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  Extraction of ultrashort DNA molecules from herbarium specimens

Gutaker, R., Reiter, E., Furtwängler, A., Schuenemann, V., & Burbano, H. (2017). Extraction of ultrashort DNA molecules from herbarium specimens. Biotechniques, 62(2), 76-79. doi:10.2144/000114517.

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Genre: Journal Article

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 Creators:
Gutaker, RM1, Author           
Reiter, E, Author
Furtwängler, A, Author
Schuenemann, VJ, Author
Burbano, HA1, Author           
Affiliations:
1Department Molecular Biology, Max Planck Institute for Developmental Biology, Max Planck Society, ou_3375790              

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Free keywords: ANCIENT DNA; LIBRARY PREPARATION; GENOME SEQUENCE; STRANDED-DNA; NEANDERTHALBiochemistry & Molecular Biology; ancient DNA; herbarium; DNA extraction; paleogenomics; next-generation sequencing;
 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.

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Language(s): eng - English
 Dates: 2017-02
 Publication Status: Published in print
 Pages: -
 Publishing info: -
 Table of Contents: -
 Rev. Type: -
 Identifiers: DOI: 10.2144/000114517
PMID: 28193151
 Degree: -

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Title: Biotechniques
  Other : Biotechniques
Source Genre: Journal
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Publ. Info: [Natick, MA : Eaton Pub. Co.
Pages: - Volume / Issue: 62 (2) Sequence Number: - Start / End Page: 76 - 79 Identifier: ISSN: 0736-6205
CoNE: https://pure.mpg.de/cone/journals/resource/954925536105