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Re-evaluating data quality of dog mitochondrial,Y chromosomal,and autosomal SNPs genotyped by SNP array

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Zoological Research 2016年第6期37卷 356-360页

作者： Newton O.OTECKO min-sheng peng He-Chuan YANG Ya-Ping ZHANG Guo-Dong WANG State Key Laboratory of Genetic Resources and Evolution Yunnan Key Laboratory of Molecular Biology of Domestic AnimalsGermplasm Bank of Wild SpeciesKunming Institute of ZoologyChinese Academy of Sciences Kunming College of Life Science University of Chinese Academy of Sciences State Key Laboratory for Conservation and Utilization of Bio-Resources Yunnan University

Quality deficiencies in single nucleotide polymorphism （SNP） analyses have important implications. We used missingness rates to investigate the quality of a recently published dataset containing 424 mitochonddal, 211 Y chromosomal, and 160 432 autosomal SNPs generated by a semicustom Illumina SNP array from 5 392 dogs and 14 grey wolves. Overall, the individual missingness rate for mitochondrial SNPs was -43.8%, with 980 （18.1%）individuals completely missing mitochondrial SNP genotyping （missingness rate=l）. In males, the genotype missingness rate was -28.8% for Y chromosomal SNPs, with 374 males recording rates above 0.96. These 374 males also exhibited completely failed mitochondrial SNPs genotyping, indicative of a batch effect. Individual missingness rates for autosomal markers were greater than zero, but less than 0.5. Neither mitochondrial nor Y chromosomal SNPs achieved complete genotyping （locus missingness rate=0）, whereas 5.9% of autosomal SNPs had a locus missingness rate=l. The high missingness rates and possible batch effect show that caution and rigorous measures are vital when genotyping and analyzing SNP array data for domestic animals. Further improvements of these arrays will be helpful to future studies.

关键词： SNP array Dog Mitochondrial Ychromosomal Autosomal

A Matrilineal Genetic Legacy from the Last Glacial Maximum Confers Susceptibility to Schizophrenia in Han Chinese

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Journal of Genetics and Genomics 2014年第7期41卷 397-407页

作者： Wen Zhang Jinsong Tang A-Mei Zhang min-sheng peng Hai-Bing Xie Liwen Tan Lin Xu Ya-Ping Zhang Xiaogang Chen Yong-Gang Yao Key Laboratory of Animal Models and Human Disease Mechanisms Kunming Institute of ZoologyChinese Academy of Sciences The Institute of Mental Health the Second Xiangya HospitalCentral South University State Key Laboratory of Genetic Resources and Evolution Kunming Institute of ZoologyChinese Academy of Sciences National Technology Institute of Psychiatry Key Laboratory of Psychiatry and Mental Health of Hunan ProvinceCentral South University

Mitochondrial dysfunction has been widely reported in schizophrenia patients. To dissect the matrilineal structure of Han Chinese with or without schizophrenia and to decipher the maternal influence and evolutionary history of schizophrenia, a total of 1212 schizophrenia patients and 1005 matched healthy controls, all of Han Chinese origin, were recruited in Hunan Province, China. We classified haplogroup for each individual based on mitochondrial DNA （mtDNA） sequence variations and compared the haplogroup distribution pattern between cases and controls. Haplogroup B5a presented a higher frequency in cases than in controls （P = 0.02, OR = 1.67, 95% CI = [1.09, 2.56]）, and this result could be confirmed by permutation analysis. Age estimation of haplogroup B5a in cases revealed a much younger age than that of controls, which was coincident with the Northern Hemisphere deglaciation at the end of the Last Glacial Maximum. Analysis of complete mtDNA in five patients belonging to haplogroup B5a showed that this background effect might be caused by haplogroup- defining variants m.8584G〉A and m.10398A〉G. Our results showed that matrilineal risk factor for schizophrenia had an ancient origin and might acquire a predisposing effect on schizophrenia due to the environment change and/or orchestration with other nuclear genetic factors appeared recently in human evolutionary history.

关键词： mtDNA haplogroup Schizophrenia Association Last Glacial Maximum Evolutionary medicine

A paratlei mechanism underlying frizzle in domestic chickens

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Journal of Molecular Cell Biology 2018年第6期10卷 589-591页

作者： Xing Guo Yan-Qing Li ming-Shan Wang Zhi-Bin Wang Quan Zhang Yong Shao Run-Shen Jiang sheng Wang Chen-Dong Ma Robert W.Murphy Guang-Qin Wang Jing Dong Li Zhang Dong-Dong Wu Bing-Wang Du min-sheng peng Ya-Ping Zhang State Key Laboratory of Genetic Resources and Evolution and Yunnan Laboratory of Molecular Biology of Domestic Animals Kunmin8 Institute of ZoologyChinese Academy of SciencesKunming 650223 China College of Agricultural Guangdong Ocean UniversityZhanjiang 524088China College of Animal Science and Technology Anhui Agricultural UniversityHefei 230036 China Laboratory of Animal Genetics Breeding and ReproductionMinistry of Agriculture of ChinaNational Engineering Laboratory for Animal BreedingCollege of Animal Science and TechnologyChina Agricultural UniversityBeijing 100193 China Centre for Biodiversity and Conservation Biology Royal Ontario MuseumTorontoM5S2C6Canada 6Jinsheng Animal Husbandry Technology Co. Ltd Zhanjiang 524025China Kunming College of Life Science University of Chinese Academy of SciencesKunming 650204China Center for Excellence in Animal Evolution and Genetics Chinese Academy of Sciences Kunming 650223China State Key Laboratory for Conservation and Utilization of Bio-resources Yunnan University Kunming 650091China

Dear Editor,The feather,a highly keratinized tissue with variations in the shape,distribution,pigmentation,and structure,is an attractive topic in developmental and evolutionary biology (Boer et al.,2017).

关键词： evolutionary biology domestic chickens

Comparative population genomics reveals genetic basis underlying body size of domestic chickens

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Journal of Molecular Cell Biology 2016年第6期8卷 542-552页

作者： ming-Shan Wang Yong-Xia Huo Yan Li Newton OOtecko Ling-Yan Su Hai-Bo Xu Shi-Fang Wu min-sheng peng He-Qun Liu Lin Zeng David M.Irwin Yong-Gang Yao Dong-Dong Wu Ya-Ping Zhang State Key Laboratory of Genetic Resources and Evolution Yunnan Laboratory of Molecular Biology of Domestic AnimalsKunming Institute of ZoologyChinese Academy of SciencesKunming 650223China Kunming College of Life Science University of Chinese Academy of SciencesKunming 650204China College of Life Science Anhui UniversityHefei 230601China Laboratory for Conservation and Utilization of Bio-Resource Yunnan UniversityKunming 650091China Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences&Yunnan Province Kunming Institute of ZoologyKunming 650223China Department of Laboratory Medicine and Pathobiology University of TorontoTorontoOntario M5S 1A8Canada Banting and Best Diabetes Centre University of TorontoTorontoOntario M5G 2C4Canada

Body size is the most important economic trait for animal production and *** hundreds of loci have been reported to be associated with growth trait and body weight in *** loci are mapped to large genomic regions due to the low density and limited number of genetic markers in previous ***,we employed comparative population genomics to identify genetic basis underlying the small body size of Yuanbao chicken(a famous ornamental chicken)based on 89 whole *** most significant signal was mapped to the BMP10 gene,whose expression was upregulated in the Yuanbao *** of BMP10 induced a significant decrease in body length by inhibiting angiogenic vessel development in *** addition,three other loci on chromosomes 1,2,and 24 were also identified to be potentially involved in the development of body *** results provide a paradigm shift in identification of novel loci controlling body size variation,availing a fast and efficient *** loci,particularly BMP10,add insights into ongoing research of the evolution of body size under artificial selection and have important implications for future chicken breeding.

关键词： body size artificial selection comparative population genomics domestication

Natatanuran frogs used the Indian Plate to step-stone disperse and radiate across the Indian Ocean

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National Science Review 2019年第1期6卷 10-14页

作者： Zhi-Yong Yuan Bao-Lin Zhang Christopher J.Raxworthy David W.Weisrock Paul M.Hime Jie-Qiong Jin Emily M.Lemmon Alan R.Lemmon Sean D.Holland Michelle L.Kortyna Wei-Wei Zhou min-sheng peng Jing Che Elizabeth Prendini State Key Laboratory of Genetic Resources and Evolution Kunming Institute of Zoology Chinese Academy of Sciences Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China Ministry of Education Southwest Forestry University Kunming College of Life Science University of Chinese Academy of Sciences Department of Herpetology American Museum of Natural History Department of Biology University of Kentucky Biodiversity Institute University of Kansas Southeast Asia Biodiversity Research Institute Chinese Academy of Sciences Department of Biological Science Florida State University Department of Scientific Computing Florida State University Sino-Africa Joint Research Center Chinese Academy of Sciences Center for Excellence in Animal Evolution andGenetics Chinese Academy of Sciences

Investigating the evolutionary history of widespread higher taxa, subjected to multiple tectonic events, can provide evidence for or against various palaeogeographical models of early Earth history [1,2]. Contemporary biotic distributions have been strongly influenced by events associated with the breakup of Gondwana into present-day Africa,Antarctica, Australia, South America,Madagascar and India, during the Late Mesozoic and Early Palaeogene [2]. The fragmentation of Gondwana and subsequent tectonic drift ultimately allowed biotic exchanges between Laurasia and Gondwana [2,3], influencing the global distributions of many taxa.

关键词： In Natatanuran frogs used the Indian Plate to step-stone disperse and radiate across the Indian Ocean

Extramedullary plasmacytoma with the uvula as first affected site:A case report

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World Journal of Clinical Oncology 2025年第1期16卷 53-58页

作者： Jing Yang Hui peng sheng-Ke Tu min Li Kui Song Department of Hematology The First Affiliated Hospital of Jishou UniversityJishou 416000Hunan ProvinceChina Department of Pharmacy The First Affiliated Hospital of Jishou UniversityJishou 416000Hunan ProvinceChina

BACKGROUND Extramedullary plasmacytoma(EMP)represents one of the rarer forms of plasma cell malignancies,capable of impacting a variety of tissues and organs throughout the *** majority of EMP cases are predominantly found in the head and neck region,especially within the laryngopharynx,as well as in the gastrointestinal *** there have been documented instances of oropharyngeal involvement in EMP cases in the academic literature,it is important to note that EMP specifically affecting the uvula is exceedingly ***,it is noteworthy that over 60% of epithelial carcinomas in the upper respiratory tract and oropharynx tend to metastasize to the cervical lymph nodes,indicating a propensity for regional spread in these types of *** this context,we present a rare case of extramedullary plasmacytoma where the uvula served as the initially affected *** case emphasizes the need for heightened awareness among clinicians regarding such unusual comorbidities,as early recognition and diagnosis can significantly influence patient management and treatment *** addition,a review of the relevant literature is included to further educate and inform healthcare professionals about this rare presentation,ultimately aiming to enhance clinical understanding and improve patient care in similar *** SUMMARY A 51-year-old man was admitted to our hospital because of a slowly enlarging neck mass.A physical examination revealed a palpable left lymph node,and magnetic resonance imaging(MRI)of the oropharynx and the neck showed a soft tissue mass in the oropharynx and enlargement of multiple lymph nodes in the *** soft tissue mass was diagnosed as plasmacytoma by immunohistochemical *** immunoglobulins and bone marrow biopsy showed normal ***,we diagnosed that as EMP of the *** four cycles of adjuvant chemotherapy dominated by bortezomib,MRI reexamination showed a significant reduction of the mass

关键词： Extramedullary plasmacytoma Plasmacytoma Uvula Multiple myeloma Case report

The high diversity of SARS-CoV-2-related coronaviruses in pangolins alerts potential ecological risks

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Zoological Research 2021年第6期42卷 834-844页

作者： min-sheng peng Jian-Bo Li Zheng-Fei Cai Hang Liu Xiaolu Tang Ruochen Ying Jia-Nan Zhang Jia-Jun Tao Ting-Ting Yin Tao Zhang Jing-Yang Hu Ru-Nian Wu Zhong-Yin Zhou Zhi-Gang Zhang Li Yu Yong-Gang Yao Zheng-Li Shi Xue-Mei Lu Jian Lu Ya-Ping Zhang State Key Laboratory of Genetic Resources and Evolution Yunnan Laboratory of Molecular Biology of Domestic AnimalsKunming Institute of ZoologyChinese Academy of SciencesKunmingYunnan 650201China Kunming College of Life Science University of Chinese Academy of SciencesKunmingYunnan 650204China KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases Kunming Institute of ZoologyChinese Academy of SciencesKunmingYunnan 650201China State Key Laboratory for Conservation and Utilization of Bio-resources in Yunnan Yunnan UniversityKunmingYunnan 650091China State Key Laboratory of Protein and Plant Gene Research Center for BioinformaticsSchool of Life SciencesPeking UniversityBeijing 100871China Molbreeding Biotechnology Co. Ltd.ShijiazhuangHebei 050035China Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences&Yunnan Province Kunming Institute of ZoologyKunmingYunnan 650201China CAS Key Laboratory of Special Pathogens and Biosafety Wuhan Institute of VirologyChinese Academy of SciencesWuhanHubei 430071China Center for Excellence in Animal Evolution and Genetics Chinese Academy of SciencesKunmingYunnan 650201China

Understanding the zoonotic origin and evolution history of SARS-CoV-2 will provide critical insights for alerting and preventing future outbreaks.A significant gap remains for the possible role of pangolins as a reservoir of SARS-CoV-2 related coronaviruses(SC2r-CoVs).Here,we screened SC2r-CoVs in 172 samples from 163 pangolin individuals of four species,and detected positive signals in muscles of four Manis javanica and,for the first time,one *** analysis of pangolin mitochondrial DNA traced their origins from Southeast *** in-solution hybridization capture sequencing,we assembled a partial pangolin SC2r-CoV(pangolin-CoV)genome sequence of 22895 bp(MP20)from the *** *** analyses revealed MP20 was very closely related to pangolin-CoVs that were identified in *** seized by Guangxi Customs.A genetic contribution of bat coronavirus to pangolin-CoVs via recombination was *** analysis revealed that the genetic diversity of pangolin-CoVs is substantially higher than previously *** the potential infectivity of pangolin-CoVs,the high genetic diversity of pangolin-CoVs alerts the ecological risk of zoonotic evolution and transmission of pathogenic SC2r-CoVs.

关键词： SARS-CoV-2 Pangolin Recombination Diversity Sequencing mtDNA

A cryptic mitochondrial DNA link between North European and West African dogs

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Journal of Genetics and Genomics 2017年第3期44卷 163-170页

作者： Adeniyi C.Adeola Sheila C.Ommeh Jiao-Jiao Song S.Charles Olaogun Oscar J.Sanke Ting-Ting Yin Guo-Dong Wang Shi-Fang Wu Zhong-Yin Zhou Jacqueline K.Lichoti Bernard R.Agwanda Philip M.Dawuda Robert W.Murphy min-sheng peng Ya-Ping Zhang State Key Laboratory for Conservation and Utilization of Bio-Resources Yunnan University Kunming 650091 China

Domestic dogs have an ancient origin and a long history in Africa. Nevertheless, the timing and sources of their introduction into Africa remain enigmatic. Herein, we analyse variation in mitochondrial DNA（mt DNA） D-loop sequences from 345 Nigerian and 37 Kenyan village dogs plus 1530 published sequences of dogs from other parts of Africa, Europe and West Asia. All Kenyan dogs can be assigned to one of three haplogroups（matrilines; clades）： A, B, and C, while Nigerian dogs can be assigned to one of four haplogroups A, B, C, and D. None of the African dogs exhibits a matrilineal contribution from the African wolf（Canis lupus lupaster）. The genetic signal of a recent demographic expansion is detected in Nigerian dogs from West Africa. The analyses of mitochondrial genomes reveal a maternal genetic link between modern West African and North European dogs indicated by sub-haplogroup D1（but not the entire haplogroup D） coalescing around 12,000 years ago. Incorporating molecular anthropological evidence,we propose that sub-haplogroup D1 in West African dogs could be traced back to the late-glacial dispersals, potentially associated with human hunter-gatherer migration from southwestern Europe.

关键词： Dog Mitochondrial DNA Africa Haplogroup D Late-glacial dispersal Hybridization

The Lactase Persistence-22018G＞A Allele Increase Body Mass Index in Asian Populations

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The Lactase Persistence-22018G＞A Allele Increase Body Mass ...