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An Efficient Pipeline for Ancient DNA Mapping and Recovery of Endogenous Ancient DNA from Whole-Genome Sequencing Data
  • +10
  • Wenhao Xu,
  • Yu Lin,
  • Ke Zhao,
  • Hai Li,
  • Yin Tian,
  • Jacob Ngatia,
  • Yue Ma,
  • Hua Guo,
  • Xiao Guo,
  • Yan Xu,
  • Karsten Kristiansen,
  • Tian Lan,
  • Xin Zhou
Wenhao Xu
Chinese Academy of Sciences
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Yu Lin
BGI-Shenzhen
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Ke Zhao
Chinese Academy of Sciences
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Hai Li
BGI-Shenzhen
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Yin Tian
BGI-Shenzhen
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Jacob Ngatia
Northeast Forestry University
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Yue Ma
Northeast Forestry University
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Hua Guo
Forest Inventory and Planning Institute of Jilin Province
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Xiao Guo
BGI-Shenzhen
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Yan Xu
Northeast Forestry University
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Karsten Kristiansen
BGI-Shenzhen
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Tian Lan
BGI-Shenzhen
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Xin Zhou
Chinese Academy of Sciences
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Peer review status:IN REVISION

16 Apr 2020Submitted to Ecology and Evolution
17 Apr 2020Submission Checks Completed
17 Apr 2020Assigned to Editor
20 Apr 2020Reviewer(s) Assigned
25 May 2020Review(s) Completed, Editorial Evaluation Pending
28 May 2020Editorial Decision: Revise Minor
02 Jul 20201st Revision Received
03 Jul 2020Submission Checks Completed
03 Jul 2020Assigned to Editor
03 Jul 2020Review(s) Completed, Editorial Evaluation Pending
05 Aug 2020Editorial Decision: Revise Minor

Abstract

Ancient DNA research has developed rapidly over the past few decades due to the improvement 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 the raw sequencing data. This is often difficult due to the degradation of ancient DNA and high levels of contamination, especially homologous contamination. 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 the homologous contaminations, we attempted to recover reads based on the 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 the homologous contaminations to a very low proportion. Overall, these recommendations for ancient DNA mapping and separation of endogenous DNA in this study could facilitate future studies of ancient DNA.