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

文献类型：期刊论文

作者Xu, Wenhao9,10; Lin, Yu7,8; Zhao, Keliang6; Li, Haimeng5,8; Tian, Yinping8; Ngatia, Jacob Njaramba4; Ma, Yue4; Sahu, Sunil Kumar8; Guo, Huabing3; Guo, Xiaosen2,8
刊名ECOLOGY AND EVOLUTION
出版日期2021
卷号11期号:1页码:390-401
关键词ancient DNA BWA mem deamination DNA damage genome mapping
ISSN号2045-7758
DOI10.1002/ece3.7056
英文摘要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.
WOS关键词POPULATION HISTORY ; READ ALIGNMENT ; EXTINCT ; DAMAGE
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
语种英语
WOS记录号WOS:000600540600001
出版者WILEY
源URL[http://119.78.100.205/handle/311034/18802]  
专题古脊椎动物与古人类研究所_图书馆1
通讯作者Lan, Tianming; Zhou, Xinying
作者单位1.Univ Copenhagen, Lab Genom & Mol Biomed, Dept Biol, Copenhagen, Denmark
2.BGI Shenzhen, Guangdong Prov Acad Workstat BGI Synthet Genom, Shenzhen, Peoples R China
3.Forest Inventory & Planning Inst Jilin Prov, Changchun, Peoples R China
4.Northeast Forestry Univ, Coll Wildlife Resources, Harbin, Peoples R China
5.Univ Chinese Acad Sci, Sch Future Technol, Beijing, Peoples R China
6.CAS Ctr Excellence Life & Paleoenvironm, Beijing, Peoples R China
7.BGI Shenzhen, Guangdong Prov Key Lab Genome Read & Write, Shenzhen, Peoples R China
8.BGI Shenzhen, State Key Lab Agr Genom, Shenzhen 518083, Peoples R China
9.Huazhong Agr Univ, Coll Informat, Wuhan, Peoples R China
10.Chinese Acad Sci, Inst Vertebrate Paleontol & Paleoanthropol, 142 Xizhimenwai St, Beijing 100044, Peoples R China
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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来源：古脊椎动物与古人类研究所

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