Skip to main content
SpringerLink
Log in
SpringerLink
Log in

Double-Stranded Library Preparation for Ancient and Other Degraded Samples

  • Protocol
  • First Online:
Ancient DNA

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1963))

Abstract

High-throughput sequencing (HTS) allows fast and cost-efficient sequencing of ancient DNA (aDNA) without prior information about what sequences should be targeted. One necessary step for HTS is the preparation of a sequencing library. Commercial kits are available for this purpose, but many of these are not suitable for aDNA or other types of damaged DNA. Here, we outline a protocol for HTS library preparation that is optimized for ancient DNA. We report the library conversion rate for a range of input template and adapter concentrations. Our results show that the protocol performs at a high efficiency.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Protocol
USD 49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 119.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Hardcover Book
USD 159.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  1. Green RE, Krause J, Ptak SE et al (2006) Analysis of one million base pairs of Neanderthal DNA. Nature 444:330–336. https://doi.org/10.1038/nature05336

    Article  CAS  PubMed  Google Scholar 

  2. Hofreiter M, Paijmans JLA, Goodchild H et al (2014) The future of ancient DNA: technical advances and conceptual shifts. BioEssays 37:284–293. https://doi.org/10.1002/bies.201400160

    Article  PubMed  Google Scholar 

  3. Noonan JP, Priest JR, Rohland N et al (2012) Genomic sequencing of Pleistocene cave bears. Science 597:597–599. https://doi.org/10.1126/science.1113485

    Article  CAS  Google Scholar 

  4. Briggs AW, Heyn P (2012) Preparation of next-generation sequencing libraries from damaged DNA. Methods Mol Biol 840:143–154

    Article  CAS  Google Scholar 

  5. Gansauge M-T, Meyer M (2013) Single-stranded DNA library preparation for the sequencing of ancient or damaged DNA. Nat Protoc 8:737–748. https://doi.org/10.1038/nprot.2013.038

    Article  CAS  PubMed  Google Scholar 

  6. Fortes GG, Paijmans JLA (2015) Analysis of whole mitogenomes from ancient samples. Methods Mol Biol 1347:179–195

    Article  CAS  Google Scholar 

  7. Barlow A, Gonzalez Fortes GM, Dalen L et al (2016) Massive influence of DNA isolation and library preparation approaches on palaeogenomic sequencing data. bioRxiv. https://doi.org/10.1101/075911

  8. Brace S, Thomas JA, Dalén L et al (2016) Evolutionary history of the Nesophontidae, the last unplaced recent mammal family. Mol Biol Evol 33:msw186. https://doi.org/10.1093/molbev/msw186

    Article  CAS  Google Scholar 

  9. Gaubert P, Patel R, Veron G et al (2017) Phylogeography of the Small Indian Civet and Origin of Introductions to Western Indian Ocean Islands. J Hered 108:270–279. https://doi.org/10.1093/jhered/esw085

    Article  CAS  PubMed  Google Scholar 

  10. Martins RF, Fickel J, Le M et al (2017) Phylogeography of red muntjacs reveals three distinct mitochondrial lineages. BMC Evol Biol 17:34. https://doi.org/10.1186/s12862-017-0888-0

    Article  PubMed  PubMed Central  Google Scholar 

  11. Palkopoulou E, Mallick S, Skoglund P et al (2015) Complete genomes reveal signatures of demographic and genetic declines in the woolly mammoth. Curr Biol 25:1395–1400. https://doi.org/10.1016/j.cub.2015.04.007

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. Patel RP, Förster DW, Kitchener AC et al (2016) Two species of Southeast Asian cats in the genus Catopuma with diverging histories: an island endemic forest specialist and a widespread habitat generalist. R Soc Open Sci 3:160350. https://doi.org/10.1098/rsos.160350

    Article  PubMed  PubMed Central  Google Scholar 

  13. Meyer M, Kircher M (2010) Illumina sequencing library preparation for highly multiplexed target capture and sequencing. Cold Spring Harb Protoc. https://doi.org/10.1101/pdb.prot5448

  14. Kircher M, Sawyer S, Meyer M (2012) Double indexing overcomes inaccuracies in multiplex sequencing on the Illumina platform. Nucleic Acids Res 40:1–8. https://doi.org/10.1093/nar/gkr771

    Article  CAS  Google Scholar 

  15. Lehman IR (1974) DNA ligase: structure, mechanism, and function

    Google Scholar 

  16. Dabney J, Meyer M (2012) Length and GC-biases during sequencing library amplification: a comparison of various polymerase-buffer systems with ancient and modern DNA sequencing libraries. BioTechniques. https://doi.org/10.2144/000113809

Download references

Author information

Authors and Affiliations

  1. Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany

    Kirstin Henneberger, Axel Barlow & Johanna L. A. Paijmans

Authors
  1. Kirstin Henneberger
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Axel Barlow
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Johanna L. A. Paijmans
    View author publications

    You can also search for this author in PubMed Google Scholar

Editor information

Editors and Affiliations

  1. Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, USA

    Beth Shapiro

  2. Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany

    Axel Barlow

  3. Tromsø University Museum, UiT—The Arctic University of Norway, Tromsø, Norway

    Peter D. Heintzman

  4. Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany

    Michael Hofreiter

  5. Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany

    Johanna L. A. Paijmans

  6. Laboratório Nacional de Computação Científica, Petrópolis, Rio de Janeiro, Brazil

    André E. R. Soares

Rights and permissions

Reprints and permissions

Copyright information

© 2019 Springer Science+Business Media, LLC, part of Springer Nature

About this protocol

Check for updates. Verify currency and authenticity via CrossMark

Cite this protocol

Henneberger, K., Barlow, A., Paijmans, J.L.A. (2019). Double-Stranded Library Preparation for Ancient and Other Degraded Samples. In: Shapiro, B., Barlow, A., Heintzman, P., Hofreiter, M., Paijmans, J., Soares, A. (eds) Ancient DNA. Methods in Molecular Biology, vol 1963. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-9176-1_8

Download citation

  • DOI: https://doi.org/10.1007/978-1-4939-9176-1_8

  • Published:

  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-9175-4

  • Online ISBN: 978-1-4939-9176-1

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics

Search

Navigation