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Lu Z, Yuan C, An X, Chen Z, Guo T, Liu J. Chromosome-level genome assembly of Guide Black-Fur sheep (Ovis aries). Sci Data 2024; 11:711. [PMID: 38951548 PMCID: PMC11217409 DOI: 10.1038/s41597-024-03564-x] [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: 12/25/2023] [Accepted: 06/24/2024] [Indexed: 07/03/2024] Open
Abstract
Guide Black-Fur sheep (GD) is a breed of Tibetan sheep (Ovis aries) that lives in the Qinghai-Tibetan plateau region at an altitude of over 4,000 m. However, a lack of genomic information has made it difficult to understand the high-altitude adaptation of these sheep. We sequenced and assembled the GD reference genome using PacBio, Hi-C, and Illumina sequencing technologies. The final assembled genome size was 2.73 Gb, with a contig N50 of 20.30 Mb and a scaffold N50 of 107.63 Mb. The genome is predicted to contain 20,759 protein-coding genes, of which 98.42 have functional annotations. Repeat elements account for approximately 52.2% of the genomic landscape. The completeness of the GD genome assembly is highlighted by a BUSCO score of 93.1%. This high-quality genome assembly provides a critical resource for future molecular breeding and genetic improvement of Tibetan sheep.
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Affiliation(s)
- Zengkui Lu
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, 730050, China
- Sheep Breeding Engineering Technology Research Center of Chinese Academy of Agricultural Sciences, Lanzhou, 730050, China
| | - Chao Yuan
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, 730050, China
- Sheep Breeding Engineering Technology Research Center of Chinese Academy of Agricultural Sciences, Lanzhou, 730050, China
| | - Xuejiao An
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, 730050, China
- Sheep Breeding Engineering Technology Research Center of Chinese Academy of Agricultural Sciences, Lanzhou, 730050, China
| | | | - Tingting Guo
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, 730050, China
- Sheep Breeding Engineering Technology Research Center of Chinese Academy of Agricultural Sciences, Lanzhou, 730050, China
| | - Jianbin Liu
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, 730050, China.
- Sheep Breeding Engineering Technology Research Center of Chinese Academy of Agricultural Sciences, Lanzhou, 730050, China.
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2
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Atağ G, Kaptan D, Yüncü E, Başak Vural K, Mereu P, Pirastru M, Barbato M, Leoni GG, Güler MN, Er T, Eker E, Yazıcı TD, Kılıç MS, Altınışık NE, Çelik EA, Morell Miranda P, Dehasque M, Floridia V, Götherström A, Bilgin CC, Togan İ, Günther T, Özer F, Hadjisterkotis E, Somel M. Population Genomic History of the Endangered Anatolian and Cyprian Mouflons in Relation to Worldwide Wild, Feral, and Domestic Sheep Lineages. Genome Biol Evol 2024; 16:evae090. [PMID: 38670119 PMCID: PMC11109821 DOI: 10.1093/gbe/evae090] [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: 01/15/2024] [Revised: 04/09/2024] [Accepted: 04/22/2024] [Indexed: 04/28/2024] Open
Abstract
Once widespread in their homelands, the Anatolian mouflon (Ovis gmelini anatolica) and the Cyprian mouflon (Ovis gmelini ophion) were driven to near extinction during the 20th century and are currently listed as endangered populations by the International Union for Conservation of Nature. While the exact origins of these lineages remain unclear, they have been suggested to be close relatives of domestic sheep or remnants of proto-domestic sheep. Here, we study whole genome sequences of n = 5 Anatolian mouflons and n = 10 Cyprian mouflons in terms of population history and diversity, comparing them with eight other extant sheep lineages. We find reciprocal genetic affinity between Anatolian and Cyprian mouflons and domestic sheep, higher than all other studied wild sheep genomes, including the Iranian mouflon (O. gmelini). Studying diversity indices, we detect a considerable load of short runs of homozygosity blocks (<2 Mb) in both Anatolian and Cyprian mouflons, reflecting small effective population size (Ne). Meanwhile, Ne and mutation load estimates are lower in Cyprian compared with Anatolian mouflons, suggesting the purging of recessive deleterious variants in Cyprian sheep under a small long-term Ne, possibly attributable to founder effects, island isolation, introgression from domestic lineages, or differences in their bottleneck dynamics. Expanding our analyses to worldwide wild and feral Ovis genomes, we observe varying viability metrics among different lineages and a limited consistency between viability metrics and International Union for Conservation of Nature conservation status. Factors such as recent inbreeding, introgression, and unique population dynamics may have contributed to the observed disparities.
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Affiliation(s)
- Gözde Atağ
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
| | - Damla Kaptan
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
| | - Eren Yüncü
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
| | - Kıvılcım Başak Vural
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
| | - Paolo Mereu
- Department of Biochemical Sciences, University of Sassari, Sassari, Italy
| | - Monica Pirastru
- Department of Biochemical Sciences, University of Sassari, Sassari, Italy
| | - Mario Barbato
- Department of Veterinary Sciences, University of Messina, Messina, Italy
| | | | - Merve Nur Güler
- Department of Health Informatics, Graduate School of Informatics, Middle East Technical University, Ankara, Turkey
| | - Tuğçe Er
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
| | - Elifnaz Eker
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
| | - Tunca Deniz Yazıcı
- Graduate School for Evolution, Ecology and Systematics, Ludwig Maximillian University of Munich, Munich, Germany
| | - Muhammed Sıddık Kılıç
- Department of Health Informatics, Graduate School of Informatics, Middle East Technical University, Ankara, Turkey
| | | | - Ecem Ayşe Çelik
- Department of Settlement Archeology, Middle East Technical University, Ankara, Turkey
| | - Pedro Morell Miranda
- Human Evolution, Department of Organismal Biology, Uppsala University, Uppsala, Sweden
| | - Marianne Dehasque
- Human Evolution, Department of Organismal Biology, Uppsala University, Uppsala, Sweden
| | - Viviana Floridia
- Department of Veterinary Sciences, University of Messina, Messina, Italy
| | - Anders Götherström
- Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden
- Centre for Palaeogenetics, Stockholm University, Stockholm, Sweden
| | - Cemal Can Bilgin
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
| | - İnci Togan
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
| | - Torsten Günther
- Human Evolution, Department of Organismal Biology, Uppsala University, Uppsala, Sweden
| | - Füsun Özer
- Department of Anthropology, Hacettepe University, Ankara, Turkey
| | - Eleftherios Hadjisterkotis
- Agricultural Research Institute, Ministry of Agriculture, Rural Development and Environment, Nicosia, Cyprus
| | - Mehmet Somel
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
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3
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Chen ZH, Xu YX, Xie XL, Wang DF, Aguilar-Gómez D, Liu GJ, Li X, Esmailizadeh A, Rezaei V, Kantanen J, Ammosov I, Nosrati M, Periasamy K, Coltman DW, Lenstra JA, Nielsen R, Li MH. Whole-genome sequence analysis unveils different origins of European and Asiatic mouflon and domestication-related genes in sheep. Commun Biol 2021; 4:1307. [PMID: 34795381 PMCID: PMC8602413 DOI: 10.1038/s42003-021-02817-4] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 10/27/2021] [Indexed: 02/06/2023] Open
Abstract
The domestication and subsequent development of sheep are crucial events in the history of human civilization and the agricultural revolution. However, the impact of interspecific introgression on the genomic regions under domestication and subsequent selection remains unclear. Here, we analyze the whole genomes of domestic sheep and their wild relative species. We found introgression from wild sheep such as the snow sheep and its American relatives (bighorn and thinhorn sheep) into urial, Asiatic and European mouflons. We observed independent events of adaptive introgression from wild sheep into the Asiatic and European mouflons, as well as shared introgressed regions from both snow sheep and argali into Asiatic mouflon before or during the domestication process. We revealed European mouflons might arise through hybridization events between a now extinct sheep in Europe and feral domesticated sheep around 6000-5000 years BP. We also unveiled later introgressions from wild sheep to their sympatric domestic sheep after domestication. Several of the introgression events contain loci with candidate domestication genes (e.g., PAPPA2, NR6A1, SH3GL3, RFX3 and CAMK4), associated with morphological, immune, reproduction or production traits (wool/meat/milk). We also detected introgression events that introduced genes related to nervous response (NEURL1), neurogenesis (PRUNE2), hearing ability (USH2A), and placental viability (PAG11 and PAG3) into domestic sheep and their ancestral wild species from other wild species.
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Affiliation(s)
- Ze-Hui Chen
- grid.9227.e0000000119573309CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences (UCAS), Beijing, China ,grid.22935.3f0000 0004 0530 8290College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Ya-Xi Xu
- grid.22935.3f0000 0004 0530 8290College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Xing-Long Xie
- grid.9227.e0000000119573309CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences (UCAS), Beijing, China
| | - Dong-Feng Wang
- grid.9227.e0000000119573309CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences (UCAS), Beijing, China
| | - Diana Aguilar-Gómez
- grid.47840.3f0000 0001 2181 7878Center for Computational Biology, University of California at Berkeley, Berkeley, CA 94720 USA
| | | | - Xin Li
- grid.9227.e0000000119573309CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences (UCAS), Beijing, China
| | - Ali Esmailizadeh
- grid.412503.10000 0000 9826 9569Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, Kerman, Iran
| | - Vahideh Rezaei
- grid.412503.10000 0000 9826 9569Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, Kerman, Iran
| | - Juha Kantanen
- grid.22642.300000 0004 4668 6757Natural Resources Institute Finland (Luke), Jokioinen, Finland
| | - Innokentyi Ammosov
- grid.495192.2Laboratory of Reindeer Husbandry and Traditional Industries, Yakut Scientific Research Institute of Agriculture, The Sakha Republic (Yakutia), Yakutsk, Russia
| | - Maryam Nosrati
- grid.412462.70000 0000 8810 3346Department of Agriculture, Payame Noor University, Tehran, Iran
| | - Kathiravan Periasamy
- grid.420221.70000 0004 0403 8399Animal Production and Health Laboratory, Joint FAO/IAEA Division of Nuclear Techniques in Food and Agriculture, International Atomic Energy Agency, Vienna, Austria
| | - David W. Coltman
- grid.17089.37Department of Biological Sciences, University of Alberta, Edmonton, AB T6G2E9 Canada
| | - Johannes A. Lenstra
- grid.5477.10000000120346234Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
| | - Rasmus Nielsen
- Department of Integrative Biology, University of California at Berkeley, Berkeley, CA, 94720, USA. .,Department of Statistics, UC Berkeley, Berkeley, CA, 94707, USA. .,Globe Institute, University of Copenhagen, 1350, København K, Denmark.
| | - Meng-Hua Li
- College of Animal Science and Technology, China Agricultural University, Beijing, China.
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4
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Gelabert P, Sawyer S, Bergström A, Margaryan A, Collin TC, Meshveliani T, Belfer-Cohen A, Lordkipanidze D, Jakeli N, Matskevich Z, Bar-Oz G, Fernandes DM, Cheronet O, Özdoğan KT, Oberreiter V, Feeney RNM, Stahlschmidt MC, Skoglund P, Pinhasi R. Genome-scale sequencing and analysis of human, wolf, and bison DNA from 25,000-year-old sediment. Curr Biol 2021; 31:3564-3574.e9. [PMID: 34256019 PMCID: PMC8409484 DOI: 10.1016/j.cub.2021.06.023] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 04/23/2021] [Accepted: 06/09/2021] [Indexed: 01/07/2023]
Abstract
Cave sediments have been shown to preserve ancient DNA but so far have not yielded the genome-scale information of skeletal remains. We retrieved and analyzed human and mammalian nuclear and mitochondrial environmental "shotgun" genomes from a single 25,000-year-old Upper Paleolithic sediment sample from Satsurblia cave, western Georgia:first, a human environmental genome with substantial basal Eurasian ancestry, which was an ancestral component of the majority of post-Ice Age people in the Near East, North Africa, and parts of Europe; second, a wolf environmental genome that is basal to extant Eurasian wolves and dogs and represents a previously unknown, likely extinct, Caucasian lineage; and third, a European bison environmental genome that is basal to present-day populations, suggesting that population structure has been substantially reshaped since the Last Glacial Maximum. Our results provide new insights into the Late Pleistocene genetic histories of these three species and demonstrate that direct shotgun sequencing of sediment DNA, without target enrichment methods, can yield genome-wide data informative of ancestry and phylogenetic relationships.
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Affiliation(s)
- Pere Gelabert
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria.
| | - Susanna Sawyer
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
| | - Anders Bergström
- Ancient Genomics Laboratory, Francis Crick Institute, London, UK.
| | - Ashot Margaryan
- Center for Evolutionary Hologenomics, University of Copenhagen, Copenhagen, Denmark
| | - Thomas C Collin
- School of Medicine, University College Dublin, Dublin, Ireland
| | - Tengiz Meshveliani
- Georgian National Museum, Institute of Paleoanthropology and Paleobiology, Tbilisi, Georgia
| | - Anna Belfer-Cohen
- Institute of Archaeology, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - David Lordkipanidze
- Georgian National Museum, Institute of Paleoanthropology and Paleobiology, Tbilisi, Georgia
| | - Nino Jakeli
- Georgian National Museum, Institute of Paleoanthropology and Paleobiology, Tbilisi, Georgia
| | | | - Guy Bar-Oz
- Zinman Institute of Archaeology, University of Haifa, Haifa, Israel
| | - Daniel M Fernandes
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria; CIAS, Department of Life Sciences, University of Coimbra, Coimbra, Portugal
| | - Olivia Cheronet
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
| | - Kadir T Özdoğan
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
| | - Victoria Oberreiter
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
| | | | - Mareike C Stahlschmidt
- Department of Human Evolution, Max-Planck-Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Pontus Skoglund
- Ancient Genomics Laboratory, Francis Crick Institute, London, UK.
| | - Ron Pinhasi
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria.
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5
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Cao YH, Xu SS, Shen M, Chen ZH, Gao L, Lv FH, Xie XL, Wang XH, Yang H, Liu CB, Zhou P, Wan PC, Zhang YS, Yang JQ, Pi WH, Hehua EE, Berry DP, Barbato M, Esmailizadeh A, Nosrati M, Salehian-Dehkordi H, Dehghani-Qanatqestani M, Dotsev AV, Deniskova TE, Zinovieva NA, Brem G, Štěpánek O, Ciani E, Weimann C, Erhardt G, Mwacharo JM, Ahbara A, Han JL, Hanotte O, Miller JM, Sim Z, Coltman D, Kantanen J, Bruford MW, Lenstra JA, Kijas J, Li MH. Historical Introgression from Wild Relatives Enhanced Climatic Adaptation and Resistance to Pneumonia in Sheep. Mol Biol Evol 2021; 38:838-855. [PMID: 32941615 PMCID: PMC7947771 DOI: 10.1093/molbev/msaa236] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
How animals, particularly livestock, adapt to various climates and environments over short evolutionary time is of fundamental biological interest. Further, understanding the genetic mechanisms of adaptation in indigenous livestock populations is important for designing appropriate breeding programs to cope with the impacts of changing climate. Here, we conducted a comprehensive genomic analysis of diversity, interspecies introgression, and climate-mediated selective signatures in a global sample of sheep and their wild relatives. By examining 600K and 50K genome-wide single nucleotide polymorphism data from 3,447 samples representing 111 domestic sheep populations and 403 samples from all their seven wild relatives (argali, Asiatic mouflon, European mouflon, urial, snow sheep, bighorn, and thinhorn sheep), coupled with 88 whole-genome sequences, we detected clear signals of common introgression from wild relatives into sympatric domestic populations, thereby increasing their genomic diversities. The introgressions provided beneficial genetic variants in native populations, which were significantly associated with local climatic adaptation. We observed common introgression signals of alleles in olfactory-related genes (e.g., ADCY3 and TRPV1) and the PADI gene family including in particular PADI2, which is associated with antibacterial innate immunity. Further analyses of whole-genome sequences showed that the introgressed alleles in a specific region of PADI2 (chr2: 248,302,667-248,306,614) correlate with resistance to pneumonia. We conclude that wild introgression enhanced climatic adaptation and resistance to pneumonia in sheep. This has enabled them to adapt to varying climatic and environmental conditions after domestication.
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Affiliation(s)
- Yin-Hong Cao
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences (UCAS), Beijing, China
| | - Song-Song Xu
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences (UCAS), Beijing, China
| | - Min Shen
- Institute of Animal Husbandry and Veterinary Medicine, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, China
- Xinjiang Academy of Agricultural and Reclamation Sciences, State Key Laboratory of Sheep Genetic Improvement and Healthy Breeding, Shihezi, China
| | - Ze-Hui Chen
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences (UCAS), Beijing, China
| | - Lei Gao
- Institute of Animal Husbandry and Veterinary Medicine, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, China
- Xinjiang Academy of Agricultural and Reclamation Sciences, State Key Laboratory of Sheep Genetic Improvement and Healthy Breeding, Shihezi, China
| | - Feng-Hua Lv
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, China
- College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Xing-Long Xie
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences (UCAS), Beijing, China
| | - Xin-Hua Wang
- Institute of Animal Husbandry and Veterinary Medicine, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, China
- Xinjiang Academy of Agricultural and Reclamation Sciences, State Key Laboratory of Sheep Genetic Improvement and Healthy Breeding, Shihezi, China
| | - Hua Yang
- Institute of Animal Husbandry and Veterinary Medicine, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, China
- Xinjiang Academy of Agricultural and Reclamation Sciences, State Key Laboratory of Sheep Genetic Improvement and Healthy Breeding, Shihezi, China
| | - Chang-Bin Liu
- Institute of Animal Husbandry and Veterinary Medicine, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, China
- Xinjiang Academy of Agricultural and Reclamation Sciences, State Key Laboratory of Sheep Genetic Improvement and Healthy Breeding, Shihezi, China
| | - Ping Zhou
- Institute of Animal Husbandry and Veterinary Medicine, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, China
- Xinjiang Academy of Agricultural and Reclamation Sciences, State Key Laboratory of Sheep Genetic Improvement and Healthy Breeding, Shihezi, China
| | - Peng-Cheng Wan
- Institute of Animal Husbandry and Veterinary Medicine, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, China
- Xinjiang Academy of Agricultural and Reclamation Sciences, State Key Laboratory of Sheep Genetic Improvement and Healthy Breeding, Shihezi, China
| | - Yun-Sheng Zhang
- Institute of Animal Husbandry and Veterinary Medicine, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, China
- Xinjiang Academy of Agricultural and Reclamation Sciences, State Key Laboratory of Sheep Genetic Improvement and Healthy Breeding, Shihezi, China
| | - Jing-Quan Yang
- Institute of Animal Husbandry and Veterinary Medicine, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, China
- Xinjiang Academy of Agricultural and Reclamation Sciences, State Key Laboratory of Sheep Genetic Improvement and Healthy Breeding, Shihezi, China
| | - Wen-Hui Pi
- Institute of Animal Husbandry and Veterinary Medicine, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, China
- Xinjiang Academy of Agricultural and Reclamation Sciences, State Key Laboratory of Sheep Genetic Improvement and Healthy Breeding, Shihezi, China
| | - EEr Hehua
- Institute of Animal Science, Ningxia Academy of Agriculture and Forestry Sciences, Hui Autonomous Region, Yinchuan, Ningxia, China
| | - Donagh P Berry
- Animal and Grassland Research and Innovation Centre, Teagasc, Moorepark, Fermoy, Co. Cork, Ireland
| | - Mario Barbato
- Department of Animal Sciences, Food and Nutrition, Università Cattolica del Sacro Cuore, Piacenza, Italy
| | - Ali Esmailizadeh
- Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, Kerman, Iran
| | - Maryam Nosrati
- Department of Agriculture, Payame Noor University, Tehran, Iran
| | - Hosein Salehian-Dehkordi
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences (UCAS), Beijing, China
| | | | - Arsen V Dotsev
- L.K. Ernst Federal Science Center for Animal Husbandry, Moscow Region, Podolsk, Russian Federation
| | - Tatiana E Deniskova
- L.K. Ernst Federal Science Center for Animal Husbandry, Moscow Region, Podolsk, Russian Federation
| | - Natalia A Zinovieva
- L.K. Ernst Federal Science Center for Animal Husbandry, Moscow Region, Podolsk, Russian Federation
| | - Gottfried Brem
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine, Vienna, Austria
| | - Ondřej Štěpánek
- Department of Virology, State Veterinary Institute Jihlava, Jihlava, Czech Republic
| | - Elena Ciani
- Dipartimento di Bioscienze, Biotecnologie e Biofarmaceutica, Università degli Studi di Bari Aldo 24, Moro, Bari, Italy
| | - Christina Weimann
- Department of Animal Breeding and Genetics, Justus-Liebig-University Giessen, Giessen, Germany
| | - Georg Erhardt
- Department of Animal Breeding and Genetics, Justus-Liebig-University Giessen, Giessen, Germany
| | - Joram M Mwacharo
- Small Ruminant Genomics, International Center for Agricultural Research in the Dry Areas (ICARDA), Addis Ababa, Ethiopia
| | - Abulgasim Ahbara
- School of Life Sciences, University of Nottingham, University Park, Nottingham, United Kingdom
| | - 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
- Livestock Genetics Program, International Livestock Research Institute (ILRI), Nairobi, Kenya
| | - Olivier Hanotte
- School of Life Sciences, University of Nottingham, University Park, Nottingham, United Kingdom
- Livestock Genetics Program, International Livestock Research Institute (ILRI), Addis Abeba, Ethiopia
- Center for Tropical Livestock Genetics and Health (CTLGH), The Roslin Institute, University of Edinburgh, Easter Bush, Midlothian, United Kingdom
| | - Joshua M Miller
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
| | - Zijian Sim
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
- Fish and Wildlife Enforcement Branch Forensic Unit, Government of Alberta, Edmonton, AB, Canada
| | - David Coltman
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
| | - Juha Kantanen
- Production Systems, Natural Resources Institute Finland (Luke), Jokioinen, Finland
| | - Michael W Bruford
- School of Biosciences, Cardiff University, Cathays Park, Cardiff, United Kingdom
- Sustainable Places Research Institute, Cardiff University, Cardiff, United Kingdom
| | - Johannes A Lenstra
- Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - James Kijas
- Commonwealth Scientific and Industrial Research Organisation Agriculture and Food, Queensland Bioscience Precinct, St Lucia, Brisbane, QLD, Australia
| | - Meng-Hua Li
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, China
- College of Animal Science and Technology, China Agricultural University, Beijing, China
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6
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Su R, Qiao X, Gao Y, Li X, Jiang W, Chen W, Fan Y, Zheng B, Zhang Y, Liu Z, Wang R, Wang Z, Wang Z, Wan W, Dong Y, Li J. Draft Genome of the European Mouflon ( Ovis orientalis musimon). Front Genet 2020; 11:533611. [PMID: 33329689 PMCID: PMC7710762 DOI: 10.3389/fgene.2020.533611] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2020] [Accepted: 10/26/2020] [Indexed: 11/13/2022] Open
Abstract
Mouflon (Ovis orientalis) with its huge and beautiful horns is considered as one of the ancestors of domesticated sheep. The European mouflon (Ovis orientalis musimon) is in the Asiatic mouflon (O. orientalis) clade. In order to provide novel genome information for mouflon, moreover promote genetic analysis of genus Ovis both domestic and wild, we propose to sequence the mouflon genome. We assembled the highly heterozygous mouflon genome based on Illumina HiSeq platform using the next-generation sequencing technology. Finally, the draft genome we accessed approximately 2.69 Gb (42.15% GC), while N50 sizes of contig and scaffold are 110.1 kb and 10.4 Mb, respectively. The contiguity of this assembly is obviously better than earlier versions. Further analyses predicted 20,814 protein-coding genes in the mouflon genome and 12,390 shared gene families among bovine species. It is estimated that the divergence time between O. orientalis musimon and Ovis aries was 7.6 million years ago. The draft mouflon genome assembly will provide data support and theoretical basis for various investigations of the genus Ovis species in future.
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Affiliation(s)
- Rui Su
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Inner Mongolia Autonomous Region, Hohhot, China
- Key Laboratory of Mutton Sheep Genetics and Breeding, Ministry of Agriculture, Hohhot, China
- Engineering Research Center for Goat Genetics and Breeding, Inner Mongolia Autonomous Region, Hohhot, China
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Xian Qiao
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
| | - Yun Gao
- NOWBIO Technology Co. Ltd, Kunming, China
| | - Xiaokai Li
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
| | - Wei Jiang
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
| | - Wei Chen
- College of Biological Big Data, Yunnan Agricultural University, Kunming, China
- Yunnan Research Institute for Local Plateau Agriculture and Industry, Kunming, China
| | - Yixing Fan
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
| | - Bingwu Zheng
- Daqingshan Wild Animal Park, Hohhot Gardens Management Bureau, Hohhot, China
| | - Yanjun Zhang
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Inner Mongolia Autonomous Region, Hohhot, China
- Key Laboratory of Mutton Sheep Genetics and Breeding, Ministry of Agriculture, Hohhot, China
- Engineering Research Center for Goat Genetics and Breeding, Inner Mongolia Autonomous Region, Hohhot, China
| | - Zhihong Liu
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Inner Mongolia Autonomous Region, Hohhot, China
- Key Laboratory of Mutton Sheep Genetics and Breeding, Ministry of Agriculture, Hohhot, China
- Engineering Research Center for Goat Genetics and Breeding, Inner Mongolia Autonomous Region, Hohhot, China
| | - Ruijun Wang
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Inner Mongolia Autonomous Region, Hohhot, China
- Key Laboratory of Mutton Sheep Genetics and Breeding, Ministry of Agriculture, Hohhot, China
- Engineering Research Center for Goat Genetics and Breeding, Inner Mongolia Autonomous Region, Hohhot, China
| | - Zhiying Wang
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Inner Mongolia Autonomous Region, Hohhot, China
- Key Laboratory of Mutton Sheep Genetics and Breeding, Ministry of Agriculture, Hohhot, China
- Engineering Research Center for Goat Genetics and Breeding, Inner Mongolia Autonomous Region, Hohhot, China
| | - Zhixin Wang
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Inner Mongolia Autonomous Region, Hohhot, China
- Key Laboratory of Mutton Sheep Genetics and Breeding, Ministry of Agriculture, Hohhot, China
- Engineering Research Center for Goat Genetics and Breeding, Inner Mongolia Autonomous Region, Hohhot, China
| | - Wenting Wan
- Key Laboratory for Space Bioscience and Biotechnology, Center for Ecological and Environmental Sciences, Northwestern Polytechnical University, Xi’an, China
| | - Yang Dong
- College of Biological Big Data, Yunnan Agricultural University, Kunming, China
- Yunnan Research Institute for Local Plateau Agriculture and Industry, Kunming, China
| | - Jinquan Li
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Inner Mongolia Autonomous Region, Hohhot, China
- Key Laboratory of Mutton Sheep Genetics and Breeding, Ministry of Agriculture, Hohhot, China
- Engineering Research Center for Goat Genetics and Breeding, Inner Mongolia Autonomous Region, Hohhot, China
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7
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Goat Genomic Resources: The Search for Genes Associated with Its Economic Traits. Int J Genomics 2020; 2020:5940205. [PMID: 32904540 PMCID: PMC7456479 DOI: 10.1155/2020/5940205] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 06/30/2020] [Accepted: 07/24/2020] [Indexed: 11/25/2022] Open
Abstract
Goat plays a crucial role in human livelihoods, being a major source of meat, milk, fiber, and hides, particularly under adverse climatic conditions. The goat genomics related to the candidate gene approach is now being used to recognize molecular mechanisms that have different expressions of growth, reproductive, milk, wool, and disease resistance. The appropriate literature on this topic has been reviewed in this article. Several genetic characterization attempts of different goats have reported the existence of genotypic and morphological variations between different goat populations. As a result, different whole-genome sequences along with annotated gene sequences, gene function, and other genomic information of different goats are available in different databases. The main objective of this review is to search the genes associated with economic traits in goats. More than 271 candidate genes have been discovered in goats. Candidate genes influence the physiological pathway, metabolism, and expression of phenotypes. These genes have different functions on economically important traits. Some genes have pleiotropic effect for expression of phenotypic traits. Hence, recognizing candidate genes and their mutations that cause variations in gene expression and phenotype of an economic trait can help breeders look for genetic markers for specific economic traits. The availability of reference whole-genome assembly of goats, annotated genes, and transcriptomics makes comparative genomics a useful tool for systemic genetic upgradation. Identification and characterization of trait-associated sequence variations and gene will provide powerful means to give positive influences for future goat breeding program.
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8
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Upadhyay M, Hauser A, Kunz E, Krebs S, Blum H, Dotsev A, Okhlopkov I, Bagirov V, Brem G, Zinovieva N, Medugorac I. The First Draft Genome Assembly of Snow Sheep (Ovis nivicola). Genome Biol Evol 2020; 12:1330-1336. [PMID: 32592471 PMCID: PMC7487135 DOI: 10.1093/gbe/evaa124] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/08/2020] [Indexed: 12/30/2022] Open
Abstract
The snow sheep, Ovis nivicola, which is endemic to the mountain ranges of northeastern Siberia, are well adapted to the harsh cold climatic conditions of their habitat. In this study, using long reads of Nanopore sequencing technology, whole-genome sequencing, assembly, and gene annotation of a snow sheep were carried out. Additionally, RNA-seq reads from several tissues were also generated to supplement the gene prediction in snow sheep genome. The assembled genome was ∼2.62 Gb in length and was represented by 7,157 scaffolds with N50 of about 2 Mb. The repetitive sequences comprised of 41% of the total genome. BUSCO analysis revealed that the snow sheep assembly contained full-length or partial fragments of 97% of mammalian universal single-copy orthologs (n = 4,104), illustrating the completeness of the assembly. In addition, a total of 20,045 protein-coding sequences were identified using comprehensive gene prediction pipeline. Of which 19,240 (∼96%) sequences were annotated using protein databases. Moreover, homology-based searches and de novo identification detected 1,484 tRNAs; 243 rRNAs; 1,931 snRNAs; and 782 miRNAs in the snow sheep genome. To conclude, we generated the first de novo genome of the snow sheep using long reads; these data are expected to contribute significantly to our understanding related to evolution and adaptation within the Ovis genus.
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Affiliation(s)
- Maulik Upadhyay
- Population Genomics Group, Department of Veterinary Sciences, Ludwig Maximilian University of Munich, Munich, Germany
| | - Andreas Hauser
- Laboratory for Functional Genome Analysis, Gene Center, Ludwig Maximilian University of Munich, Munich, Germany
| | - Elisabeth Kunz
- Population Genomics Group, Department of Veterinary Sciences, Ludwig Maximilian University of Munich, Munich, Germany
| | - Stefan Krebs
- Laboratory for Functional Genome Analysis, Gene Center, Ludwig Maximilian University of Munich, Munich, Germany
| | - Helmut Blum
- Laboratory for Functional Genome Analysis, Gene Center, Ludwig Maximilian University of Munich, Munich, Germany
| | - Arsen Dotsev
- L.K. Ernst Federal Science Center for Animal Husbandry, Moscow Region, Podolsk, Russia
| | | | - Vugar Bagirov
- L.K. Ernst Federal Science Center for Animal Husbandry, Moscow Region, Podolsk, Russia
| | - Gottfried Brem
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine, Vienna, Austria
| | - Natalia Zinovieva
- L.K. Ernst Federal Science Center for Animal Husbandry, Moscow Region, Podolsk, Russia
| | - Ivica Medugorac
- Population Genomics Group, Department of Veterinary Sciences, Ludwig Maximilian University of Munich, Munich, Germany
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9
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Liu G, Zhao C, Xu D, Zhang H, Monakhov V, Shang S, Gao X, Sha W, Ma J, Zhang W, Tang X, Li B, Hua Y, Cao X, Liu Z, Zhang H. First Draft Genome of the Sable, Martes zibellina. Genome Biol Evol 2020; 12:59-65. [PMID: 32058545 PMCID: PMC7144822 DOI: 10.1093/gbe/evaa029] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/05/2020] [Indexed: 11/28/2022] Open
Abstract
Members of genus Martes provide early warning signals about forest ecosystem health and are designated as a Management Indicator Species. As one of the most widespread members in Martes, the sable (Martes zibellina) is a circumboreal small predator found throughout all taiga zoogeographical zones of Eurasia and shows distinct population differentiation and morphological variations. To support further studies on striking local adaptation and population evolution, we present the first sable genome, assembled de novo from an individual originating in the Great Khingan Mountains (China). The assembled genome is 2.42 Gb, consisting of 15,814 scaffolds with a scaffold N50 of 5.20 Mb. Searches for complete Mammalia BUSCO (Benchmarking Universal Single-Copy Ortholog) gene groups found that 95.15% of the curated single-copy orthologs were assembled as complete, suggesting a high level of completeness of the genome. We totally predicted 19,413 protein-coding genes, and 0.82 Gb of repeat sequences was annotated. We also detected 1,257 olfactory receptor genes and found more functional olfactory receptor genes in sable than in other Mustelidae species, which provide a possible genetic explanation for the acute sense of smell of the sable for searching the preys under deep snow. Phylogenetic analyses revealed that the ferret (Mustela putorius furo) and sea otter (Enhydra lutris) form a clade that is sister to the sable, which was dated ∼16.4 Ma. Overall, our study provided the first reference genome for research in a broad range of areas including local adaptations, population evolution, conservation, and management for sable.
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Affiliation(s)
- Guangshuai Liu
- College of Life Science, Qufu Normal University, China
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Chao Zhao
- College of Life Science, Qufu Normal University, China
| | - Dongming Xu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Huanxin Zhang
- College of Marine Life Science, Ocean University of China, Qingdao, Shandong, China
| | - Vladimir Monakhov
- Institute of Plant and Animal Ecology, Ural Branch, Russian Academy of Sciences, Yekaterinburg, Russia
| | - Shuai Shang
- College of Marine Life Science, Ocean University of China, Qingdao, Shandong, China
- College of Biological and Environmental Engineering, Binzhou University, China
| | - Xiaodong Gao
- College of Life Science, Qufu Normal University, China
| | - Weilai Sha
- College of Life Science, Qufu Normal University, China
| | - Jianzhang Ma
- College of Wildlife Resources, Northeast Forestry University, Harbin, China
| | - Wei Zhang
- College of Wildlife Resources, Northeast Forestry University, Harbin, China
| | - Xuexi Tang
- College of Marine Life Science, Ocean University of China, Qingdao, Shandong, China
| | - Bo Li
- College of Wildlife Resources, Northeast Forestry University, Harbin, China
| | - Yan Hua
- College of Wildlife Resources, Northeast Forestry University, Harbin, China
| | - Xiaofang Cao
- Novogene Bioinformatics Institute, Beijing, China
| | - Zhen Liu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Honghai Zhang
- College of Life Science, Qufu Normal University, China
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10
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Pascoal S, Risse JE, Zhang X, Blaxter M, Cezard T, Challis RJ, Gharbi K, Hunt J, Kumar S, Langan E, Liu X, Rayner JG, Ritchie MG, Snoek BL, Trivedi U, Bailey NW. Field cricket genome reveals the footprint of recent, abrupt adaptation in the wild. Evol Lett 2019; 4:19-33. [PMID: 32055408 PMCID: PMC7006468 DOI: 10.1002/evl3.148] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Revised: 10/21/2019] [Accepted: 11/13/2019] [Indexed: 12/31/2022] Open
Abstract
Evolutionary adaptation is generally thought to occur through incremental mutational steps, but large mutational leaps can occur during its early stages. These are challenging to study in nature due to the difficulty of observing new genetic variants as they arise and spread, but characterizing their genomic dynamics is important for understanding factors favoring rapid adaptation. Here, we report genomic consequences of recent, adaptive song loss in a Hawaiian population of field crickets (Teleogryllus oceanicus). A discrete genetic variant, flatwing, appeared and spread approximately 15 years ago. Flatwing erases sound‐producing veins on male wings. These silent flatwing males are protected from a lethal, eavesdropping parasitoid fly. We sequenced, assembled and annotated the cricket genome, produced a linkage map, and identified a flatwing quantitative trait locus covering a large region of the X chromosome. Gene expression profiling showed that flatwing is associated with extensive genome‐wide effects on embryonic gene expression. We found that flatwing male crickets express feminized chemical pheromones. This male feminizing effect, on a different sexual signaling modality, is genetically associated with the flatwing genotype. Our findings suggest that the early stages of evolutionary adaptation to extreme pressures can be accompanied by greater genomic and phenotypic disruption than previously appreciated, and highlight how abrupt adaptation might involve suites of traits that arise through pleiotropy or genomic hitchhiking.
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Affiliation(s)
- Sonia Pascoal
- Department of Zoology University of Cambridge Cambridge CB2 3EJ United Kingdom
| | - Judith E Risse
- Division of Bioinformatics, Department of Plant Sciences Wageningen University & Research Wageningen 6708 PB The Netherlands.,Animal Ecology Netherlands Institute of Ecology Wageningen 6700 AB The Netherlands
| | - Xiao Zhang
- School of Biology University of St Andrews St Andrews Fife KY16 9TH United Kingdom
| | - Mark Blaxter
- Edinburgh Genomics University of Edinburgh Edinburgh EH9 3JT United Kingdom.,Institute of Evolutionary Biology University of Edinburgh Edinburgh EH9 3JT United Kingdom
| | - Timothee Cezard
- Edinburgh Genomics University of Edinburgh Edinburgh EH9 3JT United Kingdom
| | - Richard J Challis
- Edinburgh Genomics University of Edinburgh Edinburgh EH9 3JT United Kingdom
| | - Karim Gharbi
- Edinburgh Genomics University of Edinburgh Edinburgh EH9 3JT United Kingdom.,Earlham Institute Norwich Research Park Norwich NR4 7UZ United Kingdom
| | - John Hunt
- School of Science and Health and the Hawkesbury Institute for the Environment Western Sydney University Penrith NSW 2751 Australia.,Centre for Ecology and Conservation University of Exeter Penryn TR10 9FE United Kingdom
| | - Sujai Kumar
- Edinburgh Genomics University of Edinburgh Edinburgh EH9 3JT United Kingdom
| | - Emma Langan
- Edinburgh Genomics University of Edinburgh Edinburgh EH9 3JT United Kingdom.,School of Environmental Sciences University of East Anglia Norwich NR4 7UZ United Kingdom
| | - Xuan Liu
- Centre for Genomic Research University of Liverpool Liverpool L69 7ZB United Kingdom
| | - Jack G Rayner
- School of Biology University of St Andrews St Andrews Fife KY16 9TH United Kingdom
| | - Michael G Ritchie
- School of Biology University of St Andrews St Andrews Fife KY16 9TH United Kingdom
| | - Basten L Snoek
- Theoretical Biology and Bioinformatics Utrecht University Utrecht 3584 CH The Netherlands.,Terrestrial Ecology Netherlands Institute of Ecology Wageningen 6700 AB The Netherlands
| | - Urmi Trivedi
- Edinburgh Genomics University of Edinburgh Edinburgh EH9 3JT United Kingdom
| | - Nathan W Bailey
- School of Biology University of St Andrews St Andrews Fife KY16 9TH United Kingdom
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11
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Abstract
Ruminants (Ruminantia) are among the most successful herbivorous mammals, exhibiting wide-ranging morphological and ecological characteristics (such as headgear and multichambered stomach) and including various key livestock species (e.g., cattle, buffalo, yak, sheep, and goat). Understanding their evolution is of great significance not only in scientific research but also in applications potential for human society. The rapid growth of genomic resources provides unprecedented opportunities to dissect the evolutionary histories and molecular mechanisms underlying the distinct characteristics of ruminants. Here we summarize our current understanding of the genetic, morphological, and ecological diversity of ruminants and provide prospects for future studies.
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Affiliation(s)
- Bao Wang
- 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
| | - Le Chen
- Center for Ecological and Environmental Sciences, Northwestern Polytechnical University, Xi'an Shaanxi 710072, China, E-mail:chen_
| | - Wen Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming Yunnan 650223, China, E-mail:.,Center for Ecological and Environmental Sciences, Northwestern Polytechnical University, Xi'an Shaanxi 710072, China.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming Yunnan 650223, China
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12
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Li R, Fu W, Su R, Tian X, Du D, Zhao Y, Zheng Z, Chen Q, Gao S, Cai Y, Wang X, Li J, Jiang Y. Towards the Complete Goat Pan-Genome by Recovering Missing Genomic Segments From the Reference Genome. Front Genet 2019; 10:1169. [PMID: 31803240 PMCID: PMC6874019 DOI: 10.3389/fgene.2019.01169] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Accepted: 10/23/2019] [Indexed: 01/08/2023] Open
Abstract
It is broadly expected that next generation sequencing will ultimately generate a complete genome as is the latest goat reference genome (ARS1), which is considered to be one of the most continuous assemblies in livestock. However, the rich diversity of worldwide goat breeds indicates that a genome from one individual would be insufficient to represent the whole genomic contents of goats. By comparing nine de novo assemblies from seven sibling species of domestic goat with ARS1 and using resequencing and transcriptome data from goats for verification, we identified a total of 38.3 Mb sequences that were absent in ARS1. The pan-sequences contain genic fractions with considerable expression. Using the pan-genome (ARS1 together with the pan-sequences) as a reference genome, variation calling efficacy can be appreciably improved. A total of 56,657 spurious SNPs per individual were repressed and 24,414 novel SNPs per individual on average were recovered as a result of better reads mapping quality. The transcriptomic mapping rate was also increased by ∼1.15%. Our study demonstrated that comparing de novo assemblies from closely related species is an efficient and reliable strategy for finding missing sequences from the reference genome and could be applicable to other species. Pan-genome can serve as an improved reference genome in animals for a better exploration of the underlying genomic variations and could increase the probability of finding genotype-phenotype associations assessed by a comprehensive variation database containing much more differences between individuals. We have constructed a goat pan-genome web interface for data visualization (http://animal.nwsuaf.edu.cn/panGoat).
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Affiliation(s)
- Ran Li
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Weiwei Fu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Rui Su
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
| | - Xiaomeng Tian
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Duo Du
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Yue Zhao
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Zhuqing Zheng
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Qiuming Chen
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Shan Gao
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Yudong Cai
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Xihong Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Jinquan Li
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
| | - Yu Jiang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
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13
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Chen L, Qiu Q, Jiang Y, Wang K, Lin Z, Li Z, Bibi F, Yang Y, Wang J, Nie W, Su W, Liu G, Li Q, Fu W, Pan X, Liu C, Yang J, Zhang C, Yin Y, Wang Y, Zhao Y, Zhang C, Wang Z, Qin Y, Liu W, Wang B, Ren Y, Zhang R, Zeng Y, da Fonseca RR, Wei B, Li R, Wan W, Zhao R, Zhu W, Wang Y, Duan S, Gao Y, Zhang YE, Chen C, Hvilsom C, Epps CW, Chemnick LG, Dong Y, Mirarab S, Siegismund HR, Ryder OA, Gilbert MTP, Lewin HA, Zhang G, Heller R, Wang W. Large-scale ruminant genome sequencing provides insights into their evolution and distinct traits. Science 2019; 364:364/6446/eaav6202. [DOI: 10.1126/science.aav6202] [Citation(s) in RCA: 163] [Impact Index Per Article: 32.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Accepted: 05/16/2019] [Indexed: 12/17/2022]
Abstract
The ruminants are one of the most successful mammalian lineages, exhibiting morphological and habitat diversity and containing several key livestock species. To better understand their evolution, we generated and analyzed de novo assembled genomes of 44 ruminant species, representing all six Ruminantia families. We used these genomes to create a time-calibrated phylogeny to resolve topological controversies, overcoming the challenges of incomplete lineage sorting. Population dynamic analyses show that population declines commenced between 100,000 and 50,000 years ago, which is concomitant with expansion in human populations. We also reveal genes and regulatory elements that possibly contribute to the evolution of the digestive system, cranial appendages, immune system, metabolism, body size, cursorial locomotion, and dentition of the ruminants.
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14
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Hu XJ, Yang J, Xie XL, Lv FH, Cao YH, Li WR, Liu MJ, Wang YT, Li JQ, Liu YG, Ren YL, Shen ZQ, Wang F, Hehua EE, Han JL, Li MH. The Genome Landscape of Tibetan Sheep Reveals Adaptive Introgression from Argali and the History of Early Human Settlements on the Qinghai-Tibetan Plateau. Mol Biol Evol 2019; 36:283-303. [PMID: 30445533 PMCID: PMC6367989 DOI: 10.1093/molbev/msy208] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Tibetan sheep are the most common and widespread domesticated animals on the Qinghai-Tibetan Plateau (QTP) and have played an essential role in the permanent human occupation of this high-altitude region. However, the precise timing, route, and process of sheep pastoralism in the QTP region remain poorly established, and little is known about the underlying genomic changes that occurred during the process. Here, we investigate the genomic variation in Tibetan sheep using whole-genome sequences, single nucleotide polymorphism arrays, mitochondrial DNA, and Y-chromosomal variants in 986 samples throughout their distribution range. We detect strong signatures of selection in genes involved in the hypoxia and ultraviolet signaling pathways (e.g., HIF-1 pathway and HBB and MITF genes) and in genes associated with morphological traits such as horn size and shape (e.g., RXFP2). We identify clear signals of argali (Ovis ammon) introgression into sympatric Tibetan sheep, covering 5.23-5.79% of their genomes. The introgressed genomic regions are enriched in genes related to oxygen transportation system, sensory perception, and morphological phenotypes, in particular the genes HBB and RXFP2 with strong signs of adaptive introgression. The spatial distribution of genomic diversity and demographic reconstruction of the history of Tibetan sheep show a stepwise pattern of colonization with their initial spread onto the QTP from its northeastern part ∼3,100 years ago, followed by further southwest expansion to the central QTP ∼1,300 years ago. Together with archeological evidence, the date and route reveal the history of human expansions on the QTP by the Tang-Bo Ancient Road during the late Holocene. Our findings contribute to a depth understanding of early pastoralism and the local adaptation of Tibetan sheep as well as the late-Holocene human occupation of the QTP.
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Affiliation(s)
- Xiao-Ju Hu
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, China.,College of Life Sciences, University of Chinese Academy of Sciences (UCAS), Beijing, China
| | - Ji Yang
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, China
| | - Xing-Long Xie
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, China.,College of Life Sciences, University of Chinese Academy of Sciences (UCAS), Beijing, China
| | - Feng-Hua Lv
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, China
| | - Yin-Hong Cao
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, China.,College of Life Sciences, University of Chinese Academy of Sciences (UCAS), Beijing, China
| | - Wen-Rong Li
- Animal Biotechnological Research Center, Xinjiang Academy of Animal Science, Urumqi, China
| | - Ming-Jun Liu
- Animal Biotechnological Research Center, Xinjiang Academy of Animal Science, Urumqi, China
| | - Yu-Tao Wang
- College of Life and Geographic Sciences, Kashi University, Kashi, 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
| | - Yan-Lin Ren
- Shandong Binzhou Academy of Animal Science and Veterinary Medicine, Binzhou, 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
| | - EEr Hehua
- Grass-Feeding Livestock Engineering Technology Research Center, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, 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, China.,Livestock Genetics Program, 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.,College of Life Sciences, University of Chinese Academy of Sciences (UCAS), Beijing, China
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15
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Comparison of Element Concentrations (Ba, Mn, Pb, Sr, Zn) in the Bones and Teeth of Wild Ruminants from the West Carpathians and the Tian-Shan Mountains as Indicators of Air Pollution. ATMOSPHERE 2019. [DOI: 10.3390/atmos10020064] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Through analyzing the concentrations of selected heavy metals (Ba, Mn, Pb, Sr, Zn) in the bones and teeth of wild living and ecologically equivalent ruminants from the Tian-Shan (Capra sibirica and Ovis ammon polii) and the West Carpathians (Rupicapra rupicapra tatrica) we compared the environmental pollution levels of these two mountain ranges. The samples were analyzed by X-ray fluorescence. Significantly higher contents of Zn and Mn as well as a higher frequency of measurable occurrences of Mn, Ba, and Pb in samples from the West Carpathians confirmed the results of our previous study, that the West Carpathians are relatively more polluted by heavy metals than the Tian-Shan Mountains. The most probably contamination sources are mining and smelting as well as traffic emissions, which can reach remote mountain ranges through long distance atmospheric transport.
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Yang Y, Wang Y, Zhao Y, Zhang X, Li R, Chen L, Zhang G, Jiang Y, Qiu Q, Wang W, Wei HJ, Wang K. Draft genome of the Marco Polo Sheep (Ovis ammon polii). Gigascience 2018; 6:1-7. [PMID: 29112761 PMCID: PMC5740985 DOI: 10.1093/gigascience/gix106] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Accepted: 10/30/2017] [Indexed: 11/14/2022] Open
Abstract
Background The Marco Polo Sheep (Ovis ammon polii), a subspecies of argali (Ovis ammon) that is distributed mainly in the Pamir Mountains, provides a mammalian model to study high altitude adaptation mechanisms. Due to over-hunting and subsistence poaching, as well as competition with livestock and habitat loss, O. ammon has been categorized as an endangered species on several lists. It can have fertile offspring with sheep. Hence, a high-quality reference genome of the Marco Polo Sheep will be very helpful in conservation genetics and even in exploiting useful genes in sheep breeding. Findings A total of 1022.43 Gb of raw reads resulting from whole-genome sequencing of a Marco Polo Sheep were generated using an Illumina HiSeq2000 platform. The final genome assembly (2.71 Gb) has an N50 contig size of 30.7 Kb and a scaffold N50 of 5.49 Mb. The repeat sequences identified account for 46.72% of the genome, and 20 336 protein-coding genes were predicted from the masked genome. Phylogenetic analysis indicated a close relationship between Marco Polo Sheep and the domesticated sheep, and the time of their divergence was approximately 2.36 million years ago. We identified 271 expanded gene families and 168 putative positively selected genes in the Marco Polo Sheep lineage. Conclusions We provide the first genome sequence and gene annotation for the Marco Polo Sheep. The availability of these resources will be of value in the future conservation of this endangered large mammal, for research into high altitude adaptation mechanisms, for reconstructing the evolutionary history of the Caprinae, and for the future conservation of the Marco Polo Sheep.
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Affiliation(s)
- Yongzhi Yang
- Center for Ecological and Environmental Sciences, Northwestern Polytechnical University, Xi'an 710072, China
| | - Yutao Wang
- College of Life and Geographic Sciences, Kashgar University, Kashgar 844000, China.,The Key Laboratory of Ecology and Biological Resources in Yark and Oasis at Colleges and Universities under the Department of Education of Xinjiang Uygur Autonomous Region, Kashgar University, Kashgar 844000, China
| | - Yue Zhao
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Xiuying Zhang
- College of Life and Geographic Sciences, Kashgar University, Kashgar 844000, China.,The Key Laboratory of Ecology and Biological Resources in Yark and Oasis at Colleges and Universities under the Department of Education of Xinjiang Uygur Autonomous Region, Kashgar University, Kashgar 844000, China
| | - Ran Li
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Lei Chen
- Center for Ecological and Environmental Sciences, Northwestern Polytechnical University, Xi'an 710072, China
| | - Guojie Zhang
- Centre for Social Evolution, Department of Biology, Universitetsparken 15, University of Copenhagen, Copenhagen 2100, Denmark
| | - Yu Jiang
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Qiang Qiu
- Center for Ecological and Environmental Sciences, Northwestern Polytechnical University, Xi'an 710072, China
| | - Wen Wang
- Center for Ecological and Environmental Sciences, Northwestern Polytechnical University, Xi'an 710072, China
| | - Hong-Jiang Wei
- Key Laboratory Animal Nutrition and Feed of Yunnan Province, Yunnan Agricultural University, Kunming 650201, China
| | - Kun Wang
- Center for Ecological and Environmental Sciences, Northwestern Polytechnical University, Xi'an 710072, China
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Genome Sequence of the Freshwater Yangtze Finless Porpoise. Genes (Basel) 2018; 9:genes9040213. [PMID: 29659530 PMCID: PMC5924555 DOI: 10.3390/genes9040213] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Revised: 04/06/2018] [Accepted: 04/11/2018] [Indexed: 11/17/2022] Open
Abstract
The Yangtze finless porpoise (Neophocaena asiaeorientalis ssp. asiaeorientalis) is a subspecies of the narrow-ridged finless porpoise (N. asiaeorientalis). In total, 714.28 gigabases (Gb) of raw reads were generated by whole-genome sequencing of the Yangtze finless porpoise, using an Illumina HiSeq 2000 platform. After filtering the low-quality and duplicated reads, we assembled a draft genome of 2.22 Gb, with contig N50 and scaffold N50 values of 46.69 kilobases (kb) and 1.71 megabases (Mb), respectively. We identified 887.63 Mb of repetitive sequences and predicted 18,479 protein-coding genes in the assembled genome. The phylogenetic tree showed a relationship between the Yangtze finless porpoise and the Yangtze River dolphin, which diverged approximately 20.84 million years ago. In comparisons with the genomes of 10 other mammals, we detected 44 species-specific gene families, 164 expanded gene families, and 313 positively selected genes in the Yangtze finless porpoise genome. The assembled genome sequence and underlying sequence data are available at the National Center for Biotechnology Information under BioProject accession number PRJNA433603.
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