1
|
Peng Y, Li H, Liu Z, Zhang C, Li K, Gong Y, Geng L, Su J, Guan X, Liu L, Zhou R, Zhao Z, Guo J, Liang Q, Li X. Chromosome-level genome assembly of the Arctic fox (Vulpes lagopus) using PacBio sequencing and Hi-C technology. Mol Ecol Resour 2021; 21:2093-2108. [PMID: 33829635 DOI: 10.1111/1755-0998.13397] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 03/28/2021] [Accepted: 03/30/2021] [Indexed: 10/21/2022]
Abstract
The Arctic fox (Vulpes lagopus) is the only fox species occurring in the Arctic and has adapted to its extreme climatic conditions. Currently, the molecular basis of its adaptation to the extreme climate has not been characterized. Here, we applied PacBio sequencing and chromosome structure capture technique to assemble the first V. lagopus genome assembly, which is assembled into chromosome fragments. The genome assembly has a total length of 2.345 Gb with a contig N50 of 31.848 Mb and a scaffold N50 of 131.537 Mb, consisting of 25 pseudochromosomal scaffolds. The V. lagopus genome had approximately 32.33% repeat sequences. In total, 21,278 protein-coding genes were predicted, of which 99.14% were functionally annotated. Compared with 12 other mammals, V. lagopus was most closely related to V. Vulpes with an estimated divergence time of ~7.1 Ma. The expanded gene families and positively selected genes potentially play roles in the adaptation of V. lagopus to Arctic extreme environment. This high-quality assembled genome will not only promote future studies of genetic diversity and evolution in foxes and other canids but also provide important resources for conservation of Arctic species.
Collapse
Affiliation(s)
- Yongdong Peng
- Hebei Key Laboratory of Specialty Animal Germplasm Resources Exploration and Innovation (Under Planning), College of Animal Science and Technology, Hebei Normal University of Science and Technology, Qinhuangdao, China
| | - Hong Li
- Novogene Bioinformatics Institute, Beijing, China
| | - Zhengzhu Liu
- Hebei Key Laboratory of Specialty Animal Germplasm Resources Exploration and Innovation (Under Planning), College of Animal Science and Technology, Hebei Normal University of Science and Technology, Qinhuangdao, China
| | - Chuansheng Zhang
- Hebei Key Laboratory of Specialty Animal Germplasm Resources Exploration and Innovation (Under Planning), College of Animal Science and Technology, Hebei Normal University of Science and Technology, Qinhuangdao, China
| | - Keqiang Li
- Hebei Key Laboratory of Specialty Animal Germplasm Resources Exploration and Innovation (Under Planning), College of Mathematics and Information Science, Hebei Normal University of Science and Technology, Qinhuangdao, China
| | - Yuanfang Gong
- Hebei Key Laboratory of Specialty Animal Germplasm Resources Exploration and Innovation (Under Planning), College of Animal Science and Technology, Hebei Normal University of Science and Technology, Qinhuangdao, China
| | - Liying Geng
- Hebei Key Laboratory of Specialty Animal Germplasm Resources Exploration and Innovation (Under Planning), College of Agronomy and Biotechnology, Hebei Normal University of Science and Technology, Qinhuangdao, China
| | - Jingjing Su
- Hebei Key Laboratory of Applied Chemistry, School of Environmental and Chemical Engineering, Yanshan University, Qinhuangdao, China
| | - Xuemin Guan
- Hebei Key Laboratory of Specialty Animal Germplasm Resources Exploration and Innovation (Under Planning), College of Agronomy and Biotechnology, Hebei Normal University of Science and Technology, Qinhuangdao, China
| | - Lei Liu
- College of Animal Science and Technology, Shandong Agricultural University, Tai-an, China
| | - Ruihong Zhou
- Hebei Key Laboratory of Specialty Animal Germplasm Resources Exploration and Innovation (Under Planning), College of Animal Science and Technology, Hebei Normal University of Science and Technology, Qinhuangdao, China
| | - Ziya Zhao
- Hebei Key Laboratory of Specialty Animal Germplasm Resources Exploration and Innovation (Under Planning), College of Animal Science and Technology, Hebei Normal University of Science and Technology, Qinhuangdao, China
| | - Jianxu Guo
- Hebei Key Laboratory of Specialty Animal Germplasm Resources Exploration and Innovation (Under Planning), College of Animal Science and Technology, Hebei Normal University of Science and Technology, Qinhuangdao, China
| | - Qiqi Liang
- Novogene Bioinformatics Institute, Beijing, China
| | - Xianglong Li
- Hebei Key Laboratory of Specialty Animal Germplasm Resources Exploration and Innovation (Under Planning), College of Animal Science and Technology, Hebei Normal University of Science and Technology, Qinhuangdao, China
| |
Collapse
|
2
|
Martinez B, Ortiz RM. Thyroid Hormone Regulation and Insulin Resistance: Insights From Animals Naturally Adapted to Fasting. Physiology (Bethesda) 2017; 32:141-151. [PMID: 28202624 DOI: 10.1152/physiol.00018.2016] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The contribution of thyroidal status in insulin signaling and glucose homeostasis has been implicated as a potential pathophysiological factor in humans, but the specific mechanisms remain largely elusive. Fasting induces changes in both thyroid hormone secretion and insulin signaling. Here, we explore how mammals that undergo natural, prolonged bouts of fasting provide unique insight into evolved physiological adaptations that allow them to tolerate such conditions despite intermittent states of reversible insulin resistance. Such insights from nature may provide clues to better understand the basis of thyroidal involvement in insulin dysregulation in humans.
Collapse
Affiliation(s)
- Bridget Martinez
- Department of Molecular & Cellular Biology, University of California, Merced, California
| | - Rudy M Ortiz
- Department of Molecular & Cellular Biology, University of California, Merced, California
| |
Collapse
|
3
|
Mustonen AM, Bowman J, Sadowski C, Nituch LA, Bruce L, Halonen T, Puukka K, Rouvinen-Watt K, Aho J, Nieminen P. Physiological adaptations to prolonged fasting in the overwintering striped skunk (Mephitis mephitis). Comp Biochem Physiol A Mol Integr Physiol 2013; 166:555-63. [DOI: 10.1016/j.cbpa.2013.08.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2013] [Revised: 08/15/2013] [Accepted: 08/15/2013] [Indexed: 10/26/2022]
|
4
|
The effects of an abundant ectoparasite, the deer ked (Lipoptena cervi), on the health of moose (Alces alces) in Finland. Parasitol Res 2012; 111:1223-32. [DOI: 10.1007/s00436-012-2956-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2012] [Accepted: 05/03/2012] [Indexed: 11/25/2022]
|
5
|
Paakkonen T, Mustonen AM, Käkelä R, Kiljander T, Kynkäänniemi SM, Laaksonen S, Solismaa M, Aho J, Kortet R, Puukka K, Saarela S, Härkönen L, Kaitala A, Ylönen H, Nieminen P. Experimental infection of the deer ked (Lipoptena cervi) has no negative effects on the physiology of the captive reindeer (Rangifer tarandus tarandus). Vet Parasitol 2011; 179:180-8. [DOI: 10.1016/j.vetpar.2011.02.017] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2010] [Revised: 02/15/2011] [Accepted: 02/22/2011] [Indexed: 10/18/2022]
Affiliation(s)
- Tommi Paakkonen
- University of Eastern Finland, Faculty of Science and Forestry, Department of Biology, P.O. Box 111, 80101 Joensuu, Finland.
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
6
|
Sonne C. Health effects from long-range transported contaminants in Arctic top predators: An integrated review based on studies of polar bears and relevant model species. ENVIRONMENT INTERNATIONAL 2010; 36:461-491. [PMID: 20398940 DOI: 10.1016/j.envint.2010.03.002] [Citation(s) in RCA: 139] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2010] [Revised: 03/06/2010] [Accepted: 03/10/2010] [Indexed: 05/29/2023]
Abstract
The aim of this review is to provide a thorough overview of the health effects from the complexed biomagnified mixture of long-range transported industrial organochlorines (OCs), polybrominated diphenyl ethers (PBDEs), perfluorinated compounds (PFCs) and mercury (Hg) on polar bear (Ursus maritimus) health. Multiple scientific studies of polar bears indicate negative relationships between exposure to these contaminants and health parameters; however, these are all of a correlative nature and do not represent true cause-and-effects. Therefore, information from controlled studies of farmed Norwegian Arctic foxes (Vulpes lagopus) and housed East and West Greenland sledge dogs (Canis familiaris) were included as supportive weight of evidence in the clarification of contaminant exposure and health effects in polar bears. The review showed that hormone and vitamin concentrations, liver, kidney and thyroid gland morphology as well as reproductive and immune systems of polar bears are likely to be influenced by contaminant exposure. Furthermore, exclusively based on polar bear contaminant studies, bone density reduction and neurochemical disruption and DNA hypomethylation of the brain stem seemed to occur. The range of tissue concentration, at which these alterations were observed in polar bears, were ca. 1-70,000 ng/g lw for OCs (blood plasma concentrations of some PCB metabolites even higher), ca. 1-1000 ng/g lw for PBDEs and for PFCs and Hg 114-3052 ng/g ww and 0.1-50 microg/g ww, respectively. Similar concentrations were found in farmed foxes and housed sledge dogs while the lack of dose response designs did not allow an estimation of threshold levels for oral exposure and accumulated tissue concentrations. Nor was it possible to pinpoint a specific group of contaminants being more important than others nor analyze their interactions. For East Greenland polar bears the corresponding daily SigmaOC and SigmaPBDE oral exposure was estimated to be 35 and 0.34 microg/kg body weight, respectively. Furthermore, PFC concentrations, at which population effect levels could occur, are likely to be reached around year 2012 for the East Greenland polar bear subpopulation if current increasing temporal trends continue. Such proposed reproductive population effects were supported by physiological based pharmacokinetic (PBPK) modelling of critical body residues (CBR) with risk quotients >or=1 for SigmaPCB, dieldrin, SigmaPFC and SigmaOHC (organohalogen contaminant). The estimated daily TEQ for East Greenland polar bears and East Greenland sledge dogs were 32-281-folds above WHO SigmaTEQ guidelines for humans. Compared to human tolerable daily intake (TDI), these were exceeded for PCBs, dieldrin, chlordanes and SigmaHCH in East Greenland polar bears. Comparisons like these should be done with caution, but together with the CBR modelling and T-score estimations, these were the only available tools for polar bear risk evaluation. In conclusion, polar bears seem to be susceptible to contaminant induced stress that may have an overall sub-clinical impact on their health and population status via impacts on their immune and reproductive systems.
Collapse
Affiliation(s)
- Christian Sonne
- Section for Contaminants, Effects and Marine Mammals, Department of Arctic Environment, National Environmental Research Institute, University of Aarhus, DK-4000 Roskilde, Denmark.
| |
Collapse
|
7
|
Response to Fasting in an Unnaturally Obese Carnivore, the Captive European Polecat Mustela putorius. Exp Biol Med (Maywood) 2009; 234:1287-95. [DOI: 10.3181/0904-rm-140] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
The European polecat ( Mustela putorius) is a naturally lean carnivore prone to excessive weight gain in captivity. This study assessed its suitability to investigate the natural history of the obese phenotype displayed in overweight humans, domestic animals, and seasonally obese wild mammals. Ten farm-bred polecats were subjected to a 5-day fast with 10 controls. Obesity (40% body fat) was associated with an unfavorable plasma lipid profile and high glucose and insulin concentrations. The polecats were in phase II of fasting with normoglycemia, low liver carbohydrate stores, and decreased plasma concentrations of urea and most amino acids. Although the plasma nonesterified fatty acid (NEFA) levels were elevated, the adipose tissue lipase activities suggested a blunted lipolytic response. Lipid mobilization was more efficient from intraabdominal fat. The animals developed hepatic lipidosis with elevated NEFA influx into the liver and losses of n-3 polyunsaturated fatty acids and arginine as hypothetical etiological factors. The plasma leptin, insulin, and triiodothyronine levels decreased but were not accompanied by reduced sex steroid or increased stress hormone concentrations. The blunted lipolytic response often encountered in obesity suggests that the organism is trying to defend the obese phenotype. Liver lipidosis and decreased insulin and triiodothyronine levels seem to be among the most consistent responses to fasting manifested in diverse mammalian orders and different levels of body fatness. The polecat could be recommended as an easily accessible carnivorean model to study the natural history of the obese phenotype and its comorbidities.
Collapse
|
8
|
Sonne C, Wolkers H, Rigét FF, Jensen JEB, Teilmann J, Jenssen BM, Fuglei E, Ahlstrøm Ø, Dietz R, Muir DCG, Jørgensen EH. Mineral density and biomechanical properties of bone tissue from male Arctic foxes (Vulpes lagopus) exposed to organochlorine contaminants and emaciation. Comp Biochem Physiol C Toxicol Pharmacol 2009; 149:97-103. [PMID: 18761108 DOI: 10.1016/j.cbpc.2008.07.015] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/02/2008] [Revised: 07/20/2008] [Accepted: 07/22/2008] [Indexed: 01/22/2023]
Abstract
We investigated the impact from dietary OC (organochlorine) exposure and restricted feeding (emaciation) on bone mineral density (BMD; g hydroxy-apatite cm(-2)) in femoral, vertebrate, skull and baculum osteoid tissue from farmed Arctic blue foxes (Vulpes lagopus). For femur, also biomechanical properties during bending (displacement [mm], load [N], energy absorption [J] and stiffness [N/mm]) were measured. Sixteen foxes (EXP) were fed a wet food containing 7.7% OC-polluted minke whale (Balaenoptera acutorostrata) blubber in two periods of body fat deposition (Aug-Dec) and two periods of body fat mobilisation (Jan-July) in which the food contained less energy and only 2% blubber. SigmaOC food concentration in the food containing 7.7% whale blubber was 309 ng/g wet mass. This corresponded to a SigmaOC exposure of ca. 17 microg/kg body mass/d and a responding SigmaOC residue in subcutaneous adipose tissue of ca. 1700 ng/g live mass in the 8 EXP fat foxes euthanized after 16 months. A control group (CON) composed of 15 foxes were fed equal daily caloric amounts of clean pork (Sus scrofa) fat. After 16 months, 8 EXP and 7 CON foxes were euthanized (mean body mass=9.25 kg) while the remaining 8 EXP and 8 CON foxes were given restricted food rations for 6 months resulting in a body weight reduction (mean body mass=5.46 kg). The results showed that only BMD(skull) vs. BMD(vertebrae) were significantly correlated (R=0.68; p=0.03; n=10) probably due to a similar composition of trabecular and cortical osteoid tissue. No difference in any of the BMD measurements or femoral biomechanical properties was found between EXP and CON foxes although BMD baculum was 1.6-folds lower in the EXP group. However, lean summer foxes had significantly lower femoral biomechanical properties measured as displacement (mm), energy absorption (J) and time (s) biomechanical properties than fat winter foxes (all p<0.004). This indicates lower stiffness and softer bones from fasting which is in agreement with previous studies. Further, it should be kept in mind when studying bone tissues in Arctic mammals also in order to avoid confounding effects from body condition.
Collapse
Affiliation(s)
- Christian Sonne
- Department of Arctic Environment, National Environmental Research Institute, University of Aarhus, Roskilde, Denmark.
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
9
|
Cherry SG, Derocher AE, Stirling I, Richardson ES. Fasting physiology of polar bears in relation to environmental change and breeding behavior in the Beaufort Sea. Polar Biol 2008. [DOI: 10.1007/s00300-008-0530-0] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|