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Biotechniques. 2017 Feb 1;62(2):76-79. doi: 10.2144/000114517.

Extraction of ultrashort DNA molecules from herbarium specimens.

Author information

1
Research Group for Ancient Genomics and Evolution, Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany.
2
Institute of Archaeological Sciences, University of Tübingen, Tübingen, Germany.
3
Institute of Archaeological Sciences, University of Tübingen, Tübingen, Germany; Senckenberg Center for Human Evolution and Paleoenvironment, University of Tübingen, Tübingen, Germany.

Abstract

DNA extracted from herbarium specimens is highly fragmented; therefore, it is crucial to use extraction protocols that retrieve short DNA molecules. Improvements in extraction and DNA library preparation protocols for animal remains have allowed efficient retrieval of molecules shorter than 50 bp. Here, we applied these improvements to DNA extraction protocols for herbarium specimens and evaluated extraction performance by shotgun sequencing, which allows an accurate estimation of the distribution of DNA fragment lengths. Extraction with N-phenacylthiazolium bromide (PTB) buffer decreased median fragment length by 35% when compared with cetyl-trimethyl ammonium bromide (CTAB); modifying the binding conditions of DNA to silica allowed for an additional decrease of 10%. We did not observe a further decrease in length for single-stranded DNA (ssDNA) versus double-stranded DNA (dsDNA) library preparation methods. Our protocol enables the retrieval of ultrashort molecules from herbarium specimens, which will help to unlock the genetic information stored in herbaria.

KEYWORDS:

DNA extraction; ancient DNA; herbarium; next-generation sequencing; paleogenomics

PMID:
28193151
DOI:
10.2144/000114517
[Indexed for MEDLINE]
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