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.
Highlights
Under favourable conditions DNA fragments can survive in plant [1] and animal tissues [2] for hundreds of thousands of years providing a molecular record of the past
The typical sign of depurination, which is the excess of both adenine (A) and guanine (G) before DNA breaking points, has been detected by high throughput sequencing (HTS) in libraries constructed from ancient DNA (aDNA) [9]
We used a group of multiple species herbarium samples and freshly prepared herbarium samples of Arabidopsis thaliana dried using a wooden press
Summary
Under favourable conditions DNA fragments can survive in plant [1] and animal tissues [2] for hundreds of thousands of years providing a molecular record of the past. The vast majority of ancient DNA (aDNA) studies have focused on animal remains, whereas plant remains have received less attention [3] despite the abundance of historic plant specimens. The aDNA comes in small fragment sizes [5] and holds various modifications that distinguish it from DNA extracted from fresh tissue [6]. DNA degradation is marked by an increase of cytosine (C) to thymine (T) substitutions towards the end of aDNA fragments. This pattern results from spontaneous deamination of C residues to uracils (U) that are read as T by the polymerase and occur in higher proportion in single-stranded DNA overhangs [9,10]. A biochemical definition of aDNA includes all above-mentioned characteristics but does not delineate a time boundary between ancient and modern DNA [3]
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