T2T-YAO: A Telomere-to-telomere Assembled Diploid Reference Genome for Han Chinese.

IF 11.5 2区 生物学 Q1 GENETICS & HEREDITY
Genomics, Proteomics & Bioinformatics Pub Date : 2023-12-01 Epub Date: 2023-08-16 DOI:10.1016/j.gpb.2023.08.001
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
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引用次数: 0

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.

T2T-YAO:从端粒到端粒的汉族二倍体参考基因组。
自2001年首次发布以来,人类参考基因组的质量不断提高,最近发布的端粒到端粒(T2T)版本--T2T-CHM13--经过20年的努力,在简化的、近乎同源的水滴形痣细胞系基因组的基础上,达到了连续性和准确性的最高水平。在这里,为了给世界上人口最多的汉族提供一个真实完整的二倍体人类基因组参考,我们组装了一个汉族男性个体的基因组 T2T-YAO,其中包括单倍体中所有 22 + X + M 和 22 + Y 染色体的 T2T 组装。T2T-YAO 的质量远远优于目前所有的二倍体基因组,其单倍体版本 T2T-YAO-hp 是通过为每个常染色体选择更好的基因组而生成的,达到了每 29.5 Mb 只有不到一个错误的最高质量,甚至高于 T2T-CHM13 的质量。T2T-YAO 源自一个生活在汉族原住民地区的个体,显示出与远古祖先清晰的祖先关系和潜在的遗传连续性。与 CHM13 相比,T2T-YAO 的每个单倍型拥有 330-Mb 的独有序列,3100 个独特基因,以及数以万计的核苷酸和结构变异,凸显了人群分层参考基因组的必要性。T2T-YAO是一个真正准确和真实的中国人群代表,它的构建将有助于精确划分基因组变异,推进我们对疾病和表型遗传性的理解,尤其是在中国人群独特变异的背景下。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
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来源期刊
Genomics, Proteomics & Bioinformatics
Genomics, Proteomics & Bioinformatics Biochemistry, Genetics and Molecular Biology-Biochemistry
CiteScore
14.30
自引率
4.20%
发文量
844
审稿时长
61 days
期刊介绍: Genomics, Proteomics and Bioinformatics (GPB) is the official journal of the Beijing Institute of Genomics, Chinese Academy of Sciences / China National Center for Bioinformation and Genetics Society of China. It aims to disseminate new developments in the field of omics and bioinformatics, publish high-quality discoveries quickly, and promote open access and online publication. GPB welcomes submissions in all areas of life science, biology, and biomedicine, with a focus on large data acquisition, analysis, and curation. Manuscripts covering omics and related bioinformatics topics are particularly encouraged. GPB is indexed/abstracted by PubMed/MEDLINE, PubMed Central, Scopus, BIOSIS Previews, Chemical Abstracts, CSCD, among others.
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