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Robust DNA Isolation and High-throughput Sequencing Library Construction for Herbarium Specimens
Published on: March 8, 2018
DNA damage in plant herbarium tissue.
Martijn Staats1, Argelia Cuenca, James E Richardson
1Biosystematics Group, Wageningen University, Wageningen, The Netherlands.
Plos One
|December 14, 2011
Summary
Herbarium specimens contain degraded DNA, but this study shows reliable genetic data is obtainable. Most DNA damage occurs during specimen preparation, not long-term storage, with minimal organelle or nuclear genome degradation.
Area of Science:
- Molecular Biology
- Genetics
- Botany
Background:
- Dried plant herbarium specimens are a valuable DNA source but often yield degraded DNA, hindering genetic research.
- DNA post-mortem damage can reduce amplifiable DNA and introduce sequencing errors, necessitating careful assessment.
Purpose of the Study:
- To quantitatively and qualitatively assess DNA post-mortem damage in herbarium specimens.
- To determine the accuracy of molecular data obtained from herbarium samples.
- To evaluate DNA degradation and miscoding lesions in relation to specimen preparation and storage duration.
Main Methods:
- Utilized 454-sequencing of amplicons from plastid, mitochondrial, and nuclear DNA to assess miscoding lesions.
- Employed quantitative real-time PCR to evaluate DNA degradation from strand breaks.
- Compared fresh and herbarium specimens from the same individuals to quantify post-mortem damage.
Main Results:
- DNA quantity was reduced to 2.4-3.8% after preparation and 1.0-1.3% after long-term storage, indicating most damage occurs early.
- No preferential degradation was observed between organelle (plastid, mitochondrial) and nuclear genomes.
- Increased C→T/G→A transitions in old plastid DNA suggest cytosine deamination during storage.
Conclusions:
- Reliable sequence data can be obtained from herbarium specimens despite DNA degradation.
- DNA damage is primarily associated with the initial specimen preparation process.
- Understanding DNA damage mechanisms is crucial for accurate molecular data from historical samples.
