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DNA analysis of molluscs from a museum wet collection: a comparison of different extraction methods

BACKGROUND: DNA isolation and PCR amplification from molluscan taxa is considered as problematic because polysaccharides in tissue and mucus presumably co-precipitate with the DNA and inhibit the activity of DNA polymerase. In the present study we tested two common extraction methods on specimens fr...

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Autores principales: Jaksch, Katharina, Eschner, Anita, Rintelen, Thomas V., Haring, Elisabeth
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2016
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4950716/
https://www.ncbi.nlm.nih.gov/pubmed/27430899
http://dx.doi.org/10.1186/s13104-016-2147-7
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author Jaksch, Katharina
Eschner, Anita
Rintelen, Thomas V.
Haring, Elisabeth
author_facet Jaksch, Katharina
Eschner, Anita
Rintelen, Thomas V.
Haring, Elisabeth
author_sort Jaksch, Katharina
collection PubMed
description BACKGROUND: DNA isolation and PCR amplification from molluscan taxa is considered as problematic because polysaccharides in tissue and mucus presumably co-precipitate with the DNA and inhibit the activity of DNA polymerase. In the present study we tested two common extraction methods on specimens from the mollusc collection of the Natural History Museum Vienna (NHMW). We analysed a broad variety of taxa covering a large temporal span (acquisition years 1877 to 1999), which distinguishes our study from previous ones where mostly fresh material was used. We also took other factors into account: effects of sample age, effects of formaldehyde treatment and taxon-specific problems. We used several primer combinations to amplify amplicons of different lengths of two mitochondrial genes: cytochrome c oxidase subunit 1 (COI) and 16S rRNA gene (16S). RESULTS: Overall PCR success was 43 % in the 576 extractions (including all primer combinations). The smallest amplicon (~240 bp) showed the best results (49 % positive reactions), followed by the 400 bp amplicon (40.5 %). Both short sections yielded significantly better results than the 700 bp long amplicon (27 %). Comparatively, the Gen-ial-First, All-tissue DNA-Kit—extraction method performed significantly better than Promega-Tissue and Hair Extraction Kit. Generally, PCR success is age-dependent. Nonetheless, we were able to obtain the longest amplicon even from 137-year-old material. Importantly, formaldehyde traces did not totally inhibit amplification success, although very high concentrations did. CONCLUSIONS: Museum material has gained importance for DNA analysis in recent years, especially for DNA barcoding projects. In some cases, however, the amplification of the standard barcoding region (partial sequence of the COI) is problematic with old material. Our study clearly shows that the COI barcoding region could be amplified in up to 49 % of PCRs (varying with amplicon length), which is, for museum samples, quite a high percentage. The difference between extraction methods was minimal and we recommend using an established kit for a first attempt because experience and routine in handling might be more important than slight performance differences of the various kits. Finally, we identify fixation, storage, sample conservation and documentation of the specimens’ history rather than the DNA extraction method to be the most crucial factors for PCR success. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s13104-016-2147-7) contains supplementary material, which is available to authorized users.
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spelling pubmed-49507162016-07-20 DNA analysis of molluscs from a museum wet collection: a comparison of different extraction methods Jaksch, Katharina Eschner, Anita Rintelen, Thomas V. Haring, Elisabeth BMC Res Notes Research Article BACKGROUND: DNA isolation and PCR amplification from molluscan taxa is considered as problematic because polysaccharides in tissue and mucus presumably co-precipitate with the DNA and inhibit the activity of DNA polymerase. In the present study we tested two common extraction methods on specimens from the mollusc collection of the Natural History Museum Vienna (NHMW). We analysed a broad variety of taxa covering a large temporal span (acquisition years 1877 to 1999), which distinguishes our study from previous ones where mostly fresh material was used. We also took other factors into account: effects of sample age, effects of formaldehyde treatment and taxon-specific problems. We used several primer combinations to amplify amplicons of different lengths of two mitochondrial genes: cytochrome c oxidase subunit 1 (COI) and 16S rRNA gene (16S). RESULTS: Overall PCR success was 43 % in the 576 extractions (including all primer combinations). The smallest amplicon (~240 bp) showed the best results (49 % positive reactions), followed by the 400 bp amplicon (40.5 %). Both short sections yielded significantly better results than the 700 bp long amplicon (27 %). Comparatively, the Gen-ial-First, All-tissue DNA-Kit—extraction method performed significantly better than Promega-Tissue and Hair Extraction Kit. Generally, PCR success is age-dependent. Nonetheless, we were able to obtain the longest amplicon even from 137-year-old material. Importantly, formaldehyde traces did not totally inhibit amplification success, although very high concentrations did. CONCLUSIONS: Museum material has gained importance for DNA analysis in recent years, especially for DNA barcoding projects. In some cases, however, the amplification of the standard barcoding region (partial sequence of the COI) is problematic with old material. Our study clearly shows that the COI barcoding region could be amplified in up to 49 % of PCRs (varying with amplicon length), which is, for museum samples, quite a high percentage. The difference between extraction methods was minimal and we recommend using an established kit for a first attempt because experience and routine in handling might be more important than slight performance differences of the various kits. Finally, we identify fixation, storage, sample conservation and documentation of the specimens’ history rather than the DNA extraction method to be the most crucial factors for PCR success. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s13104-016-2147-7) contains supplementary material, which is available to authorized users. BioMed Central 2016-07-18 /pmc/articles/PMC4950716/ /pubmed/27430899 http://dx.doi.org/10.1186/s13104-016-2147-7 Text en © The Author(s) 2016 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Research Article
Jaksch, Katharina
Eschner, Anita
Rintelen, Thomas V.
Haring, Elisabeth
DNA analysis of molluscs from a museum wet collection: a comparison of different extraction methods
title DNA analysis of molluscs from a museum wet collection: a comparison of different extraction methods
title_full DNA analysis of molluscs from a museum wet collection: a comparison of different extraction methods
title_fullStr DNA analysis of molluscs from a museum wet collection: a comparison of different extraction methods
title_full_unstemmed DNA analysis of molluscs from a museum wet collection: a comparison of different extraction methods
title_short DNA analysis of molluscs from a museum wet collection: a comparison of different extraction methods
title_sort dna analysis of molluscs from a museum wet collection: a comparison of different extraction methods
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4950716/
https://www.ncbi.nlm.nih.gov/pubmed/27430899
http://dx.doi.org/10.1186/s13104-016-2147-7
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