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Wang C, Wu DD, Yuan YH, Yao MC, Han JL, Wu YJ, Shan F, Li WP, Zhai JQ, Huang M, Peng SM, Cai QH, Yu JY, Liu QX, Liu ZY, Li LX, Teng MS, Huang W, Zhou JY, Zhang C, Chen W, Tu XL. Population genomic analysis provides evidence of the past success and future potential of South China tiger captive conservation. BMC Biol 2023; 21:64. [PMID: 37069598 PMCID: PMC10111772 DOI: 10.1186/s12915-023-01552-y] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 02/21/2023] [Indexed: 04/19/2023] Open
Abstract
BACKGROUND Among six extant tiger subspecies, the South China tiger (Panthera tigris amoyensis) once was widely distributed but is now the rarest one and extinct in the wild. All living South China tigers are descendants of only two male and four female wild-caught tigers and they survive solely in zoos after 60 years of effective conservation efforts. Inbreeding depression and hybridization with other tiger subspecies were believed to have occurred within the small, captive South China tiger population. It is therefore urgently needed to examine the genomic landscape of existing genetic variation among the South China tigers. RESULTS In this study, we assembled a high-quality chromosome-level genome using long-read sequences and re-sequenced 29 high-depth genomes of the South China tigers. By combining and comparing our data with the other 40 genomes of six tiger subspecies, we identified two significantly differentiated genomic lineages among the South China tigers, which harbored some rare genetic variants introgressed from other tiger subspecies and thus maintained a moderate genetic diversity. We noticed that the South China tiger had higher FROH values for longer runs of homozygosity (ROH > 1 Mb), an indication of recent inbreeding/founder events. We also observed that the South China tiger had the least frequent homozygous genotypes of both high- and moderate-impact deleterious mutations, and lower mutation loads than both Amur and Sumatran tigers. Altogether, our analyses indicated an effective genetic purging of deleterious mutations in homozygous states from the South China tiger, following its population contraction with a controlled increase in inbreeding based on its pedigree records. CONCLUSIONS The identification of two unique founder/genomic lineages coupled with active genetic purging of deleterious mutations in homozygous states and the genomic resources generated in our study pave the way for a genomics-informed conservation, following the real-time monitoring and rational exchange of reproductive South China tigers among zoos.
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Affiliation(s)
- Chen Wang
- Guangzhou Zoo & Guangzhou Wildlife Research Center, Guangzhou, 510070, China
| | - Dong-Dong Wu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650201, China
- Kunming Natural History Museum of Zoology, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, Yunnan, China
- Kunming College of Life Science, University of the Chinese Academy of Sciences, Kunming, 650204, China
| | | | - Meng-Cheng Yao
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650201, China
- Kunming Natural History Museum of Zoology, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, Yunnan, China
- Kunming College of Life Science, University of the Chinese Academy of Sciences, Kunming, 650204, China
| | - Jian-Lin Han
- CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100193, China
- International Livestock Research Institute (ILRI), Nairobi, 00100, Kenya
| | - Ya-Jiang Wu
- Guangzhou Zoo & Guangzhou Wildlife Research Center, Guangzhou, 510070, China
| | - Fen Shan
- Guangzhou Zoo & Guangzhou Wildlife Research Center, Guangzhou, 510070, China
| | - Wan-Ping Li
- Guangzhou Zoo & Guangzhou Wildlife Research Center, Guangzhou, 510070, China
| | - Jun-Qiong Zhai
- Guangzhou Zoo & Guangzhou Wildlife Research Center, Guangzhou, 510070, China
| | - Mian Huang
- Guangzhou Zoo & Guangzhou Wildlife Research Center, Guangzhou, 510070, China
| | - Shi-Ming Peng
- Guangzhou Zoo & Guangzhou Wildlife Research Center, Guangzhou, 510070, China
| | - Qin-Hui Cai
- Guangzhou Zoo & Guangzhou Wildlife Research Center, Guangzhou, 510070, China
| | | | | | | | - Lin-Xiang Li
- Suzhou Shangfangshan Forest Zoo, Suzhou, 215009, China
| | | | - Wei Huang
- Nanchang Zoo, Nanchang, 330025, China
| | - Jun-Ying Zhou
- Chinese Association of Zoological Gardens, Beijing, 100037, China
| | - Chi Zhang
- Qinghai Province Key Laboratory of Crop Molecular Breeding, Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, 810008, Qinghai, China
| | - Wu Chen
- Guangzhou Zoo & Guangzhou Wildlife Research Center, Guangzhou, 510070, China.
| | - Xiao-Long Tu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650201, China.
- Kunming Natural History Museum of Zoology, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, Yunnan, China.
- Kunming College of Life Science, University of the Chinese Academy of Sciences, Kunming, 650204, China.
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2
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Zeng L, Liu HQ, Tu XL, Ji CM, Gou X, Esmailizadeh A, Wang S, Wang MS, Wang MC, Li XL, Charati H, Adeola AC, Moshood Adedokun RA, Oladipo O, Olaogun SC, Sanke OJ, Godwin F M, Cecily Ommeh S, Agwanda B, Kasiiti Lichoti J, Han JL, Zheng HK, Wang CF, Zhang YP, Frantz LAF, Wu DD. Genomes reveal selective sweeps in kiang and donkey for high-altitude adaptation. Zool Res 2021; 42:450-460. [PMID: 34156172 PMCID: PMC8317180 DOI: 10.24272/j.issn.2095-8137.2021.095] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Over the last several hundred years, donkeys have adapted to high-altitude conditions on the Tibetan Plateau. Interestingly, the kiang, a closely related equid species, also inhabits this region. Previous reports have demonstrated the importance of specific genes and adaptive introgression in divergent lineages for adaptation to hypoxic conditions on the Tibetan Plateau. Here, we assessed whether donkeys and kiangs adapted to the Tibetan Plateau via the same or different biological pathways and whether adaptive introgression has occurred. We assembled a de novo genome from a kiang individual and analyzed the genomes of five kiangs and 93 donkeys (including 24 from the Tibetan Plateau). Our analyses suggested the existence of a strong hard selective sweep at the EPAS1 locus in kiangs. In Tibetan donkeys, however, another gene, i.e., EGLN1, was likely involved in their adaptation to high altitude. In addition, admixture analysis found no evidence for interspecific gene flow between kiangs and Tibetan donkeys. Our findings indicate that despite the short evolutionary time scale since the arrival of donkeys on the Tibetan Plateau, as well as the existence of a closely related species already adapted to hypoxia, Tibetan donkeys did not acquire adaptation via admixture but instead evolved adaptations via a different biological pathway.
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Affiliation(s)
- Lin Zeng
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650204, China
| | - He-Qun Liu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China.,Department of Genetics, Albert Einstein College of Medicine, Bronx, New York, NY 10461, USA
| | - Xiao-Long Tu
- Annoroad Gene Tech. (Beijing) Co., Ltd., Beijing 100176, China
| | - Chang-Mian Ji
- Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan 571101, China.,Biomarker Technologies Corporation, Beijing 101300, China
| | - Xiao Gou
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming, Yunnan 650201, China
| | - Ali Esmailizadeh
- Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, Kerman, PB 76169-133, Iran
| | - Sheng Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
| | - Ming-Shan Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
| | | | - Xiao-Long Li
- Biomarker Technologies Corporation, Beijing 101300, China
| | - Hadi Charati
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650204, China
| | - Adeniyi C Adeola
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Germplasm Bank of Wild Species, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China.,Sino-Africa Joint Research Center, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
| | | | - Olatunbosun Oladipo
- Federal College of Animal Health and Production Technology, Moor-Plantation, Ibadan, Nigeria
| | | | - Oscar J Sanke
- Taraba State Ministry of Agriculture and Natural Resources, Jalingo 660221, Nigeria
| | | | - Sheila Cecily Ommeh
- Institute For Biotechnology Research Jomo Kenyatta University of Agriculture and Technology, Nairobi 62000-00200, Kenya.,Department of Zoology, National Museums of Kenya, Nairobi 40658-00100, Kenya
| | - Bernard Agwanda
- Department of Zoology, National Museums of Kenya, Nairobi 40658-00100, Kenya
| | - Jacqueline Kasiiti Lichoti
- State Department of Livestock, Ministry of Agriculture, Livestock, Fisheries and Irrigation, Nairobi, Kenya
| | - Jian-Lin Han
- CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China
| | - Hong-Kun Zheng
- Biomarker Technologies Corporation, Beijing 101300, China
| | - Chang-Fa Wang
- Equus Laboratory, Dairy Cattle Research Center, Shandong Academy of Agricultural Sciences, Ji'nan, Shandong 250131, China.,Liaocheng Research Institute of Donkey High-Efficiency Breeding and Ecological Feeding, Liaocheng University, Liaocheng, Shandong 252059, China. E-mail:
| | - Ya-Ping Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, Yunnan 650223, China. E-mail:
| | - Laurent A F Frantz
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK. E-mail:
| | - Dong-Dong Wu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, Yunnan 650223, China.,Institute of Three-River-Source National Park, Chinese Academy of Sciences, Qinghai 810008, China. E-mail:
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3
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Zeng L, Tu XL, Dai H, Han FM, Lu BS, Wang MS, Nanaei HA, Tajabadipour A, Mansouri M, Li XL, Ji LL, Irwin DM, Zhou H, Liu M, Zheng HK, Esmailizadeh A, Wu DD. Whole genomes and transcriptomes reveal adaptation and domestication of pistachio. Genome Biol 2019; 20:79. [PMID: 30999938 PMCID: PMC6474056 DOI: 10.1186/s13059-019-1686-3] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2018] [Accepted: 04/01/2019] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Pistachio (Pistacia vera), one of the most important commercial nut crops worldwide, is highly adaptable to abiotic stresses and is tolerant to drought and salt stresses. RESULTS Here, we provide a draft de novo genome of pistachio as well as large-scale genome resequencing. Comparative genomic analyses reveal stress adaptation of pistachio is likely attributable to the expanded cytochrome P450 and chitinase gene families. Particularly, a comparative transcriptomic analysis shows that the jasmonic acid (JA) biosynthetic pathway plays an important role in salt tolerance in pistachio. Moreover, we resequence 93 cultivars and 14 wild P. vera genomes and 35 closely related wild Pistacia genomes, to provide insights into population structure, genetic diversity, and domestication. We find that frequent genetic admixture occurred among the different wild Pistacia species. Comparative population genomic analyses reveal that pistachio was domesticated about 8000 years ago and suggest that key genes for domestication related to tree and seed size experienced artificial selection. CONCLUSIONS Our study provides insight into genetic underpinning of local adaptation and domestication of pistachio. The Pistacia genome sequences should facilitate future studies to understand the genetic basis of agronomically and environmentally related traits of desert crops.
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Affiliation(s)
- Lin Zeng
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, 650204, China
| | - Xiao-Long Tu
- Allwegene Technologies Inc., Beijing, 102209, China
| | - He Dai
- Biomarker Technologies Corporation, Beijing, China
| | | | - Bing-She Lu
- College of Landscape Architecture and Tourism, Agricultural University of Hebei, Baoding, 071000, China
| | - Ming-Shan Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
| | - Hojjat Asadollahpour Nanaei
- Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, PB 76169-133, Kerman, Iran
| | - Ali Tajabadipour
- Pistachio Research Center, Horticultural Sciences Research Institute, Agricultural Research, Education and Extension Organization (AREEO), Rafsanjan, Iran
| | - Mehdi Mansouri
- Department of Agricultural Biotechnology, Faculty of Agriculture, Shahid Bahonar University of Kerman, Kerman, Iran
| | - Xiao-Long Li
- Biomarker Technologies Corporation, Beijing, China
| | - Li-Li Ji
- Allwegene Technologies Inc., Beijing, 102209, China
| | - David M Irwin
- Department of Laboratory Medicine and Pathobiology, Banting and Best Diabetes Centre, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Hong Zhou
- Chinese Academy of Forestry Sciences, Beijing, China
| | - Min Liu
- Biomarker Technologies Corporation, Beijing, China
| | | | - Ali Esmailizadeh
- Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, PB 76169-133, Kerman, Iran.
| | - Dong-Dong Wu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, 650223, China.
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4
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Xu X, Zhang P, Shuai P, Chen RJ, Yan XL, Zhang YH, Wang M, Litvinov YA, Xu HS, Bao T, Chen XC, Chen H, Fu CY, Kubono S, Lam YH, Liu DW, Mao RS, Ma XW, Sun MZ, Tu XL, Xing YM, Yang JC, Yuan YJ, Zeng Q, Zhou X, Zhou XH, Zhan WL, Litvinov S, Blaum K, Audi G, Uesaka T, Yamaguchi Y, Yamaguchi T, Ozawa A, Sun BH, Sun Y, Dai AC, Xu FR. Identification of the Lowest T=2, J^{π}=0^{+} Isobaric Analog State in ^{52}Co and Its Impact on the Understanding of β-Decay Properties of ^{52}Ni. Phys Rev Lett 2016; 117:182503. [PMID: 27835000 DOI: 10.1103/physrevlett.117.182503] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Indexed: 06/06/2023]
Abstract
Masses of ^{52g,52m}Co were measured for the first time with an accuracy of ∼10 keV, an unprecedented precision reached for short-lived nuclei in the isochronous mass spectrometry. Combining our results with the previous β-γ measurements of ^{52}Ni, the T=2, J^{π}=0^{+} isobaric analog state (IAS) in ^{52}Co was newly assigned, questioning the conventional identification of IASs from the β-delayed proton emissions. Using our energy of the IAS in ^{52}Co, the masses of the T=2 multiplet fit well into the isobaric multiplet mass equation. We find that the IAS in ^{52}Co decays predominantly via γ transitions while the proton emission is negligibly small. According to our large-scale shell model calculations, this phenomenon has been interpreted to be due to very low isospin mixing in the IAS.
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Affiliation(s)
- X Xu
- Key Laboratory of High Precision Nuclear Spectroscopy and Center for Nuclear Matter Science, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou 730000, People's Republic of China
| | - P Zhang
- Key Laboratory of High Precision Nuclear Spectroscopy and Center for Nuclear Matter Science, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou 730000, People's Republic of China
- Graduate University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
| | - P Shuai
- Key Laboratory of High Precision Nuclear Spectroscopy and Center for Nuclear Matter Science, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou 730000, People's Republic of China
| | - R J Chen
- Key Laboratory of High Precision Nuclear Spectroscopy and Center for Nuclear Matter Science, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou 730000, People's Republic of China
| | - X L Yan
- Key Laboratory of High Precision Nuclear Spectroscopy and Center for Nuclear Matter Science, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou 730000, People's Republic of China
| | - Y H Zhang
- Key Laboratory of High Precision Nuclear Spectroscopy and Center for Nuclear Matter Science, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou 730000, People's Republic of China
| | - M Wang
- Key Laboratory of High Precision Nuclear Spectroscopy and Center for Nuclear Matter Science, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou 730000, People's Republic of China
| | - Yu A Litvinov
- Key Laboratory of High Precision Nuclear Spectroscopy and Center for Nuclear Matter Science, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou 730000, People's Republic of China
- GSI Helmholtzzentrum für Schwerionenforschung, Planckstraße 1, 64291 Darmstadt, Germany
| | - H S Xu
- Key Laboratory of High Precision Nuclear Spectroscopy and Center for Nuclear Matter Science, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou 730000, People's Republic of China
| | - T Bao
- Key Laboratory of High Precision Nuclear Spectroscopy and Center for Nuclear Matter Science, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou 730000, People's Republic of China
| | - X C Chen
- Key Laboratory of High Precision Nuclear Spectroscopy and Center for Nuclear Matter Science, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou 730000, People's Republic of China
- GSI Helmholtzzentrum für Schwerionenforschung, Planckstraße 1, 64291 Darmstadt, Germany
| | - H Chen
- Key Laboratory of High Precision Nuclear Spectroscopy and Center for Nuclear Matter Science, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou 730000, People's Republic of China
- Graduate University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
| | - C Y Fu
- Key Laboratory of High Precision Nuclear Spectroscopy and Center for Nuclear Matter Science, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou 730000, People's Republic of China
- Graduate University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
| | - S Kubono
- Key Laboratory of High Precision Nuclear Spectroscopy and Center for Nuclear Matter Science, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou 730000, People's Republic of China
| | - Y H Lam
- Key Laboratory of High Precision Nuclear Spectroscopy and Center for Nuclear Matter Science, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou 730000, People's Republic of China
| | - D W Liu
- Key Laboratory of High Precision Nuclear Spectroscopy and Center for Nuclear Matter Science, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou 730000, People's Republic of China
- Graduate University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
| | - R S Mao
- Key Laboratory of High Precision Nuclear Spectroscopy and Center for Nuclear Matter Science, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou 730000, People's Republic of China
| | - X W Ma
- Key Laboratory of High Precision Nuclear Spectroscopy and Center for Nuclear Matter Science, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou 730000, People's Republic of China
| | - M Z Sun
- Key Laboratory of High Precision Nuclear Spectroscopy and Center for Nuclear Matter Science, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou 730000, People's Republic of China
- Graduate University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
| | - X L Tu
- Key Laboratory of High Precision Nuclear Spectroscopy and Center for Nuclear Matter Science, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou 730000, People's Republic of China
- Max-Planck-Institut für Kernphysik, Saupfercheckweg 1, 69117 Heidelberg, Germany
| | - Y M Xing
- Key Laboratory of High Precision Nuclear Spectroscopy and Center for Nuclear Matter Science, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou 730000, People's Republic of China
- Graduate University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
| | - J C Yang
- Key Laboratory of High Precision Nuclear Spectroscopy and Center for Nuclear Matter Science, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou 730000, People's Republic of China
| | - Y J Yuan
- Key Laboratory of High Precision Nuclear Spectroscopy and Center for Nuclear Matter Science, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou 730000, People's Republic of China
| | - Q Zeng
- Key Laboratory of High Precision Nuclear Spectroscopy and Center for Nuclear Matter Science, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou 730000, People's Republic of China
- Research Center for Hadron Physics, National Laboratory of Heavy Ion Accelerator Facility in Lanzhou and University of Science and Technology of China, Hefei 230026, People's Republic of China
| | - X Zhou
- Key Laboratory of High Precision Nuclear Spectroscopy and Center for Nuclear Matter Science, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou 730000, People's Republic of China
- Graduate University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
| | - X H Zhou
- Key Laboratory of High Precision Nuclear Spectroscopy and Center for Nuclear Matter Science, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou 730000, People's Republic of China
| | - W L Zhan
- Key Laboratory of High Precision Nuclear Spectroscopy and Center for Nuclear Matter Science, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou 730000, People's Republic of China
| | - S Litvinov
- GSI Helmholtzzentrum für Schwerionenforschung, Planckstraße 1, 64291 Darmstadt, Germany
| | - K Blaum
- Max-Planck-Institut für Kernphysik, Saupfercheckweg 1, 69117 Heidelberg, Germany
| | - G Audi
- CSNSM, Univ Paris-Sud, CNRS/IN2P3, Université Paris-Saclay, 91405 Orsay, France
| | - T Uesaka
- RIKEN Nishina Center, RIKEN, Saitama 351-0198, Japan
| | - Y Yamaguchi
- RIKEN Nishina Center, RIKEN, Saitama 351-0198, Japan
| | - T Yamaguchi
- Department of Physics, Saitama University, Saitama 338-8570, Japan
| | - A Ozawa
- Insititute of Physics, University of Tsukuba, Ibaraki 305-8571, Japan
| | - B H Sun
- School of Physics and Nuclear Energy Engineering, Beihang University, Beijing 100191, People's Republic of China
| | - Y Sun
- Department of Physics and Astronomy, Shanghai Jiao Tong University, Shanghai 200240, People's Republic of China
| | - A C Dai
- State Key Laboratory of Nuclear Physics and Technology, School of Physics, Peking University, Beijing 100871, People's Republic of China
| | - F R Xu
- State Key Laboratory of Nuclear Physics and Technology, School of Physics, Peking University, Beijing 100871, People's Republic of China
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5
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Yang J, Li WR, Lv FH, He SG, Tian SL, Peng WF, Sun YW, Zhao YX, Tu XL, Zhang M, Xie XL, Wang YT, Li JQ, Liu YG, Shen ZQ, Wang F, Liu GJ, Lu HF, Kantanen J, Han JL, Li MH, Liu MJ. Whole-Genome Sequencing of Native Sheep Provides Insights into Rapid Adaptations to Extreme Environments. Mol Biol Evol 2016; 33:2576-92. [PMID: 27401233 PMCID: PMC5026255 DOI: 10.1093/molbev/msw129] [Citation(s) in RCA: 182] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Global climate change has a significant effect on extreme environments and a profound influence on species survival. However, little is known of the genome-wide pattern of livestock adaptations to extreme environments over a short time frame following domestication. Sheep (Ovis aries) have become well adapted to a diverse range of agroecological zones, including certain extreme environments (e.g., plateaus and deserts), during their post-domestication (approximately 8–9 kya) migration and differentiation. Here, we generated whole-genome sequences from 77 native sheep, with an average effective sequencing depth of ∼5× for 75 samples and ∼42× for 2 samples. Comparative genomic analyses among sheep in contrasting environments, that is, plateau (>4,000 m above sea level) versus lowland (<100 m), high-altitude region (>1500 m) versus low-altitude region (<1300 m), desert (<10 mm average annual precipitation) versus highly humid region (>600 mm), and arid zone (<400 mm) versus humid zone (>400 mm), detected a novel set of candidate genes as well as pathways and GO categories that are putatively associated with hypoxia responses at high altitudes and water reabsorption in arid environments. In addition, candidate genes and GO terms functionally related to energy metabolism and body size variations were identified. This study offers novel insights into rapid genomic adaptations to extreme environments in sheep and other animals, and provides a valuable resource for future research on livestock breeding in response to climate change.
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Affiliation(s)
- Ji Yang
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, China
| | - Wen-Rong Li
- Animal Biotechnology Research Institute, Xinjiang Academy of Animal Science, Urumqi, China
| | - Feng-Hua Lv
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, China
| | - San-Gang He
- Animal Biotechnology Research Institute, Xinjiang Academy of Animal Science, Urumqi, China
| | - Shi-Lin Tian
- Novogene Bioinformatics Institute, Beijing, China
| | - Wei-Feng Peng
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, China University of Chinese Academy of Sciences (UCAS), Beijing, China
| | - Ya-Wei Sun
- Animal Biotechnology Research Institute, Xinjiang Academy of Animal Science, Urumqi, China College of Animal Science and Technology, Shihezi University, Shihezi, China
| | - Yong-Xin Zhao
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, China University of Chinese Academy of Sciences (UCAS), Beijing, China
| | - Xiao-Long Tu
- Novogene Bioinformatics Institute, Beijing, China
| | - Min Zhang
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, China School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Xing-Long Xie
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, China University of Chinese Academy of Sciences (UCAS), Beijing, China
| | - Yu-Tao Wang
- College of Biological and Geographic Sciences, Kashgar University, Kashgar, China
| | - Jin-Quan Li
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
| | - Yong-Gang Liu
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming, China
| | - Zhi-Qiang Shen
- Shandong Binzhou Academy of Animal Science and Veterinary Medicine, Binzhou, China
| | - Feng Wang
- Institute of Sheep and Goat Science, Nanjing Agricultural University, Nanjing, China
| | | | - Hong-Feng Lu
- Novogene Bioinformatics Institute, Beijing, China
| | - Juha Kantanen
- Green Technology, Natural Resources Institute Finland (Luke), Jokioinen, Finland Department of Environmental and Biological Sciences, University of Eastern Finland, Kuopio, Finland
| | - Jian-Lin Han
- CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China International Livestock Research Institute (ILRI), Nairobi, Kenya
| | - Meng-Hua Li
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, China
| | - Ming-Jun Liu
- Animal Biotechnology Research Institute, Xinjiang Academy of Animal Science, Urumqi, China
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Wang MS, Li Y, Peng MS, Zhong L, Wang ZJ, Li QY, Tu XL, Dong Y, Zhu CL, Wang L, Yang MM, Wu SF, Miao YW, Liu JP, Irwin DM, Wang W, Wu DD, Zhang YP. Genomic Analyses Reveal Potential Independent Adaptation to High Altitude in Tibetan Chickens. Mol Biol Evol 2015; 32:1880-9. [DOI: 10.1093/molbev/msv071] [Citation(s) in RCA: 125] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
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7
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Wang JW, Huang M, Xiangli B, Tu XL. [Study on the characteristics of radiance calibration using nonuniformity extended source]. Guang Pu Xue Yu Guang Pu Fen Xi 2013; 33:2002-2005. [PMID: 24059219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Integrating sphere and diffuser are always used as extended source, and they have different effects on radiance calibration of imaging spectrometer with parameter difference. In the present paper, a mathematical model based on the theory of radiative transfer and calibration principle is founded to calculate the irradiance and calibration coefficients on CCD, taking relatively poor uniformity lights-board calibration system for example. The effects of the nonuniformity on the calibration was analyzed, which makes up the correlation of calibration coefficient matrix under ideal and unideal situation. The results show that the nonuniformity makes the viewing angle and the position of the point of intersection of the optical axis and the diffuse reflection plate have relatively large effects on calibration, while the observing distance's effect is small; under different viewing angles, a deviation value can be found that makes the calibration results closest to the desired results. So, the calibration error can be reduced by choosing appropriate deviation value.
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Affiliation(s)
- Jian-Wei Wang
- Academy of Opto-Electronics, Chinese Academy of Sciences, Beijing 100094, China.
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Tu XL, Huang M, Lü QB, Wang JW, Pei LL. [Interference hyperspectral data compression based on spectral classification and local DPCM]. Guang Pu Xue Yu Guang Pu Fen Xi 2013; 33:1401-1405. [PMID: 23905361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
In order to get a high compression ratio, according to the spatial dimension correlation and the interference spectral dimension correlation of interference hyperspectral image data, the present article provides a new compression algorithm that combines spectral classification with local DPCM. This algorithm requires spectral classification for the whole interference hyperspectral image to get a classification number matrix corresponding to the two-dimensional space and a spectral classification library corresponding to the interference spectra first, then local DPCM is performed for the spectral classification library to get a further compression. As the first step of the compression, the spectral classification is very important to the compression effect. This article analyzes the differences of compression effect with different standard and different accuracy of classification, the relative Euclidean distance standard is better than the angle standard and the interference RQE standard. Finally, this article chooses an appropriate standard of compression and achieves the combined compression algorithm with programming. Compared to JPEG2000, the compression effect of combined compression algorithm is better.
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Affiliation(s)
- Xiao-Long Tu
- Academy of Opto-Electronics, Chinese Academy of Sciences, Beijing 100094, China.
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9
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Zhang YH, Xu HS, Litvinov YA, Tu XL, Yan XL, Typel S, Blaum K, Wang M, Zhou XH, Sun Y, Brown BA, Yuan YJ, Xia JW, Yang JC, Audi G, Chen XC, Jia GB, Hu ZG, Ma XW, Mao RS, Mei B, Shuai P, Sun ZY, Wang ST, Xiao GQ, Xu X, Yamaguchi T, Yamaguchi Y, Zang YD, Zhao HW, Zhao TC, Zhang W, Zhan WL. Mass measurements of the neutron-deficient 41Ti, 45Cr, 49Fe, and 53Ni nuclides: first test of the isobaric multiplet mass equation in f p-shell nuclei. Phys Rev Lett 2012; 109:102501. [PMID: 23005283 DOI: 10.1103/physrevlett.109.102501] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2012] [Indexed: 06/01/2023]
Abstract
Isochronous mass spectrometry has been applied to neutron-deficient 58Ni projectile fragments at the HIRFL-CSR facility in Lanzhou, China. Masses of a series of short-lived T(z)=-3/2 nuclides including 41Ti, 45Cr, 49Fe, and 53Ni have been measured with a precision of 20-40 keV. The new data enable us to test for the first time the isobaric multiplet mass equation (IMME) in fp-shell nuclei. We observe that the IMME is inconsistent with the generally accepted quadratic form for the A=53, T=3/2 quartet. We perform full space shell model calculations and compare them with the new experimental results.
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Affiliation(s)
- Y H Zhang
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou 730000, People's Republic of China
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Tu XL, Xu HS, Wang M, Zhang YH, Litvinov YA, Sun Y, Schatz H, Zhou XH, Yuan YJ, Xia JW, Audi G, Blaum K, Du CM, Geng P, Hu ZG, Huang WX, Jin SL, Liu LX, Liu Y, Ma X, Mao RS, Mei B, Shuai P, Sun ZY, Suzuki H, Tang SW, Wang JS, Wang ST, Xiao GQ, Xu X, Yamaguchi T, Yamaguchi Y, Yan XL, Yang JC, Ye RP, Zang YD, Zhao HW, Zhao TC, Zhang XY, Zhan WL. Direct mass measurements of short-lived A=2Z-1 nuclides (63)Ge, (65)As, (67)Se, and (71)Kr and their impact on nucleosynthesis in the rp process. Phys Rev Lett 2011; 106:112501. [PMID: 21469858 DOI: 10.1103/physrevlett.106.112501] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2011] [Indexed: 05/30/2023]
Abstract
Mass excesses of short-lived A=2Z-1 nuclei (63)Ge, (65)As, (67)Se, and (71)Kr have been directly measured to be -46,921(37), -46,937(85), -46,580(67), and -46,320(141) keV, respectively. The deduced proton separation energy of -90(85) keV for (65)As shows that this nucleus is only slightly proton unbound. X-ray burst model calculations with the new mass excess of (65)As suggest that the majority of the reaction flow passes through (64)Ge via proton capture, indicating that (64)Ge is not a significant rp-process waiting point.
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Affiliation(s)
- X L Tu
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou 730000, People's Republic of China
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Tu XL. [Nursing care of direct microsurgery of intracranial aneurysm]. Zhonghua Hu Li Za Zhi 1995; 30:584-6. [PMID: 8715894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
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