文献类型： 外文期刊

作者： Yang, Chentao ¹ ; Zhou, Yang ⁴ ; Song, Yanni ⁶ ; Wu, Dongya ¹ ; Zeng, Yan ⁴ ; Nie, Lei ⁴ ; Liu, Panhong ⁴ ; Zhang, Shilong ¹⁰ ; Chen, Guangji ⁴ ; Xu, Jinjin ⁴ ; Zhou, Hongling ⁶ ; Zhou, Long ² ; Qian, Xiaobo ⁴ ; Liu, Chenlu ¹³ ; Tan, Shangjin ⁴ ; Zhou, Chengran ⁴ ; Dai, Wei ⁴ ; Xu, Mengyang ⁴ ; Qi, Yanwei ¹⁴ ; Wang, Xiaobo ⁶ ; Guo, Lidong ¹¹ ; Fan, Guangyi ¹⁴ ; Wang, Aijun ¹⁴ ; Deng, Yuan ⁴ ; Zhang, Yong ⁴ ; Jin, Jiazheng ⁴ ; He, Yunqiu ¹ ; Guo, Chunxue ⁴ ; Guo, Guoji ¹⁶ ; Zhou, Qing ⁷ ; Xu, Xun ⁴ ; Yang, Huanming ⁴ ; Wang, Jian ⁴ ; Xu, Shuhua ¹⁷ ; Mao, Yafei ¹⁰ ; Jin, Xin ⁴ ; Ruan, Jue ⁶ ; Zhang, Guojie ¹ ;

作者机构： 1.Zhejiang Univ, Affiliated Hosp 4, Sch Med, Ctr Genom Res,Int Inst Med, Yiwu, Zhejiang, Peoples R China

2.Zhejiang Univ, Sch Med, Ctr Evolutionary & Organismal Biol, Hangzhou, Zhejiang, Peoples R China

3.Zhejiang Univ, Womens Hosp, Sch Med, Hangzhou, Zhejiang, Peoples R China

4.BGI Shenzhen, Shenzhen, Guangdong, Peoples R China

5.BGI Res Wuhan, BGI, Wuhan, Hubei, Peoples R China

6.Chinese Acad Agr Sci, Minist Agr & Rural Affairs, Agr Genom Inst Shenzhen, Genome Anal Lab,Guangdong Lab Lingnan Modern Agr,S, Shenzhen, Guangdong, Peoples R China

7.Zhejiang Univ, Med Ctr, Liangzhu Lab, Hangzhou, Zhejiang, Peoples R China

8.Zhejiang Univ, Inst Crop Sci, Hangzhou, Zhejiang, Peoples R China

9.Zhejiang Univ, Inst Bioinformat, Hangzhou, Zhejiang, Peoples R China

10.Shanghai Jiao Tong Univ, Minist Educ, Bio X Inst, Key Lab Genet Dev & Neuropsychiat Disorders, Shanghai, Peoples R China

11.Univ Chinese Acad Sci, Coll Life Sci, Beijing, Peoples R China

12.Zhejiang Univ, Innovat Ctr Yangtze River Delta, Hangzhou, Zhejiang, Peoples R China

13.Zhejiang Univ, Life Sci Inst, Hangzhou, Zhejiang, Peoples R China

14.BGI Shenzhen, BGI Qingdao, Qingdao, Shandong, Peoples R China

15.BGI Hangzhou, Hangzhou, Zhejiang, Peoples R China

16.Zhejiang Univ, Sch Med, Hangzhou, Zhejiang, Peoples R China

17.Fudan Univ, Sch Life Sci, Ctr Evolutionary Biol, Collaborat Innovat Ctr Genet & Dev,State Key Lab G, Shanghai, Peoples R China

18.Fudan Univ, Human Phenome Inst, Zhangjiang Fudan Int Innovat Ctr, Shanghai, Peoples R China

19.Fudan Univ, Minist Educ, Key Lab Contemporary Anthropol, Shanghai, Peoples R China

20.Jiangsu Normal Univ, Sch Life Sci, Int Joint Ctr Genom Jiangsu Prov, Jiangsu Key Lab Phylogen & Comparat Genom, Xuzhou, Jiangsu, Peoples R China

21.Fudan Univ, Zhongshan Hosp, Dept Liver Surg, Shanghai, Peoples R China

22.Fudan Univ, Zhongshan Hosp, Transplantat Liver Canc Inst, Shanghai, Peoples R China

23.Chinese Acad Sci, Ctr Excellence Anim Evolut & Genet, Kunming, Yunnan, Peoples R China

24.Chinese Acad Sci, Kunming Inst Zool, State Key Lab Genet Resources & Evolut, Kunming, Yunnan, Peoples R China

期刊名称：CELL RESEARCH （ 影响因子：44.1； 五年影响因子：39.3 ）

ISSN： 1001-0602

年卷期： 2023 年

页码：

收录情况： SCI

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.