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An evaluation of DNA extraction methods on historical and roadkill mammalian specimen

Molbert, Noëlie LU ; Ghanavi, Hamid Reza LU orcid ; Johansson, Tomas LU ; Mostadius, Maria LU and Hansson, Maria C LU (2023) In Scientific Reports 13.
Abstract

Guidelines identifying appropriate DNA extraction methods for both museum and modern biological samples are scarce or non-existent for mammalian species. Yet, obtaining large-scale genetic material collections are vital for conservation and management purposes. In this study, we evaluated five protocols making use of either spin-column, organic solvents, or magnetic bead-based methods for DNA extraction on skin samples from both modern, traffic-killed (n = 10) and museum (n = 10) samples of European hedgehogs, Ericaneus europaeus. We showed that phenol-chloroform or silica column (NucleoSpin Tissue) protocols yielded the highest amount of DNA with satisfactory purity compared with magnetic bead-based protocols, especially for museum... (More)

Guidelines identifying appropriate DNA extraction methods for both museum and modern biological samples are scarce or non-existent for mammalian species. Yet, obtaining large-scale genetic material collections are vital for conservation and management purposes. In this study, we evaluated five protocols making use of either spin-column, organic solvents, or magnetic bead-based methods for DNA extraction on skin samples from both modern, traffic-killed (n = 10) and museum (n = 10) samples of European hedgehogs, Ericaneus europaeus. We showed that phenol-chloroform or silica column (NucleoSpin Tissue) protocols yielded the highest amount of DNA with satisfactory purity compared with magnetic bead-based protocols, especially for museum samples. Furthermore, extractions using the silica column protocol appeared to produce longer DNA fragments on average than the other methods tested. Our investigation demonstrates that both commercial extraction kits and phenol-chloroform protocol retrieve acceptable DNA concentrations for downstream processes, from degraded remnants of traffic-killed and museum samples of mammalian specimens. Although all the tested methods could be applied depending on the research questions and laboratory conditions, commercial extraction kits may be preferred due to their effectiveness, safety and the higher quality of the DNA extractions.

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author
; ; ; and
organization
publishing date
type
Contribution to journal
publication status
published
subject
keywords
Animals, Chloroform, DNA/genetics, Phenol, Phenols, Mammals/genetics, Silicon Dioxide
in
Scientific Reports
volume
13
article number
13080
publisher
Nature Publishing Group
external identifiers
  • scopus:85168221691
  • pmid:37567875
ISSN
2045-2322
DOI
10.1038/s41598-023-39465-z
language
English
LU publication?
yes
id
76800864-bb2b-4d4e-96cd-6505664a6f0e
date added to LUP
2023-08-21 12:38:20
date last changed
2024-11-02 20:48:51
@article{76800864-bb2b-4d4e-96cd-6505664a6f0e,
  abstract     = {{<p>Guidelines identifying appropriate DNA extraction methods for both museum and modern biological samples are scarce or non-existent for mammalian species. Yet, obtaining large-scale genetic material collections are vital for conservation and management purposes. In this study, we evaluated five protocols making use of either spin-column, organic solvents, or magnetic bead-based methods for DNA extraction on skin samples from both modern, traffic-killed (n = 10) and museum (n = 10) samples of European hedgehogs, Ericaneus europaeus. We showed that phenol-chloroform or silica column (NucleoSpin Tissue) protocols yielded the highest amount of DNA with satisfactory purity compared with magnetic bead-based protocols, especially for museum samples. Furthermore, extractions using the silica column protocol appeared to produce longer DNA fragments on average than the other methods tested. Our investigation demonstrates that both commercial extraction kits and phenol-chloroform protocol retrieve acceptable DNA concentrations for downstream processes, from degraded remnants of traffic-killed and museum samples of mammalian specimens. Although all the tested methods could be applied depending on the research questions and laboratory conditions, commercial extraction kits may be preferred due to their effectiveness, safety and the higher quality of the DNA extractions.</p>}},
  author       = {{Molbert, Noëlie and Ghanavi, Hamid Reza and Johansson, Tomas and Mostadius, Maria and Hansson, Maria C}},
  issn         = {{2045-2322}},
  keywords     = {{Animals; Chloroform; DNA/genetics; Phenol; Phenols; Mammals/genetics; Silicon Dioxide}},
  language     = {{eng}},
  month        = {{08}},
  publisher    = {{Nature Publishing Group}},
  series       = {{Scientific Reports}},
  title        = {{An evaluation of DNA extraction methods on historical and roadkill mammalian specimen}},
  url          = {{http://dx.doi.org/10.1038/s41598-023-39465-z}},
  doi          = {{10.1038/s41598-023-39465-z}},
  volume       = {{13}},
  year         = {{2023}},
}