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Molecular ecology resources2021; 22(3); 891-907; doi: 10.1111/1755-0998.13518

Performance and automation of ancient DNA capture with RNA hyRAD probes.

Abstract: DNA hybridization-capture techniques allow researchers to focus their sequencing efforts on preselected genomic regions. This feature is especially useful when analysing ancient DNA (aDNA) extracts, which are often dominated by exogenous environmental sources. Here, we assessed, for the first time, the performance of hyRAD as an inexpensive and design-free alternative to commercial capture protocols to obtain authentic aDNA data from osseous remains. HyRAD relies on double enzymatic restriction of fresh DNA extracts to produce RNA probes that cover only a fraction of the genome and can serve as baits for capturing homologous fragments from aDNA libraries. We found that this approach could retrieve sequence data from horse remains coming from a range of preservation environments, including beyond radiocarbon range, yielding up to 146.5-fold on-target enrichment for aDNA extracts showing extremely low endogenous content (20%-30%), while the fraction of endogenous reads mapping on- and off-target was relatively insensitive to the original endogenous DNA content. Procedures based on two instead of a single round of capture increased on-target coverage up to 3.6-fold. Additionally, we used methylation-sensitive restriction enzymes to produce probes targeting hypomethylated regions, which improved data quality by reducing post-mortem DNA damage and mapping within multicopy regions. Finally, we developed a fully automated hyRAD protocol utilizing inexpensive robotic platforms to facilitate capture processing. Overall, our work establishes hyRAD as a cost-effective strategy to recover a set of shared orthologous variants across multiple ancient samples.
© 2021 The Authors. Molecular Ecology Resources published by John Wiley & Sons Ltd.
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Publication Date: 2021-10-15 PubMed ID: 34582623PubMed Central: PMC9291508DOI: 10.1111/1755-0998.13518Google Scholar: Lookup
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  • Journal Article

Summary

This research summary has been generated with artificial intelligence and may contain errors and omissions. Refer to the original study to confirm details provided. Submit correction.

The study presents the first evaluation of hyRAD, an economical and easily customizable alternative to standard commercial protocols, to extract ancient DNA data from bone remains. The research confirms hyRAD’s effectiveness in retrieving sequence data from horse remains originating across different preservation environments, making it a cost-effective tool for capturing shared genetic variants across multiple ancient samples.

Underlying Concept

  • HyRAD is described as an inexpensive alternative to standard commercial protocols for capturing specific genomic regions in ancient DNA analyses, which are typically populated by foreign environmental elements.
  • The method uses double enzymatic restriction processes on fresh DNA extracts to produce RNA probes, which only target a fraction of the genome. These probes act as baits in capturing matching fragments in ancient DNA libraries.

Evaluation and Performance

  • The evaluation was carried out using horse remains from various preservation environments, including some that are beyond the capacity of radiocarbon dating methods.
  • The on-target enrichment achieved was up to 146.5-fold for ancient DNA extracts with very low inherent content (<1%).
  • For samples with good DNA preservation (>20%-30%), however, the performance was less significant.
  • Interestingly, the fraction of endogenous reads mapping on- and off-target was not greatly affected by the initial endogenous DNA content.
  • Procedures that employs two capture rounds instead of just one enhanced on-target coverage by up to 3.6 times.

Improvements and Innovations

  • The researchers also used methylation-sensitive restriction enzymes to create probes that target hypomethylated regions, thus improving data quality by reducing post-mortem DNA damage and sequence mapping within multicopy regions.
  • An entirely automated hyRAD protocol was developed which utilizes economical robotic platforms to enable easier capture processing.

Conclusion

  • Overall, the research validates hyRAD as a cost-effective strategy for recovering shared orthologous variants across multiple ancient samples.

Cite This Article

APA
Suchan T, Kusliy MA, Khan N, Chauvey L, Tonasso-Calvière L, Schiavinato S, Southon J, Keller M, Kitagawa K, Krause J, Bessudnov AN, Bessudnov AA, Graphodatsky AS, Valenzuela-Lamas S, Wilczyński J, Pospuła S, Tunia K, Nowak M, Moskal-delHoyo M, Tishkin AA, Pryor AJE, Outram AK, Orlando L. (2021). Performance and automation of ancient DNA capture with RNA hyRAD probes. Mol Ecol Resour, 22(3), 891-907. https://doi.org/10.1111/1755-0998.13518

Publication

Molecular ecology resources
ISSN: 1755-0998
NlmUniqueID: 101465604
Country: England
Language: English
Volume: 22
Issue: 3
Pages: 891-907

Researcher Affiliations

Suchan, Tomasz
  • Centre d'Anthropobiologie et de Génomique de Toulouse (CAGT), Université Paul Sabatier, Faculté de Médecine Purpan, Toulouse, France.
Kusliy, Mariya A
  • Centre d'Anthropobiologie et de Génomique de Toulouse (CAGT), Université Paul Sabatier, Faculté de Médecine Purpan, Toulouse, France.
  • Department of the Diversity and Evolution of Genomes, Institute of Molecular and Cellular Biology SB RAS, Novosibirsk, Russia.
Khan, Naveed
  • Centre d'Anthropobiologie et de Génomique de Toulouse (CAGT), Université Paul Sabatier, Faculté de Médecine Purpan, Toulouse, France.
  • Department of Biotechnology, Abdul Wali Khan University, Mardan, Pakistan.
Chauvey, Loreleï
  • Centre d'Anthropobiologie et de Génomique de Toulouse (CAGT), Université Paul Sabatier, Faculté de Médecine Purpan, Toulouse, France.
Tonasso-Calvière, Laure
  • Centre d'Anthropobiologie et de Génomique de Toulouse (CAGT), Université Paul Sabatier, Faculté de Médecine Purpan, Toulouse, France.
Schiavinato, Stéphanie
  • Centre d'Anthropobiologie et de Génomique de Toulouse (CAGT), Université Paul Sabatier, Faculté de Médecine Purpan, Toulouse, France.
Southon, John
  • Earth System Science Department, University of California, Irvine, Irvine, California, USA.
Keller, Marcel
  • Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu, Estonia.
Kitagawa, Keiko
  • SFB 1070 ResourceCultures, University of Tübingen, Tübingen, Germany.
  • Department of Early Prehistory and Quaternary Ecology, University of Tübingen, Tübingen, Germany.
Krause, Johannes
  • Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany.
  • Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.
Bessudnov, Alexander N
  • Lipetsk State Pedagogical P. Semyonov-Tyan-Shansky University, Lipetsk, Russia.
Bessudnov, Alexander A
  • Institute for the History of Material Culture, Russian Academy of Sciences, Saint Petersburg, Russia.
Graphodatsky, Alexander S
  • Department of the Diversity and Evolution of Genomes, Institute of Molecular and Cellular Biology SB RAS, Novosibirsk, Russia.
Valenzuela-Lamas, Silvia
  • Institución Milà i Fontanals de Humanidades, Consejo Superior de Investigaciones Científicas (IMF-CSIC), Barcelona, Spain.
Wilczyński, Jarosław
  • Institute of Systematics and Evolution of Animals, Polish Academy of Sciences, Kraków, Poland.
Pospuła, Sylwia
  • Institute of Systematics and Evolution of Animals, Polish Academy of Sciences, Kraków, Poland.
Tunia, Krzysztof
  • Institute of Archaeology and Ethnology, Polish Academy of Sciences, Kraków, Poland.
Nowak, Marek
  • Institute of Archaeology, Jagiellonian University, Kraków, Poland.
Moskal-delHoyo, Magdalena
  • W. Szafer Institute of Botany, Polish Academy of Sciences, Kraków, Poland.
Tishkin, Alexey A
  • Department of Archaeology, Ethnography and Museology, Altai State University, Barnaul, Russia.
Pryor, Alexander J E
  • Department of Archaeology, University of Exeter, Exeter, UK.
Outram, Alan K
  • Department of Archaeology, University of Exeter, Exeter, UK.
Orlando, Ludovic
  • Centre d'Anthropobiologie et de Génomique de Toulouse (CAGT), Université Paul Sabatier, Faculté de Médecine Purpan, Toulouse, France.

MeSH Terms

  • Animals
  • Automation
  • DNA, Ancient
  • Horses / genetics
  • RNA / genetics
  • RNA Probes
  • Sequence Analysis, DNA / methods

Grant Funding

  • CNRS International Research Project (IRP AMADEUS)
  • CNRS Programme de Recherche Conjoint (PRC)
  • 681605 / H2020 European Research Council
  • 797449 / H2020 Marie Sku0142odowska-Curie Actions
  • 19-59-15001 / Russian Foundation for Basic Research
  • University Paul Sabatier IDEX Chaire d'Excellence (OURASI)

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