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Su H, Wang M, Li X, Duan S, Sun Q, Sun Y, Wang Z, Yang Q, Huang Y, Zhong J, Chen J, Jiang X, Ma J, Yang T, Liu Y, Luo L, Liu Y, Yang J, Chen G, Liu C, Cai Y, He G. Population genetic admixture and evolutionary history in the Shandong Peninsula inferred from integrative modern and ancient genomic resources. BMC Genomics 2024; 25:611. [PMID: 38890579 PMCID: PMC11184692 DOI: 10.1186/s12864-024-10514-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Accepted: 06/11/2024] [Indexed: 06/20/2024] Open
Abstract
BACKGROUND Ancient northern East Asians (ANEA) from the Yellow River region, who pioneered millet cultivation, play a crucial role in understanding the origins of ethnolinguistically diverse populations in modern China and the entire landscape of deep genetic structure and variation discovery in modern East Asians. However, the direct links between ANEA and geographically proximate modern populations, as well as the biological adaptive processes involved, remain poorly understood. RESULTS Here, we generated genome-wide SNP data for 264 individuals from geographically different Han populations in Shandong. An integrated genomic resource encompassing both modern and ancient East Asians was compiled to examine fine-scale population admixture scenarios and adaptive traits. The reconstruction of demographic history and hierarchical clustering patterns revealed that individuals from the Shandong Peninsula share a close genetic affinity with ANEA, indicating long-term genetic continuity and mobility in the lower Yellow River basin since the early Neolithic period. Biological adaptive signatures, including those related to immune and metabolic pathways, were identified through analyses of haplotype homozygosity and allele frequency spectra. These signatures are linked to complex traits such as height and body mass index, which may be associated with adaptations to cold environments, dietary practices, and pathogen exposure. Additionally, allele frequency trajectories over time and a haplotype network of two highly differentiated genes, ABCC11 and SLC10A1, were delineated. These genes, which are associated with axillary odor and bilirubin metabolism, respectively, illustrate how local adaptations can influence the diversification of traits in East Asians. CONCLUSIONS Our findings provide a comprehensive genomic dataset that elucidates the fine-scale genetic history and evolutionary trajectory of natural selection signals and disease susceptibility in Han Chinese populations. This study serves as a paradigm for integrating spatiotemporally diverse ancient genomes in the era of population genomic medicine.
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Affiliation(s)
- Haoran Su
- Genetic and Prenatal Diagnosis Center, Affiliated Hospital of North Sichuan Medical College, Nanchong, 637007, Sichuan, China
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610000, China
- School of Laboratory Medicine, North Sichuan Medical College, Nanchong, 637007, Sichuan, China
| | - Mengge Wang
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610000, China.
- Center for Archaeological Science, Sichuan University, Chengdu, 610000, China.
- Research Center for Genomic Medicine, North Sichuan Medical College, Nanchong, 637100, China.
| | - Xiangping Li
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610000, China
- School of Forensic Medicine, Kunming Medical University, Kunming, 650500, China
| | - Shuhan Duan
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610000, China
- Research Center for Genomic Medicine, North Sichuan Medical College, Nanchong, 637100, China
- Institute of Basic Medicine and Forensic Medicine, North Sichuan Medical College and Genetic and Prenatal Diagnosis Center, Affiliated Hospital of North Sichuan Medical College, Nanchong, 637007, Sichuan, China
| | - Qiuxia Sun
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610000, China
- Department of Forensic Medicine, College of Basic Medicine, Chongqing Medical University, Chongqing, 400331, China
| | - Yuntao Sun
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610000, China
- West China School of Basic Science & Forensic Medicine, Sichuan University, Chengdu, 610041, China
| | - Zhiyong Wang
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610000, China
- School of Forensic Medicine, Kunming Medical University, Kunming, 650500, China
| | - Qingxin Yang
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610000, China
- School of Forensic Medicine, Kunming Medical University, Kunming, 650500, China
| | - Yuguo Huang
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610000, China
| | - Jie Zhong
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610000, China
| | - Jing Chen
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610000, China
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, 030001, China
| | - Xiucheng Jiang
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610000, China
- Research Center for Genomic Medicine, North Sichuan Medical College, Nanchong, 637100, China
- Institute of Basic Medicine and Forensic Medicine, North Sichuan Medical College and Genetic and Prenatal Diagnosis Center, Affiliated Hospital of North Sichuan Medical College, Nanchong, 637007, Sichuan, China
| | - Jinyue Ma
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610000, China
- Research Center for Genomic Medicine, North Sichuan Medical College, Nanchong, 637100, China
- Institute of Basic Medicine and Forensic Medicine, North Sichuan Medical College and Genetic and Prenatal Diagnosis Center, Affiliated Hospital of North Sichuan Medical College, Nanchong, 637007, Sichuan, China
| | - Ting Yang
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610000, China
- School of Forensic Medicine, Kunming Medical University, Kunming, 650500, China
| | - Yunhui Liu
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610000, China
- Department of Forensic Medicine, College of Basic Medicine, Chongqing Medical University, Chongqing, 400331, China
| | - Lintao Luo
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610000, China
- Department of Forensic Medicine, College of Basic Medicine, Chongqing Medical University, Chongqing, 400331, China
| | - Yan Liu
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610000, China
- Research Center for Genomic Medicine, North Sichuan Medical College, Nanchong, 637100, China
- Institute of Basic Medicine and Forensic Medicine, North Sichuan Medical College and Genetic and Prenatal Diagnosis Center, Affiliated Hospital of North Sichuan Medical College, Nanchong, 637007, Sichuan, China
| | - Junbao Yang
- Research Center for Genomic Medicine, North Sichuan Medical College, Nanchong, 637100, China
- Institute of Basic Medicine and Forensic Medicine, North Sichuan Medical College and Genetic and Prenatal Diagnosis Center, Affiliated Hospital of North Sichuan Medical College, Nanchong, 637007, Sichuan, China
| | - Gang Chen
- Hunan Key Laboratory of Bioinformatics, School of Computer Science and Engineering, Central South University, Changsha, 410075, China
| | - Chao Liu
- Anti-Drug Technology Center of Guangdong Province, Guangzhou, 510230, China.
| | - Yan Cai
- Genetic and Prenatal Diagnosis Center, Affiliated Hospital of North Sichuan Medical College, Nanchong, 637007, Sichuan, China.
| | - Guanglin He
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610000, China.
- Center for Archaeological Science, Sichuan University, Chengdu, 610000, China.
- Research Center for Genomic Medicine, North Sichuan Medical College, Nanchong, 637100, China.
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2
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Sun Y, Wang M, Sun Q, Liu Y, Duan S, Wang Z, Zhou Y, Zhong J, Huang Y, Huang X, Yang Q, Li X, Su H, Cai Y, Jiang X, Chen J, Yan J, Nie S, Hu L, Yang J, Tang R, Wang CC, Liu C, Deng X, Yun L, He G. Distinguished biological adaptation architecture aggravated population differentiation of Tibeto-Burman-speaking people. J Genet Genomics 2024; 51:517-530. [PMID: 37827489 DOI: 10.1016/j.jgg.2023.10.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 09/28/2023] [Accepted: 10/04/2023] [Indexed: 10/14/2023]
Abstract
Tibeto-Burman (TB) people have endeavored to adapt to the hypoxic, cold, and high-UV high-altitude environments in the Tibetan Plateau and complex disease exposures in lowland rainforests since the late Paleolithic period. However, the full landscape of genetic history and biological adaptation of geographically diverse TB-speaking people, as well as their interaction mechanism, remain unknown. Here, we generate a whole-genome meta-database of 500 individuals from 39 TB-speaking populations and present a comprehensive landscape of genetic diversity, admixture history, and differentiated adaptative features of geographically different TB-speaking people. We identify genetic differentiation related to geography and language among TB-speaking people, consistent with their differentiated admixture process with incoming or indigenous ancestral source populations. A robust genetic connection between the Tibetan-Yi corridor and the ancient Yellow River people supports their Northern China origin hypothesis. We finally report substructure-related differentiated biological adaptative signatures between highland Tibetans and Loloish speakers. Adaptative signatures associated with the physical pigmentation (EDAR and SLC24A5) and metabolism (ALDH9A1) are identified in Loloish people, which differed from the high-altitude adaptative genetic architecture in Tibetan. TB-related genomic resources provide new insights into the genetic basis of biological adaptation and better reference for the anthropologically informed sampling design in biomedical and genomic cohort research.
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Affiliation(s)
- Yuntao Sun
- West China School of Basic Science & Forensic Medicine, Sichuan University, Chengdu, Sichuan 610041, China; Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, Sichuan 610000, China; Center for Archaeological Science, Sichuan University, Chengdu, Sichuan 610000, China
| | - Mengge Wang
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, Sichuan 610000, China; Center for Archaeological Science, Sichuan University, Chengdu, Sichuan 610000, China; Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong 510275, China; Guangzhou Forensic Science Institute, Guangzhou, Guangdong 510055, China.
| | - Qiuxia Sun
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, Sichuan 610000, China; Department of Forensic Medicine, College of Basic Medicine, Chongqing Medical University, Chongqing 400331, China
| | - Yan Liu
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, Sichuan 610000, China; School of Clinical Medical Sciences, North Sichuan Medical College, Nanchong, Sichuan 637100, China
| | - Shuhan Duan
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, Sichuan 610000, China; School of Basic Medical Sciences, North Sichuan Medical College, Nanchong, Sichuan 637100, China
| | - Zhiyong Wang
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, Sichuan 610000, China; School of Forensic Medicine, Kunming Medical University, Kunming, Yunnan 650500, China
| | - Yunyu Zhou
- School of Stomatology, North Sichuan Medical College, Nanchong, Sichuan 637100, China
| | - Jun Zhong
- School of Basic Medical Sciences, North Sichuan Medical College, Nanchong, Sichuan 637100, China
| | - Yuguo Huang
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, Sichuan 610000, China
| | - Xinyu Huang
- West China School of Basic Science & Forensic Medicine, Sichuan University, Chengdu, Sichuan 610041, China
| | - Qingxin Yang
- School of Forensic Medicine, Kunming Medical University, Kunming, Yunnan 650500, China
| | - Xiangping Li
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, Sichuan 610000, China; School of Forensic Medicine, Kunming Medical University, Kunming, Yunnan 650500, China
| | - Haoran Su
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, Sichuan 610000, China; School of Basic Medical Sciences, North Sichuan Medical College, Nanchong, Sichuan 637100, China
| | - Yan Cai
- School of Basic Medical Sciences, North Sichuan Medical College, Nanchong, Sichuan 637100, China; Department of Medical Laboratory, North Sichuan Medical College, Nanchong, Sichuan 637007, China
| | - Xiucheng Jiang
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, Sichuan 610000, China; School of Basic Medical Sciences, North Sichuan Medical College, Nanchong, Sichuan 637100, China
| | - Jing Chen
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, Sichuan 610000, China; School of Forensic Medicine, Shanxi Medical University, Jinzhong, Shanxi, 030600, China
| | - Jiangwei Yan
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, Shanxi, 030600, China
| | - Shengjie Nie
- School of Forensic Medicine, Kunming Medical University, Kunming, Yunnan 650500, China
| | - Liping Hu
- School of Forensic Medicine, Kunming Medical University, Kunming, Yunnan 650500, China
| | - Junbao Yang
- School of Clinical Medical Sciences, North Sichuan Medical College, Nanchong, Sichuan 637100, China
| | - Renkuan Tang
- Department of Forensic Medicine, College of Basic Medicine, Chongqing Medical University, Chongqing 400331, China
| | - Chuan-Chao Wang
- School of Life Sciences, Xiamen University, Xiamen, Fujian 361005, China
| | - Chao Liu
- Anti-Drug Technology Center of Guangdong Province, Guangzhou, Guangdong 510230, China
| | - Xiaohui Deng
- West China School of Basic Science & Forensic Medicine, Sichuan University, Chengdu, Sichuan 610041, China.
| | - Libing Yun
- West China School of Basic Science & Forensic Medicine, Sichuan University, Chengdu, Sichuan 610041, China; Center for Archaeological Science, Sichuan University, Chengdu, Sichuan 610000, China.
| | - Guanglin He
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, Sichuan 610000, China; Center for Archaeological Science, Sichuan University, Chengdu, Sichuan 610000, China.
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3
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Chen J, Liu C, Li W, Zhang W, Wang Y, Clark AG, Lu J. From sub-Saharan Africa to China: Evolutionary history and adaptation of Drosophila melanogaster revealed by population genomics. SCIENCE ADVANCES 2024; 10:eadh3425. [PMID: 38630810 PMCID: PMC11023512 DOI: 10.1126/sciadv.adh3425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Accepted: 03/13/2024] [Indexed: 04/19/2024]
Abstract
Drosophila melanogaster is a widely used model organism for studying environmental adaptation. However, the genetic diversity of populations in Asia is poorly understood, leaving a notable gap in our knowledge of the global evolution and adaptation of this species. We sequenced genomes of 292 D. melanogaster strains from various ecological settings in China and analyzed them along with previously published genome sequences. We have identified six global genetic ancestry groups, despite the presence of widespread genetic admixture. The strains from China represent a unique ancestry group, although detectable differentiation exists among populations within China. We deciphered the global migration and demography of D. melanogaster, and identified widespread signals of adaptation, including genetic changes in response to insecticides. We validated the effects of insecticide resistance variants using population cage trials and deep sequencing. This work highlights the importance of population genomics in understanding the genetic underpinnings of adaptation, an effort that is particularly relevant given the deterioration of ecosystems.
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Affiliation(s)
- Junhao Chen
- State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing 100871, China
| | - Chenlu Liu
- State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing 100871, China
| | - Weixuan Li
- State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing 100871, China
| | - Wenxia Zhang
- State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing 100871, China
| | - Yirong Wang
- College of Biology, Hunan University, Changsha 410082, China
| | - Andrew G. Clark
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Jian Lu
- State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing 100871, China
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4
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Yao H, Wang K, Lu S, Cao F, Dai P. Development of an ARMS multiplex real-time PCR assay for the detection of HLA-B*13:01 genotype by detecting highly specific SNPs. Pharmacogenet Genomics 2024; 34:53-59. [PMID: 38050734 DOI: 10.1097/fpc.0000000000000517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/06/2023]
Abstract
OBJECTIVES HLA-B*13:01 was strongly associated with Dapsone Hypersensitivity Syndrome (DHS). This study aimed to develop and validate a rapid and economical method for HLA-B*13:01 genotyping. METHODS Two tubes multiplex real-time PCR detection system comprising amplification refractory mutation system primers and TaqMan probes was established for HLA-B*13:01 genotyping. Sequence-based typing was applied to validate the accuracy of the assay. RESULTS The accuracy of the assay was 100% for HLA-B*13:01 genotyping. The detection limit of the new method was 0.025 ng DNA. The positive rate of HLA-B*13:01 in the Bouyei (20%, n = 50) populations was significantly higher than that in the Uighur population (4%, n = 100), Han (4.5%, n = 200), and Tibetan (1%, n = 100) ( P < 0.05). CONCLUSION The proposed method is rapid and reliable for HLA-B*13:01 screening in a clinical setting.
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Affiliation(s)
- Hao Yao
- National Engineering Research Center for Miniaturized Detection Systems, College of Life Science, Northwest University of Xi'an
| | - Kaixuan Wang
- National Engineering Research Center for Miniaturized Detection Systems, College of Life Science, Northwest University of Xi'an
| | - Sihai Lu
- National Engineering Research Center for Miniaturized Detection Systems, College of Life Science, Northwest University of Xi'an
| | - Fang Cao
- Department of Clinical Pharmacy, Shaanxi Provincial Cancer Hospital, Shaanxi Province, China
| | - Penggao Dai
- National Engineering Research Center for Miniaturized Detection Systems, College of Life Science, Northwest University of Xi'an
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He G, Wang P, Chen J, Liu Y, Sun Y, Hu R, Duan S, Sun Q, Tang R, Yang J, Wang Z, Yun L, Hu L, Yan J, Nie S, Wei L, Liu C, Wang M. Differentiated genomic footprints suggest isolation and long-distance migration of Hmong-Mien populations. BMC Biol 2024; 22:18. [PMID: 38273256 PMCID: PMC10809681 DOI: 10.1186/s12915-024-01828-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: 01/23/2023] [Accepted: 01/12/2024] [Indexed: 01/27/2024] Open
Abstract
BACKGROUND The underrepresentation of Hmong-Mien (HM) people in Asian genomic studies has hindered our comprehensive understanding of the full landscape of their evolutionary history and complex trait architecture. South China is a multi-ethnic region and indigenously settled by ethnolinguistically diverse HM, Austroasiatic (AA), Tai-Kadai (TK), Austronesian (AN), and Sino-Tibetan (ST) people, which is regarded as East Asia's initial cradle of biodiversity. However, previous fragmented genetic studies have only presented a fraction of the landscape of genetic diversity in this region, especially the lack of haplotype-based genomic resources. The deep characterization of demographic history and natural-selection-relevant genetic architecture of HM people was necessary. RESULTS We reported one HM-specific genomic resource and comprehensively explored the fine-scale genetic structure and adaptative features inferred from the genome-wide SNP data of 440 HM individuals from 33 ethnolinguistic populations, including previously unreported She. We identified solid genetic differentiation between HM people and Han Chinese at 7.64‒15.86 years ago (kya) and split events between southern Chinese inland (Miao/Yao) and coastal (She) HM people in the middle Bronze Age period and the latter obtained more gene flow from Ancient Northern East Asians. Multiple admixture models further confirmed that extensive gene flow from surrounding ST, TK, and AN people entangled in forming the gene pool of Chinese coastal HM people. Genetic findings of isolated shared unique ancestral components based on the sharing alleles and haplotypes deconstructed that HM people from the Yungui Plateau carried the breadth of previously unknown genomic diversity. We identified a direct and recent genetic connection between Chinese inland and Southeast Asian HM people as they shared the most extended identity-by-descent fragments, supporting the long-distance migration hypothesis. Uniparental phylogenetic topology and network-based phylogenetic relationship reconstruction found ancient uniparental founding lineages in southwestern HM people. Finally, the population-specific biological adaptation study identified the shared and differentiated natural selection signatures among inland and coastal HM people associated with physical features and immune functions. The allele frequency spectrum of cancer susceptibility alleles and pharmacogenomic genes showed significant differences between HM and northern Chinese people. CONCLUSIONS Our extensive genetic evidence combined with the historical documents supported the view that ancient HM people originated from the Yungui regions associated with ancient "Three-Miao tribes" descended from the ancient Daxi-Qujialing-Shijiahe people. Then, some have recently migrated rapidly to Southeast Asia, and some have migrated eastward and mixed respectively with Southeast Asian indigenes, Liangzhu-related coastal ancient populations, and incoming southward ST people. Generally, complex population migration, admixture, and adaptation history contributed to the complicated patterns of population structure of geographically diverse HM people.
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Affiliation(s)
- Guanglin He
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610041, China.
- Center for Archaeological Science, Sichuan University, Chengdu, 610000, China.
- Anti-Drug Technology Center of Guangdong Province, Guangzhou, 510230, China.
- Research Center for Genomic Medicine, North Sichuan Medical College, Nanchong, 637100, China.
| | - Peixin Wang
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610041, China
- School of Medical Information, Chongqing Medical University, Chongqing, 400331, China
| | - Jing Chen
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610041, China
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, 030001, China
| | - Yan Liu
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610041, China
- School of Basic Medical Sciences, North Sichuan Medical College, Nanchong, 637000, China
- Research Center for Genomic Medicine, North Sichuan Medical College, Nanchong, 637100, China
| | - Yuntao Sun
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610041, China
- Institute of Forensic Medicine, West China School of Basic Science & Forensic Medicine, Sichuan University, Chengdu, 610041, China
| | - Rong Hu
- School of Sociology and Anthropology, Xiamen University, Xiamen, 361005, China
| | - Shuhan Duan
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610041, China
- School of Basic Medical Sciences, North Sichuan Medical College, Nanchong, 637000, China
- Research Center for Genomic Medicine, North Sichuan Medical College, Nanchong, 637100, China
| | - Qiuxia Sun
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610041, China
- Department of Forensic Medicine, College of Basic Medicine, Chongqing Medical University, Chongqing, 400331, China
| | - Renkuan Tang
- Department of Forensic Medicine, College of Basic Medicine, Chongqing Medical University, Chongqing, 400331, China
| | - Junbao Yang
- School of Basic Medical Sciences, North Sichuan Medical College, Nanchong, 637000, China
- Research Center for Genomic Medicine, North Sichuan Medical College, Nanchong, 637100, China
| | - Zhiyong Wang
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610041, China
- School of Forensic Medicine, Kunming Medical University, Kunming, 650500, China
| | - Libing Yun
- Institute of Forensic Medicine, West China School of Basic Science & Forensic Medicine, Sichuan University, Chengdu, 610041, China
| | - Liping Hu
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610041, China
- School of Forensic Medicine, Kunming Medical University, Kunming, 650500, China
| | - Jiangwei Yan
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, 030001, China
| | - Shengjie Nie
- School of Forensic Medicine, Kunming Medical University, Kunming, 650500, China
| | - Lanhai Wei
- School of Ethnology and Anthropology, Inner Mongolia Normal University, Inner Mongolia, 010028, China
| | - Chao Liu
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, 510275, China.
- Anti-Drug Technology Center of Guangdong Province, Guangzhou, 510230, China.
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, 510515, China.
| | - Mengge Wang
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610041, China.
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, 510275, China.
- Anti-Drug Technology Center of Guangdong Province, Guangzhou, 510230, China.
- Research Center for Genomic Medicine, North Sichuan Medical College, Nanchong, 637100, China.
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Luo H, Zhang P, Zhang W, Zheng Y, Hao D, Shi Y, Niu Y, Song T, Li Y, Zhao S, Chen H, Xu T, He S. Recent positive selection signatures reveal phenotypic evolution in the Han Chinese population. Sci Bull (Beijing) 2023; 68:2391-2404. [PMID: 37661541 DOI: 10.1016/j.scib.2023.08.027] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 05/08/2023] [Accepted: 08/10/2023] [Indexed: 09/05/2023]
Abstract
Characterizing natural selection signatures and relationships with phenotype spectra is important for understanding human evolution and both biological and pathological mechanisms. Here, we identified 24 genetic loci under recent selection by analyzing rare singletons in 3946 high-depth whole-genome sequencing data of Han Chinese. The loci include immune-related gene regions (MHC cluster, IGH cluster, STING1, and PSG), alcohol metabolism-related gene regions (ADH1B, ALDH2, and ALDH3B2), and the olfactory perception gene OR4C16, in which the MHC cluster, ADH1B, and ALDH2 were also identified by TOPMed and WestLake Biobank. Among the signals, the IGH cluster is particularly interesting, in which the favored allele of variant 14_105737776_C_T (rs117518546, IgG1-G396R) promotes immune response, but also increases the risk of an autoimmune disease systemic lupus erythematosus (SLE). It is also surprising that our newly discovered ALDH3B2 evolved in the opposite direction to ALDH2 for alcohol metabolism. Besides monogenic traits, we found that multiple complex traits experienced polygenic adaptation. Particularly, multi-methods consistently revealed that lower blood pressure was favored in natural selection. Finally, we built a database named RePoS (recent positive selection, http://bigdata.ibp.ac.cn/RePoS/) to integrate and display multi-population selection signals. Our study extended our understanding of natural evolution and phenotype adaptation in Han Chinese as well as other populations.
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Affiliation(s)
- Huaxia Luo
- Key Laboratory of Epigenetic Regulation and Intervention, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; Department of Pediatrics, Peking University First Hospital, Beijing 100034, China
| | - Peng Zhang
- Key Laboratory of Epigenetic Regulation and Intervention, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Wanyu Zhang
- Key Laboratory of Epigenetic Regulation and Intervention, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Yu Zheng
- Key Laboratory of Epigenetic Regulation and Intervention, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Di Hao
- Key Laboratory of Epigenetic Regulation and Intervention, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Yirong Shi
- Key Laboratory of Epigenetic Regulation and Intervention, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yiwei Niu
- Key Laboratory of Epigenetic Regulation and Intervention, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Tingrui Song
- Key Laboratory of Epigenetic Regulation and Intervention, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Yanyan Li
- Key Laboratory of Epigenetic Regulation and Intervention, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Shilei Zhao
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China; China National Center for Bioinformation, Beijing 100101, China
| | - Hua Chen
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China; China National Center for Bioinformation, Beijing 100101, China.
| | - Tao Xu
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; Shandong First Medical University & Shandong Academy of Medical Sciences, Taian 271016, China.
| | - Shunmin He
- Key Laboratory of Epigenetic Regulation and Intervention, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China.
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7
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Ge X, Lu Y, Chen S, Gao Y, Ma L, Liu L, Liu J, Ma X, Kang L, Xu S. Genetic Origins and Adaptive Evolution of the Deng People on the Tibetan Plateau. Mol Biol Evol 2023; 40:msad205. [PMID: 37713634 PMCID: PMC10584363 DOI: 10.1093/molbev/msad205] [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: 03/02/2023] [Revised: 07/01/2023] [Accepted: 08/30/2023] [Indexed: 09/17/2023] Open
Abstract
The Tibetan Plateau is populated by diverse ethnic groups, but most of them are underrepresented in genomics studies compared with the Tibetans (TIB). Here, to gain further insight into the genetic diversity and evolutionary history of the people living in the Tibetan Plateau, we sequenced 54 whole genomes of the Deng people with high coverage (30-60×) and analyzed the data together with that of TIB and Sherpas, as well as 968 ancient Asian genomes and available archaic and modern human data. We identified 17.74 million novel single-nucleotide variants from the newly sequenced genomes, although the Deng people showed reduced genomic diversity and a relatively small effective population size. Compared with the other Tibetan highlander groups which are highly admixed, the Deng people are dominated by a sole ancestry that could be traced to some ancient northern East Asian populations. The divergence between Deng and Tibetan people (∼4,700-7,200 years) was more recent than that between highlanders and the Han Chinese (Deng-HAN, ∼9,000-14,000 years; TIB-HAN, 7,200-10,000 years). Adaptive genetic variants (AGVs) identified in the Deng are only partially shared with those previously reported in the TIB like HLA-DQB1, whereas others like KLHL12 were not reported in TIB. In contrast, the top candidate genes harboring AGVs as previously identified in TIB, like EPAS1 and EGLN1, do not show strong positive selection signals in Deng. Interestingly, Deng also showed a different archaic introgression scenario from that observed in the TIB. Our results suggest that convergent adaptation might be prevalent on the Tibetan Plateau.
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Affiliation(s)
- Xueling Ge
- Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Yan Lu
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, Zhangjiang Fudan International Innovation Center, Center for Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, China
| | - Shuanghui Chen
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Yang Gao
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, Zhangjiang Fudan International Innovation Center, Center for Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, China
| | - Lifeng Ma
- Key Laboratory of High-Altitude Environment and Genes Related to Disease of Tibet Ministry of Education, Xizang Minzu University, Xianyang, Shaanxi, China
- Research Center for Tibetan Social Governance, Key Research Institute of Humanities and Social Sciences in Xizang Minzu University, State Ethnic Affairs Commission, Xizang Minzu University, Xianyang, Shaanxi, China
| | - Lijun Liu
- Key Laboratory of High-Altitude Environment and Genes Related to Disease of Tibet Ministry of Education, Xizang Minzu University, Xianyang, Shaanxi, China
- Research Center for Tibetan Social Governance, Key Research Institute of Humanities and Social Sciences in Xizang Minzu University, State Ethnic Affairs Commission, Xizang Minzu University, Xianyang, Shaanxi, China
| | - Jiaojiao Liu
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, Zhangjiang Fudan International Innovation Center, Center for Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, China
| | - Xixian Ma
- Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Longli Kang
- Key Laboratory of High-Altitude Environment and Genes Related to Disease of Tibet Ministry of Education, Xizang Minzu University, Xianyang, Shaanxi, China
- Research Center for Tibetan Social Governance, Key Research Institute of Humanities and Social Sciences in Xizang Minzu University, State Ethnic Affairs Commission, Xizang Minzu University, Xianyang, Shaanxi, China
| | - Shuhua Xu
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, Zhangjiang Fudan International Innovation Center, Center for Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
- Department of Liver Surgery and Transplantation Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, China
- Ministry of Education Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center for Genetics and Development, Fudan University, Shanghai, China
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8
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Dai X, Bian P, Hu D, Luo F, Huang Y, Jiao S, Wang X, Gong M, Li R, Cai Y, Wen J, Yang Q, Deng W, Nanaei HA, Wang Y, Wang F, Zhang Z, Rosen BD, Heller R, Jiang Y. A Chinese indicine pangenome reveals a wealth of novel structural variants introgressed from other Bos species. Genome Res 2023; 33:1284-1298. [PMID: 37714713 PMCID: PMC10547261 DOI: 10.1101/gr.277481.122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 06/30/2023] [Indexed: 09/17/2023]
Abstract
Chinese indicine cattle harbor a much higher genetic diversity compared with other domestic cattle, but their genome architecture remains uninvestigated. Using PacBio HiFi sequencing data from 10 Chinese indicine cattle across southern China, we assembled 20 high-quality partially phased genomes and integrated them into a multiassembly graph containing 148.5 Mb (5.6%) of novel sequence. We identified 156,009 high-confidence nonredundant structural variants (SVs) and 206 SV hotspots spanning ∼195 Mb of gene-rich sequence. We detected 34,249 archaic introgressed fragments in Chinese indicine cattle covering 1.93 Gb (73.3%) of the genome. We inferred an average of 3.8%, 3.2%, 1.4%, and 0.5% of introgressed sequence originating, respectively, from banteng-like, kouprey-like, gayal-like, and gaur-like Bos species, as well as 0.6% of unknown origin. Introgression from multiple donors might have contributed to the genetic diversity of Chinese indicine cattle. Altogether, this study highlights the contribution of interspecies introgression to the genomic architecture of an important livestock population and shows how exotic genomic elements can contribute to the genetic variation available for selection.
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Affiliation(s)
- Xuelei Dai
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Peipei Bian
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Dexiang Hu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Funong Luo
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yongzhen Huang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Shaohua Jiao
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, 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, Shaanxi 712100, China
| | - Mian Gong
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Ran Li
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, 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, Shaanxi 712100, China
| | - Jiayue Wen
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Qimeng Yang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Weidong Deng
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China
| | - Hojjat Asadollahpour Nanaei
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
- Reproductive Biotechnology Research Center, Avicenna Research Institute, ACECR, Tehran 1983969412, Iran
| | - Yu Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Fei Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Zijing Zhang
- Institute of Animal Husbandry and Veterinary Science, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
| | - Benjamin D Rosen
- Animal Genomics and Improvement Laboratory, USDA-ARS, Beltsville, Maryland 20705, USA
| | - Rasmus Heller
- Department of Biology, University of Copenhagen, 2200 Copenhagen, Denmark;
| | - Yu Jiang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China;
- Key Laboratory of Livestock Biology, Northwest A&F University, Yangling, Shaanxi 712100, China
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9
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Ning Z, Tan X, Yuan Y, Huang K, Pan Y, Tian L, Lu Y, Wang X, Qi R, Lu D, Yang Y, Guan Y, Mamatyusupu D, Xu S. Expression profiles of east-west highly differentiated genes in Uyghur genomes. Natl Sci Rev 2023; 10:nwad077. [PMID: 37138773 PMCID: PMC10150800 DOI: 10.1093/nsr/nwad077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 02/28/2023] [Indexed: 05/05/2023] Open
Abstract
It remains unknown and debatable how European-Asian-differentiated alleles affect individual phenotypes. Here, we made the first effort to analyze the expression profiles of highly differentiated genes with eastern and western origins in 90 Uyghurs using whole-genome (30× to 60×) and transcriptome data. We screened 921 872 east-west highly differentiated genetic variants, of which ∼4.32% were expression quantitative trait loci (eQTLs), ∼0.12% were alternative splicing quantitative trait loci (sQTLs), and ∼0.12% showed allele-specific expression (ASE). The 8305 highly differentiated eQTLs of strong effects appear to have undergone natural selection, associated with immunity and metabolism. European-origin alleles tend to be more biasedly expressed; highly differentiated ASEs were enriched in diabetes-associated genes, likely affecting the diabetes susceptibility in the Uyghurs. We proposed an admixture-induced expression model to dissect the highly differentiated expression profiles. We provide new insights into the genetic basis of phenotypic differentiation between Western and Eastern populations, advancing our understanding of the impact of genetic admixture.
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Affiliation(s)
| | | | | | - Ke Huang
- Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
- School of Life Science and Technology, Shanghai Tech University, Shanghai 201210, China
| | - Yuwen Pan
- Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Lei Tian
- Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yan Lu
- State Key Laboratory of Genetic Engineering, Center for Evolutionary Biology, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Xiaoji Wang
- Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Ruicheng Qi
- Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Dongsheng Lu
- Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yajun Yang
- State Key Laboratory of Genetic Engineering, Center for Evolutionary Biology, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Yaqun Guan
- Department of Biochemistry and Molecular Biology, Preclinical Medicine College, Xinjiang Medical University, Urumqi 830011, China
| | - Dolikun Mamatyusupu
- College of the Life Sciences and Technology, Xinjiang University, Urumqi 830046, China
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10
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Wu CI. The genetics of race differentiation-should it be studied? Natl Sci Rev 2023; 10:nwad068. [PMID: 37034147 PMCID: PMC10076182 DOI: 10.1093/nsr/nwad068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/16/2023] [Indexed: 03/19/2023] Open
Affiliation(s)
- Chung-I Wu
- Chung-I Wu School of Life Sciences, Sun Yat-sen University, China Associate Editor-in-Chief for Life Sciences at NSR
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11
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Guanglin H, Lan-Hai W, Mengge W. Editorial: Forensic investigative genetic genealogy and fine-scale structure of human populations. Front Genet 2023; 13:1067865. [PMID: 36685813 PMCID: PMC9849385 DOI: 10.3389/fgene.2022.1067865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 12/22/2022] [Indexed: 01/06/2023] Open
Affiliation(s)
- He Guanglin
- 1Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, China,*Correspondence: He Guanglin, ; Wang Mengge,
| | - Wei Lan-Hai
- 2School of Ethnology and Anthropology, Inner Mongolia Normal University, Hohhot, China
| | - Wang Mengge
- 3Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China,*Correspondence: He Guanglin, ; Wang Mengge,
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12
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Wang F, Li W, Wang X, Luo X, Dai P. A single-tube multiplex real-time PCR for HLA-B*38:02 genotype by detecting highly specific SNPs. Pharmacogenomics 2023; 24:5-14. [PMID: 36661044 DOI: 10.2217/pgs-2022-0132] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Purpose: HLA-B*38:02 is closely related to carbimazole/methimazole-induced agranulocytosis. This study aimed to develop and validate a rapid and economical method for HLA-B*38:02 genotyping. Methods: A single-tube multiplex real-time PCR detection system comprising amplification refractory mutation system primers and TaqMan probes was established for HLA-B*38:02 genotyping. Sequence-based typing was applied to validate the accuracy of the assay. Results: The accuracy of the assay was 100% for HLA-B*38:02 genotyping. The detection limit of the new method was 0.05 ng DNA. The positive rate of HLA-B*38:02 in the Han (8%, n = 100), Bouyei (17.8%, n = 90) and Tibetan (12.7%, n = 110) populations was significantly higher than that in the Uighur population (1%, n = 100) (p < 0.05). Conclusion: The proposed method is rapid and reliable for HLA-B*38:02 screening in a clinical setting.
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Affiliation(s)
- Fei Wang
- National Engineering Research Center for Miniaturized Detection Systems, College of Life Science, Northwest University of Xi'an, Shaanxi Province, 710069, China
| | - Wenqi Li
- National Engineering Research Center for Miniaturized Detection Systems, College of Life Science, Northwest University of Xi'an, Shaanxi Province, 710069, China
| | - Xuan Wang
- National Engineering Research Center for Miniaturized Detection Systems, College of Life Science, Northwest University of Xi'an, Shaanxi Province, 710069, China
| | - Xiang Luo
- Department of Respiratory, Tongchuan People's Hospital Tongchuan, Shaanxi Province, People's Republic of China
| | - Penggao Dai
- National Engineering Research Center for Miniaturized Detection Systems, College of Life Science, Northwest University of Xi'an, Shaanxi Province, 710069, China.,Shaanxi Lifegen Co.,Ltd, Building 1, Collaborative Innovation Port, Fengdong New City, Xixian New Area, Xi'an, Shaanxi Province, 712000, China
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13
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Ge D, Wen Z, Feijó A, Lissovsky A, Zhang W, Cheng J, Yan C, She H, Zhang D, Cheng Y, Lu L, Wu X, Mu D, Zhang Y, Xia L, Qu Y, Vogler AP, Yang Q. Genomic Consequences of and Demographic Response to Pervasive Hybridization Over Time in Climate-Sensitive Pikas. Mol Biol Evol 2022; 40:6958644. [PMID: 36562771 PMCID: PMC9847633 DOI: 10.1093/molbev/msac274] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 11/13/2022] [Accepted: 12/20/2022] [Indexed: 12/24/2022] Open
Abstract
Rare and geographically restricted species may be vulnerable to genetic effects from inbreeding depression in small populations or from genetic swamping through hybridization with common species, but a third possibility is that selective gene flow can restore fitness (genetic rescue). Climate-sensitive pikas (Ochotona spp.) of the Qinghai-Tibetan Plateau (QHTP) and its vicinity have been reduced to residual populations through the movement of climatic zones during the Pleistocene and recent anthropogenic disturbance, whereas the plateau pika (O. curzoniae) remains common. Population-level whole-genome sequencing (n = 142) of six closely related species in the subgenus Ochotona revealed several phases of ancient introgression, lineage replacement, and bidirectional introgression. The strength of gene flow was the greatest from the dominant O. curzoniae to ecologically distinct species in areas peripheral to the QHTP. Genetic analyses were consistent with environmental reconstructions of past population movements. Recurrent periods of introgression throughout the Pleistocene revealed an increase in genetic variation at first but subsequent loss of genetic variation in later phases. Enhanced dispersion of introgressed genomic regions apparently contributed to demographic recovery in three peripheral species that underwent range shifts following climate oscillations on the QHTP, although it failed to drive recovery of northeastern O. dauurica and geographically isolated O. sikimaria. Our findings highlight differences in timescale and environmental background to determine the consequence of hybridization and the unique role of the QHTP in conserving key evolutionary processes of sky island species.
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Affiliation(s)
| | | | | | | | | | - Jilong Cheng
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Chaochao Yan
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
| | - Huishang She
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Dezhi Zhang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yalin Cheng
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Liang Lu
- State Key Laboratory for Infectious Diseases Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Xinlai Wu
- The Key Laboratory of Zoological Systematics and Application, School of Life Science, Institute of Life Science and Green Development, Hebei University, Baoding, 071002, China
| | - Danping Mu
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi, 830046, China
| | - Yubo Zhang
- State Key Laboratory for Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences at College of Life Sciences, Peking University, Beijing, 100871, China
| | - Lin Xia
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
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