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21 p, 11.5 MB |
Identification of constrained sequence elements across 239 primate genomes
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Kuderna, Lukas F. K. (Illumina. Co. Illumina Artificial Intelligence Laboratory (San Diego, Estats Units)) ;
Ulirsch, Jacob C. (Illumina. Co. Illumina Artificial Intelligence Laboratory (San Diego, Estats Units)) ;
Rashid, Sabrina (Illumina. Co. Illumina Artificial Intelligence Laboratory (San Diego, Estats Units)) ;
Ameen, Mohamed (Illumina. Co. Illumina Artificial Intelligence Laboratory (San Diego, Estats Units)) ;
Sundaram, Laksshman (Illumina. Co. Illumina Artificial Intelligence Laboratory (San Diego, Estats Units)) ;
Hickey, Glenn (University of California. Santa Cruz Genomics Institute) ;
Cox, Anthony J. (Illumina. Co. Illumina Artificial Intelligence Laboratory (San Diego, Estats Units)) ;
Gao, Hong (Illumina. Co. Illumina Artificial Intelligence Laboratory (San Diego, Estats Units)) ;
Kumar, Arvind (Illumina. Co. Illumina Artificial Intelligence Laboratory (San Diego, Estats Units)) ;
Aguet, Francois (Illumina. Co. Illumina Artificial Intelligence Laboratory (San Diego, Estats Units)) ;
Christmas, Matthew J. (Uppsala University. Department of Medical Biochemistry and Microbiology) ;
Clawson, Hiram (University of California. Santa Cruz Genomics Institute) ;
Haeussler, Maximilian (University of California. Santa Cruz Genomics Institu) ;
Janiak, Mareike C. (University of Salford. School of Science, Engineering and Environment) ;
Kuhlwilm, Martin (University of Vienna. Department of Evolutionary Anthropology) ;
Orkin, Joseph D. (Université de Montréal. Département d'Anthropologie) ;
Bataillon, Thomas (Aarhus University. Bioinformatics Research Centre) ;
Shivakumara Manu (Academy of Scientific and Innovative Research (Ghaziabad, Índia)) ;
Valenzuela, Alejandro (Institut de Biologia Evolutiva (Barcelona)) ;
Bergman, Juraj (Aarhus University. Bioinformatics Research Centre) ;
Rouselle, Marjolaine (Aarhus University. Bioinformatics Research Centre) ;
Silva, Felipe Ennes (Mamirauá Institute for Sustainable Development) ;
Agueda Calpena, Lidia (Centre Nacional d'Anàlisi Genòmica (CNAG)) ;
Blanc, Julie (Centre Nacional d'Anàlisi Genòmica (CNAG)) ;
Gut, Marta (Centre Nacional d'Anàlisi Genòmica (CNAG)) ;
de Vries, Dorien (University of Salford. School of Science, Engineering and Environment) ;
Goodhead, Ian (University of Salford. School of Science, Engineering and Environment) ;
Harris, R. Alan (Baylor College of Medicine. Department of Molecular and Human Genetics) ;
Raveendran, Muthuswamy (Baylor College of Medicine. Department of Molecular and Human Genetics) ;
Jensen, Axel (Uppsala University. Department of Ecology and Genetics) ;
Chuma, Idriss S. (Tanzania National Parks) ;
Horvath, Julie E. (University of North Carolina at Chapel Hill. Renaissance Computing Institute) ;
Hvilsom, Christina (Copenhagen Zoo) ;
Juan, David (Institut de Biologia Evolutiva (Barcelona)) ;
Frandsen, Peter (Copenhagen Zoo) ;
Schraiber, Joshua G. (Illumina. Co. Illumina Artificial Intelligence Laboratory (San Diego, Estats Units)) ;
de Melo, Fabiano R. (Universidade Federal de Viçosa) ;
Bertuol, Fabrício (Universidade Federal do Amazonas. Departamento de Genética) ;
Byrne, Hazel (University of Utah. Department of Anthropology) ;
Sampaio, Iracilda (Universidade Federal do Pará (Brasil)) ;
Pires Farias, Izeni (Universidade Federal do Amazonas. Departamento de Genética) ;
Valsecchi, João (Comunidad de Manejo de Fauna Silvestre en la Amazonía y en Latinoamérica-ComFauna) ;
Messias, Malu (Universidade Federal de Rondônia) ;
da Silva, Maria N. F. (Instituto Nacional de Pesquisas da Amazônia) ;
Trivedi, Mihir (Centre for Cellular and Molecular Biology (Hyderabad, Índia)) ;
Rossi, Rogerio (Universidade Federal do Mato Grosso. Instituto de Biociências) ;
Hrbek, Tomas (Trinity University. Department of Biology) ;
Andriaholinirina, Nicole (University of Mahajanga. Faculty of Science, Technology and Environment) ;
Rabarivola, Clément J. (University of Mahajanga. Faculty of Science, Technology and Environment) ;
Zaramody, Alphonse (University of Mahajanga. Faculty of Science, Technology and Environment) ;
Jolly, Clifford J. (New York University .Department of Anthropology) ;
Phillips-Conroy, Jane (Washington University School of Medicine in St Louis. Department of Neuroscience) ;
Wilkerson, Gregory (MD Anderson Cancer Center. Keeling Center for Comparative Medicine and Research) ;
Abbee, C. (MD Anderson Cancer Center. Keeling Center for Comparative Medicine and Research) ;
Simmons, Joe H. (MD Anderson Cancer Center. Keeling Center for Comparative Medicine and Research) ;
Fernandez-Duque, Eduardo (Yale University. Department of Anthropology) ;
Kanthaswamy, Sree (University of California. California National Primate Research Center) ;
Shiferaw, Fekadu (The Carter Center Ethiopia) ;
Wu, Dong-Dong (Chinese Academy of Sciences. Kunming Institute of Zoology. State Key Laboratory of Genetic Resources and Evolution) ;
Zhou, Long (Zhejiang University School of Medicine. Center for Evolutionary and Organismal Biology) ;
Shao, Yong (Chinese Academy of Sciences. Kunming Institute of Zoology. State Key Laboratory of Genetic Resources and Evolution) ;
Zhang, Guojie (Zhejiang University Medical Center) ;
Keyyu, Julius D. (Tanzania Wildlife Research Institute) ;
Knauf, Sascha (Justus Liebig University. Faculty of Veterinary Medicine) ;
Le, Minh D. (Vietnam National University. Department of Environmental Ecology) ;
Lizano, Esther (Institut Català de Paleontologia Miquel Crusafont) ;
Merker, Stefan epartment of Environmental Ecology (State Museum of Natural History Stuttgart. Department of Zoology) ;
Navarro, Arcadi, 1969- (Institut de Biologia Evolutiva (Barcelona)) ;
Nadler, Tilo (Cuc Phuong Commune) ;
Khor, Chiea Chuen (Genome Institute of Singapore) ;
Lee, Jessica (Mandai Nature) ;
Tan, Patrick (Duke-NUS Medical School) ;
Lim, Weng Khong (SingHealth Duke-NUS Genomic Medicine Centre) ;
Kitchener, Andrew C. (School of Geosciences) ;
Zinner, Dietmar (Leibniz ScienceCampus Primate Cognition) ;
Gut, Ivo (Centre Nacional d'Anàlisi Genòmica (CNAG)) ;
Melin, Amanda D. (University of Calgary. Alberta Children's Hospital Research Institute) ;
Guschanski, Katerina (University of Edinburgh. School of Biological Sciences) ;
Schierup, Mikkel Heide (Aarhus University. Bioinformatics Research Centre) ;
Beck, Robin (University of Salford. School of Science, Engineering and Environment) ;
Karakikes, Ioannis (Stanford University. Department of Cardiothoracic Surgery) ;
Wang, Kevin C. (Veterans Affairs Palo Alto Healthcare System) ;
Umapathy, Govindhaswamy (Centre for Cellular and Molecular Biology (Hyderabad, Índia)) ;
Roos, Christian (Leibniz Institute for Primate Research. German Primate Center) ;
Boubli, Jean (University of Salford. School of Science, Engineering and Environment) ;
Siepel, Adam (Simons Center for Quantitative Biology. Cold Spring Harbor Laboratory) ;
Kundaje, Anshul (Stanford University. Department of Genetics) ;
Paten, Benedict (University of California. Santa Cruz Genomics Institute) ;
Lindblad-Toh, Kerstin (Uppsala University. Department of Medical Biochemistry and Microbiology) ;
Rogers, Jeffrey (Baylor College of Medicine. Department of Molecular and Human Genetics) ;
Marques-Bonet, Tomas 1975- (Institut Català de Paleontologia Miquel Crusafont) ;
Farh, Kyle Kai-How (Illumina. Co. Illumina Artificial Intelligence Laboratory (San Diego, Estats Units))
Noncoding DNA is central to our understanding of human gene regulation and complex diseases and measuring the evolutionary sequence constraint can establish the functional relevance of putative regulatory elements in the human genome. [...]
2023 -  10.1038/s41586-023-06798-8
Nature, Published online nov. 2023
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2.
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14 p, 1.4 MB |
Comparative genomics reveals the hybrid origin of a macaque group
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Zhang, Baolin (Chinese Academy of Sciences) ;
Chen, Wu (Guangzhou Zoo and Guangzhou Wildlife Research Center) ;
Wang, Zefu (Sichuan University) ;
Pang, Wey (Chinese Academy of Sciences) ;
Luo, Meng-Ting (Chinese Academy of Sciences) ;
Wang, Sheng (Chinese Academy of Sciences) ;
Shao, Yong (Chinese Academy of Sciences) ;
He, Wen-Qiang (Chinese Academy of Sciences) ;
Deng, Yuan (University of Copenhagen) ;
Zhou, Long (Zhejiang University School of Medicine) ;
Chen, Jiawei (BGI-Shenzhen) ;
Yang, Min-Min (Chinese Academy of Sciences) ;
Wu, Yajiang (Guangzhou Zoo and Guangzhou Wildlife Research Center) ;
Wang, Lu (Northwest University) ;
Fernández-Bellon, Hugo (Zoo de Barcelona) ;
Molloy, Sandra (Dublin Zoo) ;
Meunier, Hélène (Université de Strasbourg) ;
Wanert, Fanélie (Université de Strasbourg) ;
Kuderna, Lukas (Illumina Inc) ;
Marques-Bonet, Tomas 1975- (Institut Català de Paleontologia Miquel Crusafont) ;
Roos, Christian (German Primate Center) ;
Qi, Xiao-Guang (Northwest University) ;
Li, Ming (Chinese Academy of Sciences) ;
Liu, Zhijin (Capital Normal University) ;
Schierup, Mikkel Heide (Aarhus University) ;
Cooper, David N. (Cardiff University) ;
Liu, Jianquan (Sichuan University) ;
Zheng, Yong-Tang (Chinese Academy of Sciences) ;
Zhang, Guojie (Zhejiang University Medical Cente) ;
Wu, Dong-Dong (Chinese Academy of Sciences)
Although species can arise through hybridization, compelling evidence for hybrid speciation has been reported only rarely in animals. Here, we present phylogenomic analyses on genomes from 12 macaque species and show that the fascicularis group originated from an ancient hybridization between the sinica and silenus groups ~3. [...]
2023 - 10.1126/sciadv.add3580
Science advances, Vol. 9, Issue 22 (June 2023) , art. eadd3580
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3.
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3 p, 958.0 KB |
Initiation of the Primate Genome Project
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Wu, Dong-Dong (Chinese Academy of Sciences. Center for Excellence in Animal Evolution and Genetics) ;
Qi, Xiao-Guang (Northwest University. College of Life Sciences) ;
Yu, Li (Yunnan University) ;
Li, Ming (Chinese Academy of Sciences. Institute of Zoology) ;
Liu, Zhi-Jin (Chinese Academy of Sciences. Institute of Zoology) ;
Yoder, Anne (Duke University. Department of Biology) ;
Roos, Christian (Leibniz Institute for Primate Research. German Primate Center) ;
Hayakawa, Takashi (Japan Monkey Centre) ;
Rogers, Jeffrey (Baylor College of Medicine. Human Genome Sequencing Center) ;
Marques-Bonet, Tomas 1975- (Institut Català de Paleontologia Miquel Crusafont) ;
Su, Bing (Chinese Academy of Sciences. Center for Excellence in Animal Evolution and Genetics) ;
Yao, Yong-Gang (University of Chinese Academy of Sciences. Kunming College of Life Science) ;
Zhang, Ya-Ping (University of Chinese Academy of Sciences. Kunming College of Life Science) ;
Zhang, Guojie (China National GeneBank)
2022 - 10.24272/j.issn.2095-8137.2022.001
Zoological Research, Vol. 43, Issue 2 (March 2022) , p. 147-149
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4.
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15 p, 4.1 MB |
Donkey genomes provide new insights into domestication and selection for coat color
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Wang, Changfa (Liaocheng University. Liaocheng Research Institute of Donkey High-Efficiency Breeding and Ecological Feeding) ;
Li, Haijing (National Engineering Research Center for Gelatin-based Traditional Chinese Medicine) ;
Guo, Yu (BGI-Shenzhen) ;
Huang, Jinming (Shandong Academy of Agricultural Sciences. Dairy Cattle Research Center) ;
Sun, Yan (Shandong Academy of Agricultural Sciences. Dairy Cattle Research Center) ;
Min, Jiumeng (BGI-Shenzhen) ;
Wang, Jinpeng (Shandong Academy of Agricultural Sciences. Dairy Cattle Research Center) ;
Fang, Xiaodong (BGI-Shenzhen) ;
Zhao, Zicheng (City University of Hong Kong. Department of Computer Science) ;
Wang, Shuai (City University of Hong Kong. Department of Computer Science) ;
Zhang, Yanlin (City University of Hong Kong. Department of Computer Science) ;
Liu, Qingfeng (BGI-Shenzhen) ;
Jiang, Qiang (Shandong Academy of Agricultural Sciences. Dairy Cattle Research Center) ;
Wang, Xiuge (Shandong Academy of Agricultural Sciences. Dairy Cattle Research Center) ;
Guo, Yijun (BGI-Shenzhen) ;
Yang, Chunhong (Shandong Academy of Agricultural Sciences. Dairy Cattle Research Center) ;
Wang, Yinchao (National Engineering Research Center for Gelatin-based Traditional Chinese Medicine) ;
Tian, Fang (National Engineering Research Center for Gelatin-based Traditional Chinese Medicine) ;
Zhuang, Guilong (Shandong Academy of Agricultural Sciences. Dairy Cattle Research Center) ;
Fan, Yanna (Shandong Academy of Agricultural Sciences. Dairy Cattle Research Center) ;
Gao, Qican (Shandong Academy of Agricultural Sciences. Dairy Cattle Research Center) ;
Li, Yuhua (Liaocheng University. Liaocheng Research Institute of Donkey High-Efficiency Breeding and Ecological Feeding) ;
Ju, Zhihua (Shandong Academy of Agricultural Sciences. Dairy Cattle Research Center) ;
Li, Jianbin (Shandong Academy of Agricultural Sciences. Dairy Cattle Research Center) ;
Li, Rongling (Shandong Academy of Agricultural Sciences. Dairy Cattle Research Center) ;
Hou, Minghai (Shandong Academy of Agricultural Sciences. Dairy Cattle Research Center) ;
Yang, Guiwen (Shandong Normal University. College of Life Science) ;
Liu, Guiqin (Liaocheng University. Liaocheng Research Institute of Donkey High-Efficiency Breeding and Ecological Feeding) ;
Liu, Wenqiang (Liaocheng University Liaocheng Research Institute of Donkey High-Efficiency Breeding and Ecological Feeding.) ;
Guo, Jiao (BGI-Shenzhen) ;
Pan, Shanshan (BGI-Shenzhen) ;
Fan, Guangyi (BGI-Shenzhen) ;
Zhang, Wei (Shandong Academy of Agricultural Sciences. Dairy Cattle Research Center) ;
Zhang, Ruitao (Liaocheng University. Liaocheng Research Institute of Donkey High-Efficiency Breeding and Ecological Feeding) ;
Yu, Jie (National Engineering Research Center for Gelatin-based Traditional Chinese Medicine) ;
Zhang, Xinhao (National Engineering Research Center for Gelatin-based Traditional Chinese Medicine) ;
Yin, Qi (BGI-Shenzhen) ;
Ji, Chuanliang (National Engineering Research Center for Gelatin-based Traditional Chinese Medicine) ;
Jin, Yuanchun (BGI-Shenzhen) ;
Yue, Guidong (BGI-Shenzhen) ;
Liu, Mei (Nanjing Normal University. Jiangsu Key Laboratory for Molecular and Medical Biotechnology) ;
Xu, Jiake (The University of Western Australia . School of Biomedical Sciences) ;
Liu, Shimin (Universitat Autònoma de Barcelona. Departament de Ciència Animal i dels Aliments) ;
Jordana i Vidal, Jordi (Universitat Autònoma de Barcelona. Departament de Ciència Animal i dels Aliments) ;
Noce, Antonia (Centre de Recerca en Agrigenòmica) ;
Amills i Eras, Marcel (Centre de Recerca en Agrigenòmica) ;
Wu, Dong-Dong (Chinese Academy of Sciences. Center for Excellence in Animal Evolution and Genetics) ;
Li, Shuaicheng (City University of Hong Kong. Department of Computer Science) ;
Zhou, Xiangshan (East China University of Science and Technology. State Key Laboratory of Bioreactor Engineering) ;
Zhong, Jifeng (Jiangsu Academy of Agricultural Sciences. Institute of Animal Science)
Current knowledge about the evolutionary history of donkeys is still incomplete due to the lack of archeological and whole-genome diversity data. To fill this gap, we have de novo assembled a chromosome-level reference genome of one male Dezhou donkey and analyzed the genomes of 126 domestic donkeys and seven wild asses. [...]
2020 - 10.1038/s41467-020-19813-7
Nature communications, Vol. 11 (December 2020) , art. 6014
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