Extracting DNA from museum bird eggs, and whole genome amplification of archive DNA

Lee, Patricia L.M. and Prys-Jones, Robert P. 2008, Extracting DNA from museum bird eggs, and whole genome amplification of archive DNA, Molecular ecology resources, vol. 8, no. 3, pp. 551-560, doi: 10.1111/j.1471-8286.2007.02042.x.

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Title Extracting DNA from museum bird eggs, and whole genome amplification of archive DNA
Author(s) Lee, Patricia L.M.ORCID iD for Lee, Patricia L.M. orcid.org/0000-0002-8489-9206
Prys-Jones, Robert P.
Journal name Molecular ecology resources
Volume number 8
Issue number 3
Start page 551
End page 560
Total pages 10
Publisher Wiley
Place of publication London, England
Publication date 2008-05
ISSN 1755-098X
Keyword(s) COI mtDNA
DNA barcoding
DNA extraction
museum collections
Summary We present a comprehensive protocol for extracting DNA from egg membranes and other internal debris recovered from the interior of blown museum bird eggs. A variety of commercially available DNA extraction methods were found to be applicable. DNA sequencing of polymerase chain reaction (PCR) products for a 176-bp fragment of mitochondrial DNA was successful for most egg samples (> 78%) even though the amount of DNA extracted (mean = 14.71 ± 4.55 ng/µL) was significantly less than that obtained for bird skin samples (mean = 67.88 ± 4.77 ng/µL). For PCR and sequencing of snipe (Gallinago) DNA, we provide eight new primers for the ‘DNA barcode’ region of COI mtDNA. In various combinations, the primers target a range of PCR products sized from 72 bp to the full ‘barcode’ of 751 bp. Not all possible combinations were tested with archive snipe DNA, but we found a significantly better success rate of PCR amplification for a shorter 176-bp target compared with a larger 288-bp fragment (67% vs. 39%). Finally, we explored the feasibility of whole genome amplification (WGA) for extending the use of archive DNA in PCR and sequencing applications. Of two WGA approaches, a PCR-based method was found to be able to amplify whole genomic DNA from archive skins and eggs from museum bird collections. After WGA, significantly more archive egg samples produced visible PCR products on agarose (56.9% before WGA vs. 79.0% after WGA). However, overall sequencing success did not improve significantly (78.8% compared with 83.0%).
Language eng
DOI 10.1111/j.1471-8286.2007.02042.x
Field of Research 060411 Population, Ecological and Evolutionary Genetics
060809 Vertebrate Biology
060208 Terrestrial Ecology
Socio Economic Objective 960899 Flora, Fauna and Biodiversity of Environments not elsewhere classified
HERDC Research category C1.1 Refereed article in a scholarly journal
Copyright notice ©2008, Wiley
Persistent URL http://hdl.handle.net/10536/DRO/DU:30056214

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