstrating that the maintenance of 3D chromatin architecture is essential for conserved genome functions. These discoveries enabled the identification of orthologous chromosomal DNA segments among related species, a method we call 3D comparative scaffotyping. The method has application for putative chromosome assignment of chromosome-scale DNA sequence scaffolds produced by de novo genome sequencing. Broadly applied to biodiversity genome sequencing efforts, the approach can reduce costs associated with karyotyping and the physical mapping of DNA segments to chromosomes. High throughput chromatin conformation capture (Hi-C) of leukocyte DNA was used to investigate the evolutionary stability of chromatin conformation at the chromosomal level in 11 species from three carnivore families: Felidae, Canidae, and Ursidae. Chromosome-scale scaffolds (C-scaffolds) of each species were initially used for whole-genome alignment to a reference genome within each family. This approach established putative orthologous relationships between C-scaffolds among the different species. Hi-C contact maps for all C-scaffolds were then visually compared and found to be distinct for a given reference chromosome or C-scaffold within a species and indistinguishable for orthologous C-scaffolds having a 1:1 relationship within a family. The visual patterns within families were strongly supported by eigenvectors from the Hi-C contact maps. Analysis of Hi-C contact maps and eigenvectors across the three carnivore families revealed that most cross-family orthologous subchromosomal fragments have a conserved three-dimensional (3D) chromatin structure and thus have been under strong evolutionary constraint for ∼54 My of carnivore evolution. The most pronounced differences in chromatin conformation were observed for the X chromosome and the red fox genome, whose chromosomes have undergone extensive rearrangements relative to other canids. We also demonstrate that Hi-C contact map pattern analysis can be used to accurately identify orthologous relationships between C-scaffolds and chromosomes, a method we termed “3D comparative scaffotyping.” This method provides a powerful means for estimating karyotypes in de novo sequenced species that have unknown karyotype and no physical mapping information.
Collapse
|
11
|
Saremi NF, Oppenheimer J, Vollmers C, O'Connell B, Milne SA, Byrne A, Yu L, Ryder OA, Green RE, Shapiro B. An Annotated Draft Genome for the Andean Bear, Tremarctos ornatus. J Hered 2021; 112:377-384. [PMID: 33882130 PMCID: PMC8280923 DOI: 10.1093/jhered/esab021] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 04/20/2021] [Indexed: 12/18/2022] Open
Abstract
The Andean bear is the only extant member of the Tremarctine subfamily and the only extant ursid species to inhabit South America. Here, we present an annotated de novo assembly of a nuclear genome from a captive-born female Andean bear, Mischief, generated using a combination of short and long DNA and RNA reads. Our final assembly has a length of 2.23 Gb, and a scaffold N50 of 21.12 Mb, contig N50 of 23.5 kb, and BUSCO score of 88%. The Andean bear genome will be a useful resource for exploring the complex phylogenetic history of extinct and extant bear species and for future population genetics studies of Andean bears.
Collapse
Affiliation(s)
- Nedda F Saremi
- Department of Biomolecular Engineering and Bioinformatics, University of California Santa Cruz, Santa Cruz, CA
| | - Jonas Oppenheimer
- Department of Biomolecular Engineering and Bioinformatics, University of California Santa Cruz, Santa Cruz, CA
| | - Christopher Vollmers
- Department of Biomolecular Engineering and Bioinformatics, University of California Santa Cruz, Santa Cruz, CA
| | - Brendan O'Connell
- Department of Medical and Molecular Genetics, Oregon Health & Science University, Portland, OR
| | - Shard A Milne
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA
| | - Ashley Byrne
- Department of Molecular, Cellular, Developmental Biology, University of California Santa Cruz, Santa Cruz, CA
| | - Li Yu
- State Key Laboratory for Conservation and Utilization of Bio-Resource in Yunnan, School of Life Sciences, Yunnan University, Kunming, China
| | | | - Richard E Green
- Department of Biomolecular Engineering and Bioinformatics, University of California Santa Cruz, Santa Cruz, CA
| | - Beth Shapiro
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA.,Howard Hughes Medical Institute, University of California Santa Cruz, Santa Cruz, CA
| |
Collapse
|
12
|
Pedersen MW, De Sanctis B, Saremi NF, Sikora M, Puckett EE, Gu Z, Moon KL, Kapp JD, Vinner L, Vardanyan Z, Ardelean CF, Arroyo-Cabrales J, Cahill JA, Heintzman PD, Zazula G, MacPhee RDE, Shapiro B, Durbin R, Willerslev E. Environmental genomics of Late Pleistocene black bears and giant short-faced bears. Curr Biol 2021; 31:2728-2736.e8. [PMID: 33878301 DOI: 10.1016/j.cub.2021.04.027] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 03/31/2021] [Accepted: 04/12/2021] [Indexed: 10/21/2022]
Abstract
Analysis of ancient environmental DNA (eDNA) has revolutionized our ability to describe biological communities in space and time,1-3 by allowing for parallel sequencing of DNA from all trophic levels.4-8 However, because environmental samples contain sparse and fragmented data from multiple individuals, and often contain closely related species,9 the field of ancient eDNA has so far been limited to organellar genomes in its contribution to population and phylogenetic studies.5,6,10,11 This is in contrast to data from fossils12,13 where full-genome studies are routine, despite these being rare and their destruction for sequencing undesirable.14-16 Here, we report the retrieval of three low-coverage (0.03×) environmental genomes from American black bear (Ursus americanus) and a 0.04× environmental genome of the extinct giant short-faced bear (Arctodus simus) from cave sediment samples from northern Mexico dated to 16-14 thousand calibrated years before present (cal kyr BP), which we contextualize with a new high-coverage (26×) and two lower-coverage giant short-faced bear genomes obtained from fossils recovered from Yukon Territory, Canada, which date to ∼22-50 cal kyr BP. We show that the Late Pleistocene black bear population in Mexico is ancestrally related to the present-day Eastern American black bear population, and that the extinct giant short-faced bears present in Mexico were deeply divergent from the earlier Beringian population. Our findings demonstrate the ability to separately analyze genomic-scale DNA sequences of closely related species co-preserved in environmental samples, which brings the use of ancient eDNA into the era of population genomics and phylogenetics.
Collapse
Affiliation(s)
- Mikkel Winther Pedersen
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Bianca De Sanctis
- Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK; Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK
| | - Nedda F Saremi
- Department of Biomolecular Engineering and Bioinformatics, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Martin Sikora
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Emily E Puckett
- Department of Biological Sciences, University of Memphis, 3770 Walker Avenue, Ellington Hall, Memphis, TN 38152, USA
| | - Zhenquan Gu
- State Key Laboratory of Tibetan Plateau Earth System Science (LATPES), Beijing 100101, China
| | - Katherine L Moon
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Joshua D Kapp
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Lasse Vinner
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Zaruhi Vardanyan
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Ciprian F Ardelean
- Unidad Académica de Antropología, Universidad Autónoma de Zacatecas, Campus II, Col. Progreso, 98066 Zacatecas, Mexico; The Archaeology Centre, Department of Anthropology, University of Toronto, 19 Ursula Franklin Street, Toronto, ON M5S 2S2, Canada
| | - Joaquin Arroyo-Cabrales
- Laboratorio de Arqueozoologia, Subdireccion de Laboratorios y Apoyo Academico, Instituto Nacional de Antropologia e Historia, Moneda 16, Col. Centro, 06060 Mexico, CdMx, Mexico
| | - James A Cahill
- Laboratory of the Neurogenetics of Language, Rockefeller University, New York, NY, USA
| | - Peter D Heintzman
- The Arctic University Museum of Norway, UiT - The Arctic University of Norway, PO Box 6050, Langnes, N-9037 Tromsø, Norway
| | - Grant Zazula
- Yukon Palaeontology Program, Department of Tourism & Culture, Government of Yukon, Whitehorse, YT Y1A 2C6, Canada
| | - Ross D E MacPhee
- Department of Mammalogy, American Museum of Natural History, New York, NY 12484, USA; American Museum of Natural History, New York, NY, USA
| | - Beth Shapiro
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA, USA; Howard Hughes Medical Institute, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Richard Durbin
- Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK; Wellcome Sanger Institute, Cambridge CB10 1SA, UK
| | - Eske Willerslev
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark; Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK; Wellcome Sanger Institute, Cambridge CB10 1SA, UK; MARUM, University of Bremen, Bremen, Germany.
| |
Collapse
|
13
|
Fazzalari A, Basadonna G, Kucukural A, Tanriverdi K, Koupenova M, Pozzi N, Kakuturu J, Friedrich AKU, Korstanje R, Fowler N, Belant JL, Beyer DE, Brooks MB, Dickson EW, Blackwood M, Mueller C, Palesty JA, Freedman JE, Cahan MA. A Translational Model for Venous Thromboembolism: MicroRNA Expression in Hibernating Black Bears. J Surg Res 2021; 257:203-212. [PMID: 32858321 PMCID: PMC11026106 DOI: 10.1016/j.jss.2020.06.027] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Revised: 05/17/2020] [Accepted: 06/16/2020] [Indexed: 01/02/2023]
Abstract
BACKGROUND Hibernating American black bears have significantly different clotting parameters than their summer active counterparts, affording them protection against venous thromboembolism during prolonged periods of immobility. We sought to evaluate if significant differences exist between the expression of microRNAs in the plasma of hibernating black bears compared with their summer active counterparts, potentially contributing to differences in hemostasis during hibernation. MATERIALS AND METHODS MicroRNA sequencing was assessed in plasma from 21 American black bears in summer active (n = 11) and hibernating states (n = 10), and microRNA signatures during hibernating and active state were established using both bear and human genome. MicroRNA targets were predicted using messenger RNA (mRNA) transcripts from black bear kidney cells. In vitro studies were performed to confirm the relationship between identified microRNAs and mRNA expression, using artificial microRNA and human liver cells. RESULTS Using the bear genome, we identified 15 microRNAs differentially expressed in the plasma of hibernating black bears. Of these microRNAs, three were significantly downregulated (miR-141-3p, miR-200a-3p, and miR-200c-3p), were predicted to target SERPINC1, the gene for antithrombin, and demonstrated regulatory control of the gene mRNA expression in cell studies. CONCLUSIONS Our findings suggest that the hibernating black bears' ability to maintain hemostasis and achieve protection from venous thromboembolism during prolonged periods of immobility may be due to changes in microRNA signatures and possible upregulation of antithrombin expression.
Collapse
Affiliation(s)
- Amanda Fazzalari
- Department of Surgery, University of Massachusetts Medical School, Worcester, Massachusetts; The Stanley J. Dudrick Department of Surgery, Saint Mary's Hospital, Waterbury, Connecticut
| | - Giacomo Basadonna
- Department of Surgery, University of Massachusetts Medical School, Worcester, Massachusetts
| | - Alper Kucukural
- Bioinformatics Core, University of Massachusetts Medical School, Worcester, Massachusetts; Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts
| | - Kahraman Tanriverdi
- Division of Cardiovascular Medicine, Department of Medicine, University of Massachusetts Medical School, Worcester, Massachusetts
| | - Milka Koupenova
- Division of Cardiovascular Medicine, Department of Medicine, University of Massachusetts Medical School, Worcester, Massachusetts
| | - Natalie Pozzi
- The Stanley J. Dudrick Department of Surgery, Saint Mary's Hospital, Waterbury, Connecticut
| | - Jahnavi Kakuturu
- The Stanley J. Dudrick Department of Surgery, Saint Mary's Hospital, Waterbury, Connecticut
| | | | - Ron Korstanje
- The Korstanje Lab, The Jackson Laboratory, Bar Harbor, Maine
| | - Nicholas Fowler
- Camp Fire Program in Wildlife Conservation, State University of New York College of Environmental Science and Forestry, Syracuse, New York
| | - Jerrold L Belant
- Camp Fire Program in Wildlife Conservation, State University of New York College of Environmental Science and Forestry, Syracuse, New York
| | - Dean E Beyer
- Department of Fisheries and Wildlife, College of Agriculture & Natural Resources, Michigan State University, East Lansing, Michigan; Michigan Department of Natural Resources, Marquette, Michigan
| | - Marjory B Brooks
- Comparative Coagulation Section, Cornell University Animal Health Diagnostic Center, Ithaca, New York
| | - Eric W Dickson
- Department of Emergency Medicine, University of Massachusetts Medical School, Worcester, Massachusetts
| | - Meghan Blackwood
- Mueller Lab for Gene Therapy, Horae Gene Therapy Center, University of Massachusetts Medical School, Worcester, Massachusetts
| | - Chris Mueller
- Mueller Lab for Gene Therapy, Horae Gene Therapy Center, University of Massachusetts Medical School, Worcester, Massachusetts
| | - J Alexander Palesty
- The Stanley J. Dudrick Department of Surgery, Saint Mary's Hospital, Waterbury, Connecticut
| | - Jane E Freedman
- Division of Cardiovascular Medicine, Department of Medicine, University of Massachusetts Medical School, Worcester, Massachusetts
| | - Mitchell A Cahan
- Department of Surgery, University of Massachusetts Medical School, Worcester, Massachusetts.
| |
Collapse
|
14
|
Ebert T, Painer J, Bergman P, Qureshi AR, Giroud S, Stalder G, Kublickiene K, Göritz F, Vetter S, Bieber C, Fröbert O, Arnemo JM, Zedrosser A, Redtenbacher I, Shiels PG, Johnson RJ, Stenvinkel P. Insights in the regulation of trimetylamine N-oxide production using a comparative biomimetic approach suggest a metabolic switch in hibernating bears. Sci Rep 2020; 10:20323. [PMID: 33230252 PMCID: PMC7684304 DOI: 10.1038/s41598-020-76346-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Accepted: 10/27/2020] [Indexed: 12/17/2022] Open
Abstract
Experimental studies suggest involvement of trimethylamine N-oxide (TMAO) in the aetiology of cardiometabolic diseases and chronic kidney disease (CKD), in part via metabolism of ingested food. Using a comparative biomimetic approach, we have investigated circulating levels of the gut metabolites betaine, choline, and TMAO in human CKD, across animal species as well as during hibernation in two animal species. Betaine, choline, and TMAO levels were associated with renal function in humans and differed significantly across animal species. Free-ranging brown bears showed a distinct regulation pattern with an increase in betaine (422%) and choline (18%) levels during hibernation, but exhibited undetectable levels of TMAO. Free-ranging brown bears had higher betaine, lower choline, and undetectable TMAO levels compared to captive brown bears. Endogenously produced betaine may protect bears and garden dormice during the vulnerable hibernating period. Carnivorous eating habits are linked to TMAO levels in the animal kingdom. Captivity may alter the microbiota and cause a subsequent increase of TMAO production. Since free-ranging bears seems to turn on a metabolic switch that shunts choline to generate betaine instead of TMAO, characterisation and understanding of such an adaptive switch could hold clues for novel treatment options in burden of lifestyle diseases, such as CKD.
Collapse
Affiliation(s)
- Thomas Ebert
- Division of Renal Medicine, Department of Clinical Science, Intervention and Technology, Karolinska Institutet, Stockholm, Sweden
| | - Johanna Painer
- Department of Interdisciplinary Life Sciences, Research Institute of Wildlife Ecology, Veterinary University Vienna, Savoyenstreet 1, 1160, Vienna, Austria
| | - Peter Bergman
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Abdul Rashid Qureshi
- Division of Renal Medicine, Department of Clinical Science, Intervention and Technology, Karolinska Institutet, Stockholm, Sweden
| | - Sylvain Giroud
- Department of Interdisciplinary Life Sciences, Research Institute of Wildlife Ecology, Veterinary University Vienna, Savoyenstreet 1, 1160, Vienna, Austria
| | - Gabrielle Stalder
- Department of Interdisciplinary Life Sciences, Research Institute of Wildlife Ecology, Veterinary University Vienna, Savoyenstreet 1, 1160, Vienna, Austria
| | - Karolina Kublickiene
- Division of Renal Medicine, Department of Clinical Science, Intervention and Technology, Karolinska Institutet, Stockholm, Sweden
| | - Frank Göritz
- Leibniz Institute for Zoo and Wildlife Ecology, Berlin, Germany
| | - Sebastian Vetter
- Department of Interdisciplinary Life Sciences, Research Institute of Wildlife Ecology, Veterinary University Vienna, Savoyenstreet 1, 1160, Vienna, Austria
| | - Claudia Bieber
- Department of Interdisciplinary Life Sciences, Research Institute of Wildlife Ecology, Veterinary University Vienna, Savoyenstreet 1, 1160, Vienna, Austria
| | - Ole Fröbert
- Department of Cardiology, Faculty of Health, Örebro University, Örebro, Sweden
| | - Jon M Arnemo
- Department of Forestry and Wildlife Management, Inland Norway University of Applied Sciences, Campus Evenstad, Koppang, Norway.,Department of Wildlife, Fish and Environmental Studies, Swedish University of Agricultural Sciences, Umeå, Sweden
| | - Andreas Zedrosser
- Department of Natural Sciences and Environmental Health, University of South-Eastern Norway, Bø i Telemark, Norway.,Institute for Wildlife Biology and Game Management, University for Natural Resources and Life Sciences, Vienna, Austria
| | | | - Paul G Shiels
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - Richard J Johnson
- Division of Renal Diseases, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Peter Stenvinkel
- Division of Renal Medicine, Department of Clinical Science, Intervention and Technology, Karolinska Institutet, Stockholm, Sweden. .,Department of Renal Medicine M99, Karolinska University Hospital, 141 86, Stockholm, Sweden.
| |
Collapse
|
15
|
Samaniego Castruita JA, Westbury MV, Lorenzen ED. Analyses of key genes involved in Arctic adaptation in polar bears suggest selection on both standing variation and de novo mutations played an important role. BMC Genomics 2020; 21:543. [PMID: 32758141 PMCID: PMC7430819 DOI: 10.1186/s12864-020-06940-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 07/22/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Polar bears are uniquely adapted to an Arctic existence. Since their relatively recent divergence from their closest living relative, brown bears, less than 500,000 years ago, the species has evolved an array of novel traits suited to its Arctic lifestyle. Previous studies sought to uncover the genomic underpinnings of these unique characteristics, and disclosed the genes showing the strongest signal of positive selection in the polar bear lineage. Here, we survey a comprehensive dataset of 109 polar bear and 33 brown bear genomes to investigate the genomic variants within these top genes present in each species. Specifically, we investigate whether fixed homozygous variants in polar bears derived from selection on standing variation in the ancestral gene pool or on de novo mutation in the polar bear lineage. RESULTS We find that a large number of sites fixed in polar bears are biallelic in brown bears, suggesting selection on standing variation. Moreover, we uncover sites in which polar bears are fixed for a derived allele while brown bears are fixed for the ancestral allele, which we suggest may be a signal of de novo mutation in the polar bear lineage. CONCLUSIONS Our findings suggest that, among other mechanisms, natural selection acting on changes in genes derived from a combination of variation already in the ancestral gene pool, and from de novo missense mutations in the polar bear lineage, may have enabled the rapid adaptation of polar bears to their new Arctic environment.
Collapse
|
16
|
Garrett MR, Korstanje R. Using Genetic and Species Diversity to Tackle Kidney Disease. Trends Genet 2020; 36:499-509. [PMID: 32362446 DOI: 10.1016/j.tig.2020.04.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 03/26/2020] [Accepted: 04/03/2020] [Indexed: 12/18/2022]
Abstract
Progress in the identification of causal genes and understanding of the mechanism underlying kidney disease is hindered by the almost exclusive use of a few animal models with restrictive monogenic backgrounds that may be more resistant to kidney disease compared with humans and, therefore, poor models. Exploring the large genetic diversity in classical animal models, such as mice and rats, and leveraging species diversity will allow us to use the genetic advantages of zebrafish, Drosophila, and other species, to develop both new animal models that are more relevant to the study of human kidney disease and potential therapies.
Collapse
Affiliation(s)
- Michael R Garrett
- Department of Pharmacology, University of Mississippi Medical Center, Jackson, MS, USA; Department of Medicine (Nephrology), University of Mississippi Medical Center, Jackson, MS, USA; Department of Pediatrics (Genetics), University of Mississippi Medical Center, Jackson, MS, USA
| | - Ron Korstanje
- The Jackson Laboratory for Mammalian Genetics, Bar Harbor, Maine, ME, USA; Mount Desert Island Biological Laboratory, Bar Harbor, Maine, ME, USA.
| |
Collapse
|
17
|
Zhu C, Xu W, Li J, Liu C, Hu M, Yuan Y, Yuan K, Zhang Y, Song X, Han J, Cui X. Draft Genome Assembly for the Tibetan Black Bear ( Ursus thibetanus thibetanus). Front Genet 2020; 11:231. [PMID: 32300354 PMCID: PMC7142260 DOI: 10.3389/fgene.2020.00231] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Accepted: 02/26/2020] [Indexed: 12/17/2022] Open
Affiliation(s)
- Chenglong Zhu
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, China
| | - Wenjie Xu
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, China
| | - Jianchuan Li
- Department of Animal Resources, Tibet Plateau Institute of Biology, Lhasa, China
| | - Chang Liu
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, China
| | - Mingliang Hu
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, China
| | - Yuan Yuan
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, China
| | - Ke Yuan
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, China
| | - Yijiuling Zhang
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, China
| | - Xingzhi Song
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, China
| | - Jin Han
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, China
| | - Xinxin Cui
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, China
| |
Collapse
|
18
|
Hawkins LJ, Storey KB. Advances and applications of environmental stress adaptation research. Comp Biochem Physiol A Mol Integr Physiol 2019; 240:110623. [PMID: 31778815 DOI: 10.1016/j.cbpa.2019.110623] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Revised: 11/19/2019] [Accepted: 11/21/2019] [Indexed: 02/06/2023]
Abstract
Evolution has produced animals that survive extreme fluctuations in environmental conditions including freezing temperatures, anoxia, desiccating conditions, and prolonged periods without food. For example, the wood frog survives whole-body freezing every winter, arresting all gross physiological functions, but recovers functions upon thawing in the spring. Likewise, many small mammals hibernate for months at a time with minimal metabolic activity, organ perfusion, and movement, yet do not suffer significant muscle atrophy upon arousal. These conditions and the biochemical adaptations employed to deal with them can be viewed as Nature's answer to problems that humans wish to answer, particularly in a biomedical context. This review focuses on recent advances in the field of animal environmental stress adaptation, starting with an emphasis on new areas of research such as epigenetics and microRNA. We then examine new and emerging technologies such as genome editing, novel sequencing applications, and single cell analysis and how these can push us closer to a deeper understanding of biochemical adaptation. Next, evaluate the potential contributions of new high-throughput technologies (e.g. next-generation sequencing, mass spectrometry proteomics) to better understanding the adaptations that support these extreme phenotypes. Concluding, we examine some of the human applications that can be gained from understanding the principles of biochemical adaptation including organ preservation and treatments for conditions such as ischemic stroke and muscle disuse atrophy.
Collapse
Affiliation(s)
- Liam J Hawkins
- Department of Biology, Carleton University, 1125 Colonel By Drive, Ottawa, ON K1S 5B6, Canada
| | - Kenneth B Storey
- Department of Biology, Carleton University, 1125 Colonel By Drive, Ottawa, ON K1S 5B6, Canada.
| |
Collapse
|
19
|
Polar bear evolution is marked by rapid changes in gene copy number in response to dietary shift. Proc Natl Acad Sci U S A 2019; 116:13446-13451. [PMID: 31209046 DOI: 10.1073/pnas.1901093116] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Polar bear (Ursus maritimus) and brown bear (Ursus arctos) are recently diverged species that inhabit vastly differing habitats. Thus, analysis of the polar bear and brown bear genomes represents a unique opportunity to investigate the evolutionary mechanisms and genetic underpinnings of rapid ecological adaptation in mammals. Copy number (CN) differences in genomic regions between closely related species can underlie adaptive phenotypes and this form of genetic variation has not been explored in the context of polar bear evolution. Here, we analyzed the CN profiles of 17 polar bears, 9 brown bears, and 2 black bears (Ursus americanus). We identified an average of 318 genes per individual that showed evidence of CN variation (CNV). Nearly 200 genes displayed species-specific CN differences between polar bear and brown bear species. Principal component analysis of gene CN provides strong evidence that CNV evolved rapidly in the polar bear lineage and mainly resulted in CN loss. Olfactory receptors composed 47% of CN differentiated genes, with the majority of these genes being at lower CN in the polar bear. Additionally, we found significantly fewer copies of several genes involved in fatty acid metabolism as well as AMY1B, the salivary amylase-encoding gene in the polar bear. These results suggest that natural selection shaped patterns of CNV in response to the transition from an omnivorous to primarily carnivorous diet during polar bear evolution. Our analyses of CNV shed light on the genomic underpinnings of ecological adaptation during polar bear evolution.
Collapse
|
20
|
Andrews MT. Molecular interactions underpinning the phenotype of hibernation in mammals. J Exp Biol 2019; 222:222/2/jeb160606. [DOI: 10.1242/jeb.160606] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
ABSTRACT
Mammals maintain a constant warm body temperature, facilitating a wide variety of metabolic reactions. Mammals that hibernate have the ability to slow their metabolism, which in turn reduces their body temperature and leads to a state of hypothermic torpor. For this metabolic rate reduction to occur on a whole-body scale, molecular interactions that change the physiology of cells, tissues and organs are required, resulting in a major departure from normal mammalian homeostasis. The aim of this Review is to cover recent advances in the molecular biology of mammalian hibernation, including the role of small molecules, seasonal changes in gene expression, cold-inducible RNA-binding proteins, the somatosensory system and emerging information on hibernating primates. To underscore the importance of differential gene expression across the hibernation cycle, mRNA levels for 14,261 ground squirrel genes during periods of activity and torpor are made available for several tissues via an interactive transcriptome browser. This Review also addresses recent findings on molecular interactions responsible for multi-day survival of near-freezing body temperatures, single-digit heart rates and a slowed metabolism that greatly reduces oxygen consumption. A better understanding of how natural hibernators survive these physiological extremes is beginning to lead to innovations in human medicine.
Collapse
Affiliation(s)
- Matthew T. Andrews
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR 97331, USA
| |
Collapse
|