ArticlePloS one2012
How to open the treasure chest? Optimising DNA extraction from herbarium specimens.
Article in PloS one, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 83 papers, 1 of them a synthesis that pooled it.
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Who cites it
83 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Type Genomics: A Framework for Integrating Genomic Data into Biodiversity and Taxonomic Research.Systematic biology · 2025Guideline
- Historical Plant Embryos as Alternative Sources of Ancient DNA for Whole Genome Sequencing.Molecular ecology resources · 2026Article
- A global phylogenetic framework for Diospyros L. (Ebenaceae, Ericales): enhanced taxon and sample coverage through NGS, Sanger sequencing and herbariomics.Annals of botany · 2026Article
- Herbariomic approach solved identity crisis of the putatively extinct Armeria arcuata Welw. ex Boiss. & Reut. (Plumbaginaceae).Annals of botany · 2026Article
- Patterns of aDNA damage through time and environments-lessons from herbarium specimens.GigaScience · 2026Article
- Ancient Microbiomes as Mirrored by DNA Extracted From Century-Old Herbarium Plants and Associated Soil.Molecular ecology resources · 2025Article
- Integrating datasets from herbarium specimens and images to treat a Neotropical myrtle species complex.Annals of botany · 2025Article
- Convergent evolution of plant prickles by repeated gene co-option over deep time.Science (New York, N.Y.) · 2024Article
- Versatile DNA extraction from diverse plant taxa using ionic liquids and magnetic ionic liquids: a methodological breakthrough for enhanced sample utility.Plant methods · 2024Article
- Molecular authentication of commercial "Qian-hu" through the integration of nrDNA internal transcribed spacer 2 and nucleotide signature.Molecular biology reports · 2024Article
- Enhancing the authenticity of animal by-products: harmonization of DNA extraction methods from novel ingredients.Frontiers in chemistry · 2024Article
- From Dormant Collections to Repositories for the Study of Habitat Changes: The Importance of Herbaria in Modern Life Sciences.Life (Basel, Switzerland) · 2023Review
- Qualitative identification of lonicerae japonicae flos in traditional chinese medicine using metabarcoding combined with specific mini-barcodes.Molecular biology reports · 2023Article
- Challenges and Opportunities behind the Use ofPlants (Basel, Switzerland) · 2023Review
- Authentication of milk thistle commercial products using UHPLC-QTOF-ESI + MS metabolomics and DNA metabarcoding.BMC complementary medicine and therapies · 2023Article
- Developing the Protocol Infrastructure for DNA Sequencing Natural History Collections.Biodiversity data journal · 2023Article
- A Review on Application of DNA Barcoding Technology for Rapid Molecular Diagnostics of Adulterants in Herbal Medicine.Drug safety · 2022Review
- A comparison of drying methods on the quality for bryophyte molecular specimens collected in the field.PloS one · 2022Article
- Pervasive Phylogenomic Incongruence Underlies Evolutionary Relationships in Eyebrights (Frontiers in plant science · 2022Article
- DNA Barcode Authentication of Devil's Claw Herbal Dietary Supplements.Plants (Basel, Switzerland) · 2021Article
23 more citing papers are in PubMed but not listed here.
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PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Herbarium collections are potentially an enormous resource for DNA studies, but the use of herbarium specimens in molecular studies has thus far been slowed down by difficulty in obtaining amplifiable DNA. Here we compare a set of commercially available DNA extraction protocols and their performance in terms of DNA purity and yield, and PCR amplification success as measured by using three differentially sized markers, the rbcL barcoding marker (cpDNA), the LEAFY exon 3 (nrDNA), and the trnL((UAA)) P6 loop (cpDNA). Results reveal large differences between extraction methods, where DNA purity rather than yield is shown to be strongly correlated with PCR success. Amplicon size shows similarly strong correlation with PCR success, with the shortest fragment showing the highest success rate (78%, P6 loop, 10-143 base pairs (bp)) and the largest fragment the lowest success (10%, rbcL, 670 bp). The effect of specimen preparation method on PCR success was also tested. Results show that drying method strongly affects PCR success, especially the availability of fragments longer than 250 bp, where longer fragments are more available for PCR amplification in air dried material compared to alcohol dried specimens. Results from our study indicate that projects relying on poor-quality starting material such as herbarium or scat samples should focus on extracting pure DNA and aim to amplify short target regions (<200-300 bp) in order to maximise outcomes. Development of shorter barcoding regions, or mini-barcodes within existing ones should be of high importance as only a few options are currently available; this is particularly important if we hope to incorporate the millions of herbarium samples available into barcoding initiatives and other molecular studies.
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