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

Jaksch, Katharina; Eschner, Anita; Rintelen, Thomas von; Haring, Elisabeth

doi:10.1186/s13104-016-2147-7

Cited by 33 publications

(22 citation statements)

References 26 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…These results are in agreement with expectations for DNA obtained from historical material which is expected to be highly degraded, and PCR amplification generally restricted to short amplicons (<200 bp) [58,59]. Amplification of the standard COI barcoding region in molluscs has proven to be particularly problematic or impossible with historical material using standard primers [64]. …”

Section: Discussionsupporting

confidence: 84%

Insights into the Evolutionary History of an Extinct South American Freshwater Snail Based on Historical DNA

et al. 2016

View full text Add to dashboard Cite

Highly oxygenated freshwater habitats in the High Paraná River (Argentina–Paraguay) were home to highly endemic snails of the genus Aylacostoma, which face extinction owing to the impoundment of the Yacyretá Reservoir in the 1990s. Two species, A. chloroticum and A. brunneum, are currently included in an ongoing ex situ conservation programme, whereas A. guaraniticum and A. stigmaticum are presumed extinct. Consequently, the validity and affinities of the latter two have remained enigmatic. Here, we provide the first molecular data on the extinct A. stigmaticum by means of historical DNA analysis. We describe patterns of molecular evolution based on partial sequences of the mitochondrial 12S ribosomal RNA gene from the extinct species and from those being bred within the ex situ programme. We further use this gene to derive a secondary structure model, to examine the specific status of A. stigmaticum and to explore the evolutionary history of these snails. The secondary structure model based on A. stigmaticum revealed that most polymorphic sites are located in unpaired regions. Our results support the view that the mitochondrial 12S region is an efficient marker for the discrimination of species, and the extinct A. stigmaticum is recognized here as a distinct evolutionary genetic species. Molecular phylogenetic analyses revealed a sister group relationship between A. chloroticum and A. brunneum, and estimated divergence times suggest that diversification of Aylacostoma in the High Paraná River might have started in the late Miocene via intra-basin speciation due to a past marine transgression. Finally, our findings reveal that DNA may be obtained from dried specimens at least 80 years after their collection, and confirms the feasibility of extracting historical DNA from museum collections for elucidating evolutionary patterns and processes in gastropods.

show abstract

Section: Discussionsupporting

confidence: 84%

Insights into the Evolutionary History of an Extinct South American Freshwater Snail Based on Historical DNA

et al. 2016

View full text Add to dashboard Cite

show abstract

“…We therefore did not analyze several other sources of genetic material in natural history collections, namely formalin-fixed specimens and tissue samples treated with RNAlater. Previous work has attempted to extract high quality DNA from formalin-fixed specimens with varying results (Hykin, Bi & McGuire, 2015;Jaksch et al, 2016). Because the procedures used for these types of extractions are more involved and less often used, we chose not to include any formalin-fixed tissue subsamples in our study but recommend repeating our study with these specimens once extractions procedures are better developed.…”

Section: Discussionmentioning

confidence: 99%

Improving sustainable use of genetic resources in biodiversity archives

Tuschhoff

Hutter

Glor

2020

PeerJ

View full text Add to dashboard Cite

Tissue sample databases housed in biodiversity archives represent a vast trove of genetic resources, and these tissues are often destructively subsampled and provided to researchers for DNA extractions and subsequent sequencing. While obtaining a sufficient quantity of DNA for downstream applications is vital for these researchers, it is also important to preserve tissue resources for future use given that the original material is destructively and consumptively sampled with each use. It is therefore necessary to develop standardized tissue subsampling and loaning procedures to ensure that tissues are being used efficiently. In this study, we specifically focus on the efficiency of DNA extraction methods by using anuran liver and muscle tissues maintained at a biodiversity archive. We conducted a series of experiments to test whether current practices involving coarse visual assessments of tissue size are effective, how tissue mass correlates with DNA yield and concentration, and whether the amount of DNA recovered is correlated with sample age. We found that tissue samples between 2 and 8 mg resulted in the most efficient extractions, with tissues at the lower end of this range providing more DNA per unit mass and tissues at the higher end of this range providing more total DNA. Additionally, we found no correlation between tissue age and DNA yield. Because we find that even very small tissue subsamples tend to yield far more DNA than is required by researchers for modern sequencing applications (including whole genome shotgun sequencing), we recommend that biodiversity archives consider dramatically improving sustainable use of their archived material by providing researchers with set quantities of extracted DNA rather than with the subsampled tissues themselves.

show abstract

“…We therefore did not analyze several other sources of genetic material in natural history collections, namely formalin-fixed specimens and tissue samples treated with RNAlater. Previous work has attempted to extract high quality DNA from formalin-fixed specimens with varying results (Hykin et al 2015, Jaksch et al 2016. Because the procedures used for these types of extractions are more involved and less often used, we chose not to include any formalin-fixed tissue subsamples in our study but recommend repeating our study with these specimens once extractions procedures are better developed.…”

Section: Discussionmentioning

confidence: 99%

“…It is not currently common practice to standardize tissue mass prior to DNA extractions (Wilcox et al 2002, Aguirre-Peñafiel et al 2014, Naccarato et al 2015 or to report masses if they were standardized (Kayes et al 2013) except in experiments to compare various protocols or methods (Drabkova et al 2002, Guo et al 2009, Abdel-Latif and Osman 2017, Yalcinkaya et al 2017. In publications, researchers tend to qualitatively report the amount of starting material with phrases such "two small pieces" or "usually minute" (Hajibabaei et al 2005, Jaksch et al 2016.…”

Section: Introductionmentioning

confidence: 99%

Peer Review #1 of "Improving sustainable use of genetic resources in biodiversity archives (v0.1)"

Chambers¹

2020

View full text Add to dashboard Cite

Tissue sample databases housed in biodiversity archives represent a vast trove of genetic resources, and these tissues are often destructively subsampled and provided to researchers for DNA extractions and subsequent sequencing. While obtaining a sufficient quantity of DNA for downstream applications is vital for these researchers, it is also important to preserve tissue resources for future use given that the original material is destructively and consumptively sampled with each use. It is therefore necessary to develop standardized tissue subsampling and loaning procedures to ensure that tissues are being used efficiently. In this study, we specifically focus on the efficiency of DNA extraction methods by using anuran liver and muscle tissues maintained at a biodiversity archive. We conducted a series of experiments to test whether current practices involving coarse visual assessments of tissue size are effective, how tissue mass correlates with DNA yield and concentration, and whether the amount of DNA recovered is correlated with sample age. We found that tissue samples between 2 mg and 8 mg resulted in the most efficient extractions, with tissues at the lower end of this range providing more DNA per unit mass and tissues at the higher end of this range providing more total DNA. Additionally, we found no correlation between tissue age and DNA yield. Because we find that even very small tissue subsamples tend to yield far more DNA than is required by researchers for modern sequencing applications (including whole genome shotgun sequencing), we recommend that biodiversity archives consider dramatically improving sustainable use of their archived material by providing researchers with set quantities of extracted DNA rather than with the subsampled tissues themselves.

show abstract

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

Cited by 33 publications

References 26 publications

Insights into the Evolutionary History of an Extinct South American Freshwater Snail Based on Historical DNA

Insights into the Evolutionary History of an Extinct South American Freshwater Snail Based on Historical DNA

Improving sustainable use of genetic resources in biodiversity archives

Peer Review #1 of "Improving sustainable use of genetic resources in biodiversity archives (v0.1)"

Contact Info

Product

Resources

About