An efficient pipeline for ancient DNA mapping and recovery of endogenous ancient DNA from whole-genome sequencing data

doi:10.1002/ece3.7056

IVPP-IR > 中科院古脊椎所（2000年以后）

	An efficient pipeline for ancient DNA mapping and recovery of endogenous ancient DNA from whole-genome sequencing data
	Xu, Wenhao 1,2; Lin, Yu 3,4; Zhao, Keliang5 ; Li, Haimeng 3,6; Tian, Yinping 3; Ngatia, Jacob Njaramba 7; Ma, Yue 7; Sahu, Sunil Kumar 3; Guo, Huabing 8; Guo, Xiaosen 3,9; Xu, Yan Chun 7; Liu, Huan 3,10; Kristiansen, Karsten 3,10; Lan, Tianming 3,10; Zhou, Xinying1,5
	2021
发表期刊	ECOLOGY AND EVOLUTION
ISSN	2045-7758
卷号	11 期号:1 页码:390-401
摘要	Ancient DNA research has developed rapidly over the past few decades due to improvements in PCR and next-generation sequencing (NGS) technologies, but challenges still exist. One major challenge in relation to ancient DNA research is to recover genuine endogenous ancient DNA sequences from raw sequencing data. This is often difficult due to degradation of ancient DNA and high levels of contamination, especially homologous contamination that has extremely similar genetic background with that of the real ancient DNA. In this study, we collected whole-genome sequencing (WGS) data from 6 ancient samples to compare different mapping algorithms. To further explore more effective methods to separate endogenous DNA from homologous contaminations, we attempted to recover reads based on ancient DNA specific characteristics of deamination, depurination, and DNA fragmentation with different parameters. We propose a quick and improved pipeline for separating endogenous ancient DNA while simultaneously decreasing homologous contaminations to very low proportions. Our goal in this research was to develop useful recommendations for ancient DNA mapping and for separation of endogenous DNA to facilitate future studies of ancient DNA.
关键词	ancient DNA BWA mem deamination DNA damage genome mapping
DOI	10.1002/ece3.7056
关键词[WOS]	POPULATION HISTORY ; READ ALIGNMENT ; EXTINCT ; DAMAGE
收录类别	SCI
语种	英语
资助项目	Shenzhen Municipal Government of China[JCYJ20170817145132389] ; Strategic Priority Research Program of the Chinese Academy of Sciences[XDB 26000000] ; Guangdong Provincial Key Laboratory of Genome Read and Write[2017B030301011] ; Fundamental Research Funds for Central Universities[DL10DA01]
WOS研究方向	Environmental Sciences & Ecology ; Evolutionary Biology
WOS类目	Ecology ; Evolutionary Biology
WOS记录号	WOS:000600540600001
出版者	WILEY
引用统计
文献类型	期刊论文
条目标识符	http://119.78.100.205/handle/311034/18803
专题	中科院古脊椎所（2000年以后）
通讯作者	Lan, Tianming; Zhou, Xinying
作者单位	1.Chinese Acad Sci, Inst Vertebrate Paleontol & Paleoanthropol, 142 Xizhimenwai St, Beijing 100044, Peoples R China 2.Huazhong Agr Univ, Coll Informat, Wuhan, Peoples R China 3.BGI Shenzhen, State Key Lab Agr Genom, Shenzhen 518083, Peoples R China 4.BGI Shenzhen, Guangdong Prov Key Lab Genome Read & Write, Shenzhen, Peoples R China 5.CAS Ctr Excellence Life & Paleoenvironm, Beijing, Peoples R China 6.Univ Chinese Acad Sci, Sch Future Technol, Beijing, Peoples R China 7.Northeast Forestry Univ, Coll Wildlife Resources, Harbin, Peoples R China 8.Forest Inventory & Planning Inst Jilin Prov, Changchun, Peoples R China 9.BGI Shenzhen, Guangdong Prov Acad Workstat BGI Synthet Genom, Shenzhen, Peoples R China 10.Univ Copenhagen, Lab Genom & Mol Biomed, Dept Biol, Copenhagen, Denmark
推荐引用方式 GB/T 7714	Xu, Wenhao,Lin, Yu,Zhao, Keliang,et al. An efficient pipeline for ancient DNA mapping and recovery of endogenous ancient DNA from whole-genome sequencing data[J]. ECOLOGY AND EVOLUTION,2021,11(1):390-401.
APA	Xu, Wenhao.,Lin, Yu.,Zhao, Keliang.,Li, Haimeng.,Tian, Yinping.,...&Zhou, Xinying.(2021).An efficient pipeline for ancient DNA mapping and recovery of endogenous ancient DNA from whole-genome sequencing data.ECOLOGY AND EVOLUTION,11(1),390-401.
MLA	Xu, Wenhao,et al."An efficient pipeline for ancient DNA mapping and recovery of endogenous ancient DNA from whole-genome sequencing data".ECOLOGY AND EVOLUTION 11.1(2021):390-401.

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