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R Soc Open Sci. 2016 Jun 22;3(6):160239. doi: 10.1098/rsos.160239. eCollection 2016 Jun.

Temporal patterns of damage and decay kinetics of DNA retrieved from plant herbarium specimens.

Author information

1
Research Group for Ancient Genomics and Evolution, Department of Molecular Biology , Max Planck Institute for Developmental Biology , Tuebingen 72076 , Germany.
2
Institute of Archaeological Sciences , University of Tübingen , Tuebingen 72076 , Germany.
3
Department of Molecular Biology , Max Planck Institute for Developmental Biology , Tuebingen 72076 , Germany.
4
Department of Ecology and Evolutionary Biology , Toronto, Ontario , Canada M5S.
5
Department of Ecology and Evolutionary Biology, Toronto, Ontario, CanadaM5S; University of Toronto, Toronto, Ontario, CanadaM5S.
6
Institute of Archaeological Sciences, University of Tübingen, Tuebingen 72076, Germany; Departments of Paleoanthropology and Archaeogenetics, Senckenberg Center for Human Evolution and Paleoenvironment, University of Tübingen, Tuebingen 72076, Germany; Max Planck Institute for the Science of Human History, Jena 07743, Germany.

Abstract

Herbaria archive a record of changes of worldwide plant biodiversity harbouring millions of specimens that contain DNA suitable for genome sequencing. To profit from this resource, it is fundamental to understand in detail the process of DNA degradation in herbarium specimens. We investigated patterns of DNA fragmentation and nucleotide misincorporation by analysing 86 herbarium samples spanning the last 300 years using Illumina shotgun sequencing. We found an exponential decay relationship between DNA fragmentation and time, and estimated a per nucleotide fragmentation rate of 1.66 × 10(-4) per year, which is six times faster than the rate estimated for ancient bones. Additionally, we found that strand breaks occur specially before purines, and that depurination-driven DNA breakage occurs constantly through time and can to a great extent explain decreasing fragment length over time. Similar to what has been found analysing ancient DNA from bones, we found a strong correlation between the deamination-driven accumulation of cytosine to thymine substitutions and time, which reinforces the importance of substitution patterns to authenticate the ancient/historical nature of DNA fragments. Accurate estimations of DNA degradation through time will allow informed decisions about laboratory and computational procedures to take advantage of the vast collection of worldwide herbarium specimens.

KEYWORDS:

DNA damage; DNA decay; ancient DNA; herbarium

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