Haplotype-resolved de novo assembly of a Tujia genome suggests the necessity for high-quality population-specific genome references

doi:10.1016/j.cels.2022.01.006

	Haplotype-resolved de novo assembly of a Tujia genome suggests the necessity for high-quality population-specific genome references
	Lou, Haiyi 1; Gao, Yang2,3 ; Xie, Bo 3; Wang, Yimin 3; Zhang, Haikuan 4; Shi, Miao 4; Ma, Sen 3; Zhang, Xiaoxi2,3 ; Liu, Chang 3; Xu, Shuhua1,2,3,5,6,7,8,9,10
	2022-04-20
发表期刊	CELL SYSTEMS (IF:9.0[JCR-2023],11.1[5-Year])
ISSN	2405-4712
EISSN	2405-4720
卷号	13 期号:4
发表状态	已发表
DOI	10.1016/j.cels.2022.01.006
摘要	Even though the human reference genome assembly is continually being improved, it remains debatable whether a population-specific reference is necessary for every ethnic group. Here, we de novo assembled an individual genome (TJ1) from the Tujia population, an ethnic minority group most closely related to the Han Chinese. TJ1 provided a high-quality haplotype-resolved assembly of chromosome-scale with a scaffold N50 size >78 Mb. Compared with GRCh38 and other de novo assemblies, TJ1 improved short-read mapping, enhanced calling precision for structural variants, and detected rare and low-frequency variants. This revealed fine-scale differences between the closely related Han and Tujia populations, such as population-stratified variants of LCT and UBXN8, and improved screening for ancestry informative markers. We demonstrated that TJ1 could reduce false positives in clinical diagnosis and analyzed the PRSS1-PRSS2 locus as a test case. Our results suggest that population-specific assemblies are necessary for genetic and medical analysis, especially when closely related populations are studied. A record of this paper???s transparent peer review process is included in the supplemental information.
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收录类别	SCI ; SCIE
语种	英语
资助项目	National Natural Science Foundation of China (NSFC)[32030020,32041008,31771388,31525014,31871256,31961130380] ; Chinese Academy of Sciences (CAS)["XDPB17","XDB38 000000"] ; National Key Research and Development Program[2016YFC0906403] ; UK Royal Society-Newton Advanced Fellowship[NAF\R1\191094] ; Shanghai Municipal Science and Technology Major Project[2017SHZDZX01]
WOS研究方向	Biochemistry & Molecular Biology ; Cell Biology
WOS类目	Biochemistry & Molecular Biology ; Cell Biology
WOS记录号	WOS:000798439400007
出版者	CELL PRESS
引用统计	正在获取...
文献类型	期刊论文
条目标识符	https://kms.shanghaitech.edu.cn/handle/2MSLDSTB/183414
专题	生命科学与技术学院_博士生生命科学与技术学院_特聘教授组_徐书华组
通讯作者	Lou, Haiyi; Xu, Shuhua
作者单位	1.Fudan Univ, Ctr Evolutionary Biol, Sch Life Sci, State Key Lab Genet Engn,Collaborat Innovat Ctr G, Shanghai 200438, Peoples R China 2.ShanghaiTech Univ, Sch Life Sci & Technol, Shanghai 201210, Peoples R China 3.Chinese Acad Sci, Univ Chinese Acad Sci, Shanghai Inst Nutr & Hlth, Key Lab Computat Biol, Shanghai 200031, Peoples R China 4.Berry Genom, Beijing 102200, Peoples R China 5.Fudan Univ, Zhongshan Hosp, Dept Liver Surg, Shanghai 200032, Peoples R China 6.Fudan Univ, Zhongshan Hosp, Transplantat Liver Canc Inst, Shanghai 200032, Peoples R China 7.Chinese Acad Sci, Ctr Excellence Anim Evolut & Genet, Kunming 650223, Yunnan, Peoples R China 8.Jiangsu Normal Univ, Sch Life Sci, Jiangsu Key Lab Phylogen & Comparat Genom, Xuzhou 221116, Jiangsu, Peoples R China 9.Zhengzhou Univ, Henan Inst Med & Pharmaceut Sci, Zhengzhou 450052, Peoples R China 10.Fudan Univ, Human Phenome Inst, Minist Educ, Key Lab Contemporary Anthropol, Shanghai 201203, Peoples R China
通讯作者单位	生命科学与技术学院
推荐引用方式 GB/T 7714	Lou, Haiyi,Gao, Yang,Xie, Bo,et al. Haplotype-resolved de novo assembly of a Tujia genome suggests the necessity for high-quality population-specific genome references[J]. CELL SYSTEMS,2022,13(4).
APA	Lou, Haiyi.,Gao, Yang.,Xie, Bo.,Wang, Yimin.,Zhang, Haikuan.,...&Xu, Shuhua.(2022).Haplotype-resolved de novo assembly of a Tujia genome suggests the necessity for high-quality population-specific genome references.CELL SYSTEMS,13(4).
MLA	Lou, Haiyi,et al."Haplotype-resolved de novo assembly of a Tujia genome suggests the necessity for high-quality population-specific genome references".CELL SYSTEMS 13.4(2022).