Unlocking the genomes of formalin‐fixed freshwater fish specimens: An assessment of factors influencing DNA extraction quantity and quality
Abstract Objective Recent technological developments may facilitate the description of evolutionary relationships and population genetic structure as well as other information relevant to fisheries management by using readily available natural history collections. Contemporary sequence capture and s...
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Online Access: | http://dx.doi.org/10.1002/nafm.10935 https://afspubs.onlinelibrary.wiley.com/doi/pdf/10.1002/nafm.10935 |
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crwiley:10.1002/nafm.10935 2024-06-02T08:05:33+00:00 Unlocking the genomes of formalin‐fixed freshwater fish specimens: An assessment of factors influencing DNA extraction quantity and quality Brino, Erin E. Schumann, David A. Rezac, Calvin R. Ellwanger, Robbie J. Osmundson, Todd W. 2023 http://dx.doi.org/10.1002/nafm.10935 https://afspubs.onlinelibrary.wiley.com/doi/pdf/10.1002/nafm.10935 en eng Wiley http://onlinelibrary.wiley.com/termsAndConditions#vor North American Journal of Fisheries Management volume 43, issue 6, page 1596-1609 ISSN 0275-5947 1548-8675 journal-article 2023 crwiley https://doi.org/10.1002/nafm.10935 2024-05-03T12:07:11Z Abstract Objective Recent technological developments may facilitate the description of evolutionary relationships and population genetic structure as well as other information relevant to fisheries management by using readily available natural history collections. Contemporary sequence capture and short‐read sequencing methods offer opportunities to analyze highly fragmented DNA from formalin‐fixed specimens so long as enough DNA of sufficient quality is recovered. Methods We compared two protocols developed to extract DNA from formalin‐fixed tissues using specimens of three freshwater fishes: the Southern Brook Lamprey Ichthyomyzon gagei , Slimy Sculpin Cottus cognatus , and Brown Trout Salmo trutta . Extractions were attempted using hot alkali digestion with and without buffer wash pretreatments to compare the DNA concentration, purity, and fragment length of DNA recovered between extraction protocols, tissue types (muscle and caudal fin tissue for Brown Trout and Slimy Sculpin), and preservation periods (5 or 7 years for Southern Brook Lamprey). Result Likelihood models generally did not detect DNA quantity differences between extraction protocols nor tissue types; however, 6.0–8.7× more DNA was recovered from Slimy Sculpin caudal fins than from muscle tissue. Extraction protocol had mixed effects on DNA purity; the wash protocol outperformed the no‐wash protocol for Slimy Sculpin and Brown Trout, but the reverse was true for the lamprey. Purer DNA was recovered from the caudal fins; however, fragment lengths were generally greater from muscle tissue for both ray‐finned species. Conclusion Our results suggest that the best tissue for sampling may depend on the quality metric considered most important for a study's objectives and that omitting time‐consuming tissue wash steps can yield DNA of quantity and quality comparable to DNA from more complex methods. Regardless of species, the DNA extracted from most samples using both protocols met quantity and quality thresholds that are likely to result in short‐read ... Article in Journal/Newspaper Cottus cognatus Slimy sculpin Wiley Online Library North American Journal of Fisheries Management 43 6 1596 1609 |
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English |
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Abstract Objective Recent technological developments may facilitate the description of evolutionary relationships and population genetic structure as well as other information relevant to fisheries management by using readily available natural history collections. Contemporary sequence capture and short‐read sequencing methods offer opportunities to analyze highly fragmented DNA from formalin‐fixed specimens so long as enough DNA of sufficient quality is recovered. Methods We compared two protocols developed to extract DNA from formalin‐fixed tissues using specimens of three freshwater fishes: the Southern Brook Lamprey Ichthyomyzon gagei , Slimy Sculpin Cottus cognatus , and Brown Trout Salmo trutta . Extractions were attempted using hot alkali digestion with and without buffer wash pretreatments to compare the DNA concentration, purity, and fragment length of DNA recovered between extraction protocols, tissue types (muscle and caudal fin tissue for Brown Trout and Slimy Sculpin), and preservation periods (5 or 7 years for Southern Brook Lamprey). Result Likelihood models generally did not detect DNA quantity differences between extraction protocols nor tissue types; however, 6.0–8.7× more DNA was recovered from Slimy Sculpin caudal fins than from muscle tissue. Extraction protocol had mixed effects on DNA purity; the wash protocol outperformed the no‐wash protocol for Slimy Sculpin and Brown Trout, but the reverse was true for the lamprey. Purer DNA was recovered from the caudal fins; however, fragment lengths were generally greater from muscle tissue for both ray‐finned species. Conclusion Our results suggest that the best tissue for sampling may depend on the quality metric considered most important for a study's objectives and that omitting time‐consuming tissue wash steps can yield DNA of quantity and quality comparable to DNA from more complex methods. Regardless of species, the DNA extracted from most samples using both protocols met quantity and quality thresholds that are likely to result in short‐read ... |
format |
Article in Journal/Newspaper |
author |
Brino, Erin E. Schumann, David A. Rezac, Calvin R. Ellwanger, Robbie J. Osmundson, Todd W. |
spellingShingle |
Brino, Erin E. Schumann, David A. Rezac, Calvin R. Ellwanger, Robbie J. Osmundson, Todd W. Unlocking the genomes of formalin‐fixed freshwater fish specimens: An assessment of factors influencing DNA extraction quantity and quality |
author_facet |
Brino, Erin E. Schumann, David A. Rezac, Calvin R. Ellwanger, Robbie J. Osmundson, Todd W. |
author_sort |
Brino, Erin E. |
title |
Unlocking the genomes of formalin‐fixed freshwater fish specimens: An assessment of factors influencing DNA extraction quantity and quality |
title_short |
Unlocking the genomes of formalin‐fixed freshwater fish specimens: An assessment of factors influencing DNA extraction quantity and quality |
title_full |
Unlocking the genomes of formalin‐fixed freshwater fish specimens: An assessment of factors influencing DNA extraction quantity and quality |
title_fullStr |
Unlocking the genomes of formalin‐fixed freshwater fish specimens: An assessment of factors influencing DNA extraction quantity and quality |
title_full_unstemmed |
Unlocking the genomes of formalin‐fixed freshwater fish specimens: An assessment of factors influencing DNA extraction quantity and quality |
title_sort |
unlocking the genomes of formalin‐fixed freshwater fish specimens: an assessment of factors influencing dna extraction quantity and quality |
publisher |
Wiley |
publishDate |
2023 |
url |
http://dx.doi.org/10.1002/nafm.10935 https://afspubs.onlinelibrary.wiley.com/doi/pdf/10.1002/nafm.10935 |
genre |
Cottus cognatus Slimy sculpin |
genre_facet |
Cottus cognatus Slimy sculpin |
op_source |
North American Journal of Fisheries Management volume 43, issue 6, page 1596-1609 ISSN 0275-5947 1548-8675 |
op_rights |
http://onlinelibrary.wiley.com/termsAndConditions#vor |
op_doi |
https://doi.org/10.1002/nafm.10935 |
container_title |
North American Journal of Fisheries Management |
container_volume |
43 |
container_issue |
6 |
container_start_page |
1596 |
op_container_end_page |
1609 |
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1800750404911235072 |