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The complete and fully-phased diploid genome of a male Han Chinese

查看全文 作　　者：Chentao [1,2,3]Yang;Yang [3,4]Zhou;Yanni [5]Song;Dongya [1,2,6,7]Wu;Yan [3]Zeng;Lei [3]Nie;Panhong [3]Liu;Shilong [8]Zhang;Guangji [3,9]Chen;Jinjin [3]Xu;Hongling [5]Zhou;Long [2,6,10]Zhou;Xiaobo [3,9]Qian;Chenlu [11]Liu;Shangjin [3]Tan;Chengran [3]Zhou;Wei [3]Dai;Mengyang [3,12]Xu;Yanwei [12]Qi;Xiaobo [5]Wang;Lidong [9,12]Guo;Guangyi [12]Fan;Aijun [12]Wang;Yuan [3]Deng;Yong [3]Zhang;Jiazheng [3]Jin;Yunqiu [1,2]He;Chunxue [3,13]Guo;Guoji [14]Guo;Qing [6,11]Zhou;Xun [3]Xu;Huanming [3]Yang;Jian [3]Wang;Shuhua [15,16,17,18,19]Xu;Yafei [8]Mao;Xin [3]Jin;Jue [5]Ruan;Guojie [1,2,6,10,20]Zhang 高影响力作者 机构地区：[1]Center for Genomic Research,International Institutes of Medicine,The Fourth Affiliated Hospital,Zhejiang University School of Medicine,Yiwu,Zhejiang,China;[2]Center for Evolutionary&Organismal Biology,&Women’s Hospital,Zhejiang University School of Medicine,Hangzhou,Zhejiang,China;[3]BGI-Shenzhen,Shenzhen,Guangdong,China;[4]BGI Research-Wuhan,BGI,Wuhan,Hubei,China;[5]Shenzhen Branch,Guangdong Laboratory for Lingnan Modern Agriculture,Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs,Agricultural Genomics Institute at Shenzhen,Chinese Academy of Agricultural Sciences,Shenzhen,Guangdong,China;[6]Liangzhu Laboratory,Zhejiang University Medical Center,Hangzhou,Zhejiang,China;[7]Institute of Crop Science&Institute of Bioinformatics,Zhejiang University,Hangzhou,Zhejiang,China;[8]Bio-X Institutes,Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders,Ministry of Education,Shanghai Jiao Tong University,Shanghai,China;[9]College of Life Sciences,University of Chinese Academy of Sciences,Beijing,China;[10]Innovation Center of Yangtze River Delta,Zhejiang University,Hangzhou,Zhejiang,China;[11]Life Sciences Institute,Zhejiang University,Hangzhou,Zhejiang,China;[12]BGI-Qingdao,BGI-Shenzhen,Qingdao,Shandong,China;[13]BGI-Hangzhou,Hangzhou,Zhejiang,China;[14]School of Medicine,Zhejiang University,Hangzhou,Zhejiang,China;[15]State Key Laboratory of Genetic Engineering,Center for Evolutionary Biology,Collaborative Innovation Center for Genetics and Development,School of Life Sciences,Fudan University,Shanghai,China;[16]Human Phenome Institute,Zhangjiang Fudan International Innovation Center,and Ministry of Education Key Laboratory of Contemporary Anthropology,Fudan University,Shanghai,China;[17]Jiangsu Key Laboratory of Phylogenomics&Comparative Genomics,International Joint Center of Genomics of Jiangsu Province School of Life Sciences,Jiangsu Normal University,Xuzhou,Jiangsu,China;[18]Department of Liver Surgery and Transplantation Liver Cancer Institute,Zhongshan Hospital,Fudan University,Shanghai,China;[19]Center for Excellence in Animal Evolution and Genetics,Chinese Academy of Sciences,Kunming,Yunnan,China;[20]State Key Laboratory of Genetic Resources and Evolution,Kunming Institute of Zoology,Chinese Academy of Sciences,Kunming,Yunnan,China高影响力机构 出　　处：《Cell Research》索引2023年第33卷第10期,共17页高影响力期刊 基　　金：supported by the funding from International Institutes of Medicine at Yiwu and Kunpeng Fellowship to G.Z.;the National Key R&D Program of China(2022YFC3400300)to J.R. 摘　　要：Since the release of the complete human genome,the priority of human genomic study has now been shifting towards closing gaps in ethnic diversity.Here,we present a fully phased and well-annotated diploid human genome from a Han Chinese male individual(CN1),in which the assemblies of both haploids achieve the telomere-to-telomere(T2T)level.Comparison of this diploid genome with the CHM13 haploid T2T genome revealed significant variations in the centromere.Outside the centromere,we discovered 11,413 structural variations,including numerous novel ones.We also detected thousands of CN1 alleles that have accumulated high substitution rates and a few that have been under positive selection in the East Asian population.Further,we found that CN1 outperforms CHM13 as a reference genome in mapping and variant calling for the East Asian population owing to the distinct structural variants of the two references.Comparison of SNP calling for a large cohort of 8869 Chinese genomes using CN1 and CHM13 as reference respectively showed that the reference bias profoundly impacts rare SNP calling,with nearly 2 million rare SNPs miss-called with different reference genomes.Finally,applying the CN1 as a reference,we discovered 5.80 Mb and 4.21 Mb putative introgression sequences from Neanderthal and Denisovan,respectively,including many East Asian specific ones undetected using CHM13 as the reference.Our analyses reveal the advances of using CN1 as a reference for population genomic studies and paleo-genomic studies.This complete genome will serve as an alternative reference for future genomic studies on the East Asian population. 关 键 词：RARE SHIFTING release
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