Genomics, Proteomics & Bioinformatics (Dec 2023)
T2T-YAO: A Telomere-to-telomere Assembled Diploid Reference Genome for Han Chinese
- Yukun He,
- Yanan Chu,
- Shuming Guo,
- Jiang Hu,
- Ran Li,
- Yali Zheng,
- Xinqian Ma,
- Zhenglin Du,
- Lili Zhao,
- Wenyi Yu,
- Jianbo Xue,
- Wenjie Bian,
- Feifei Yang,
- Xi Chen,
- Pingan Zhang,
- Rihan Wu,
- Yifan Ma,
- Changjun Shao,
- Jing Chen,
- Jian Wang,
- Jiwei Li,
- Jing Wu,
- Xiaoyi Hu,
- Qiuyue Long,
- Mingzheng Jiang,
- Hongli Ye,
- Shixu Song,
- Guangyao Li,
- Yue Wei,
- Yu Xu,
- Yanliang Ma,
- Yanwen Chen,
- Keqiang Wang,
- Jing Bao,
- Wen Xi,
- Fang Wang,
- Wentao Ni,
- Moqin Zhang,
- Yan Yu,
- Shengnan Li,
- Yu Kang,
- Zhancheng Gao
Affiliations
- Yukun He
- Department of Respiratory and Critical Care Medicine, Peking University People’s Hospital, Beijing 100044, China
- Yanan Chu
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
- Shuming Guo
- Linfen Clinical Medicine Research Center, Linfen 041000, China; Institute of Chest and Lung Diseases, Shanxi Medical University, Taiyuan 030001, China
- Jiang Hu
- GrandOmics Biosciences Co., Ltd, Wuhan 430076, China
- Ran Li
- Department of Respiratory and Critical Care Medicine, Peking University People’s Hospital, Beijing 100044, China; Beijing Key Laboratory of Genome and Precision Medicine Technologies, Beijing 100101, China
- Yali Zheng
- Department of Respiratory, Critical Care and Sleep Medicine, Xiang’an Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen 361101, China
- Xinqian Ma
- Department of Respiratory and Critical Care Medicine, Peking University People’s Hospital, Beijing 100044, China; Beijing Key Laboratory of Genome and Precision Medicine Technologies, Beijing 100101, China
- Zhenglin Du
- Institute of PSI Genomics, Wenzhou 325024, China
- Lili Zhao
- Department of Respiratory and Critical Care Medicine, Peking University People’s Hospital, Beijing 100044, China; Beijing Key Laboratory of Genome and Precision Medicine Technologies, Beijing 100101, China
- Wenyi Yu
- Department of Respiratory and Critical Care Medicine, Peking University People’s Hospital, Beijing 100044, China; Beijing Key Laboratory of Genome and Precision Medicine Technologies, Beijing 100101, China
- Jianbo Xue
- Department of Respiratory and Critical Care Medicine, Peking University People’s Hospital, Beijing 100044, China; Beijing Key Laboratory of Genome and Precision Medicine Technologies, Beijing 100101, China
- Wenjie Bian
- Department of Respiratory and Critical Care Medicine, Peking University People’s Hospital, Beijing 100044, China; Beijing Key Laboratory of Genome and Precision Medicine Technologies, Beijing 100101, China
- Feifei Yang
- Department of Respiratory and Critical Care Medicine, Peking University People’s Hospital, Beijing 100044, China; Beijing Key Laboratory of Genome and Precision Medicine Technologies, Beijing 100101, China
- Xi Chen
- Department of Respiratory and Critical Care Medicine, Peking University People’s Hospital, Beijing 100044, China; Beijing Key Laboratory of Genome and Precision Medicine Technologies, Beijing 100101, China
- Pingan Zhang
- Department of Respiratory and Critical Care Medicine, Peking University People’s Hospital, Beijing 100044, China; Beijing Key Laboratory of Genome and Precision Medicine Technologies, Beijing 100101, China
- Rihan Wu
- Department of Respiratory and Critical Care Medicine, Peking University People’s Hospital, Beijing 100044, China; Beijing Key Laboratory of Genome and Precision Medicine Technologies, Beijing 100101, China
- Yifan Ma
- Department of Respiratory and Critical Care Medicine, Peking University People’s Hospital, Beijing 100044, China; Beijing Key Laboratory of Genome and Precision Medicine Technologies, Beijing 100101, China
- Changjun Shao
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
- Jing Chen
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
- Jian Wang
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
- Jiwei Li
- Department of Respiratory, Critical Care and Sleep Medicine, Xiang’an Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen 361101, China
- Jing Wu
- Department of Respiratory, Critical Care and Sleep Medicine, Xiang’an Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen 361101, China
- Xiaoyi Hu
- Department of Respiratory, Critical Care and Sleep Medicine, Xiang’an Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen 361101, China
- Qiuyue Long
- Department of Respiratory, Critical Care and Sleep Medicine, Xiang’an Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen 361101, China
- Mingzheng Jiang
- Department of Respiratory, Critical Care and Sleep Medicine, Xiang’an Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen 361101, China
- Hongli Ye
- Department of Respiratory, Critical Care and Sleep Medicine, Xiang’an Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen 361101, China
- Shixu Song
- Department of Respiratory, Critical Care and Sleep Medicine, Xiang’an Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen 361101, China
- Guangyao Li
- Linfen Clinical Medicine Research Center, Linfen 041000, China
- Yue Wei
- Linfen Clinical Medicine Research Center, Linfen 041000, China
- Yu Xu
- Beijing Jishuitan Hospital, Capital Medical University, Beijing 100035, China
- Yanliang Ma
- Department of Respiratory and Critical Care Medicine, Peking University People’s Hospital, Beijing 100044, China; Beijing Key Laboratory of Genome and Precision Medicine Technologies, Beijing 100101, China
- Yanwen Chen
- Department of Respiratory and Critical Care Medicine, Peking University People’s Hospital, Beijing 100044, China; Beijing Key Laboratory of Genome and Precision Medicine Technologies, Beijing 100101, China
- Keqiang Wang
- Department of Respiratory and Critical Care Medicine, Peking University People’s Hospital, Beijing 100044, China; Beijing Key Laboratory of Genome and Precision Medicine Technologies, Beijing 100101, China
- Jing Bao
- Department of Respiratory and Critical Care Medicine, Peking University People’s Hospital, Beijing 100044, China; Beijing Key Laboratory of Genome and Precision Medicine Technologies, Beijing 100101, China
- Wen Xi
- Department of Respiratory and Critical Care Medicine, Peking University People’s Hospital, Beijing 100044, China; Beijing Key Laboratory of Genome and Precision Medicine Technologies, Beijing 100101, China
- Fang Wang
- Department of Respiratory and Critical Care Medicine, Peking University People’s Hospital, Beijing 100044, China; Beijing Key Laboratory of Genome and Precision Medicine Technologies, Beijing 100101, China
- Wentao Ni
- Department of Respiratory and Critical Care Medicine, Peking University People’s Hospital, Beijing 100044, China; Beijing Key Laboratory of Genome and Precision Medicine Technologies, Beijing 100101, China
- Moqin Zhang
- Department of Respiratory and Critical Care Medicine, Peking University People’s Hospital, Beijing 100044, China; Beijing Key Laboratory of Genome and Precision Medicine Technologies, Beijing 100101, China
- Yan Yu
- Department of Respiratory and Critical Care Medicine, Peking University People’s Hospital, Beijing 100044, China; Beijing Key Laboratory of Genome and Precision Medicine Technologies, Beijing 100101, China
- Shengnan Li
- Department of Respiratory and Critical Care Medicine, Peking University People’s Hospital, Beijing 100044, China; Beijing Key Laboratory of Genome and Precision Medicine Technologies, Beijing 100101, China
- Yu Kang
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100490, China; Corresponding authors.
- Zhancheng Gao
- Department of Respiratory and Critical Care Medicine, Peking University People’s Hospital, Beijing 100044, China; Institute of Chest and Lung Diseases, Shanxi Medical University, Taiyuan 030001, China; Beijing Key Laboratory of Genome and Precision Medicine Technologies, Beijing 100101, China; Corresponding authors.
- Journal volume & issue
-
Vol. 21,
no. 6
pp. 1085 – 1100
Abstract
Since its initial release in 2001, the human reference genome has undergone continuous improvement in quality, and the recently released telomere-to-telomere (T2T) version — T2T-CHM13 — reaches its highest level of continuity and accuracy after 20 years of effort by working on a simplified, nearly homozygous genome of a hydatidiform mole cell line. Here, to provide an authentic complete diploid human genome reference for the Han Chinese, the largest population in the world, we assembled the genome of a male Han Chinese individual, T2T-YAO, which includes T2T assemblies of all the 22 + X + M and 22 + Y chromosomes in both haploids. The quality of T2T-YAO is much better than those of all currently available diploid assemblies, and its haploid version, T2T-YAO-hp, generated by selecting the better assembly for each autosome, reaches the top quality of fewer than one error per 29.5 Mb, even higher than that of T2T-CHM13. Derived from an individual living in the aboriginal region of the Han population, T2T-YAO shows clear ancestry and potential genetic continuity from the ancient ancestors. Each haplotype of T2T-YAO possesses ∼ 330-Mb exclusive sequences, ∼ 3100 unique genes, and tens of thousands of nucleotide and structural variations as compared with CHM13, highlighting the necessity of a population-stratified reference genome. The construction of T2T-YAO, an accurate and authentic representative of the Chinese population, would enable precise delineation of genomic variations and advance our understandings in the hereditability of diseases and phenotypes, especially within the context of the unique variations of the Chinese population.
