Ascertaining optimal protocols for DNA extraction of different qualities of pike (Esox lucius) tissue samples - a comparison of commonly used solid phase extraction methods

• Autorzy: Eschbach E.
• Języki publikacji: EN

Abstrakty

EN

High quality DNA extractions are a prerequisite for genetic studies of a variety of organisms including fish. The current study focused on the applicability of different commercially available solid phase extraction (SPE) methods as the easiest and fastest methods for DNA extraction and their efficiency with different tissue qualities. These were represented by different kinds of pike tissues (fins, muscle, scales) preserved with different methods and stored at different temperatures over different periods of time (0.5 to 10.0 years). All DNA extractions were analysed according to their yield, purity, integrity and functionality in PCR based downstream analysis. Additionally mechanical pre-treatment of poor quality tissues (e.g. old or aged tissues) and efficient ethanol preservation of frozen bulk fin tissue were investigated. All SPE methods yielded functional DNA from very different qualities of pike tissues as shown by PCR analysis of small nuclear (microsatellite) and large mitochondrial (complete D-loop) DNA fragments. DNA from poor quality tissue can be extracted using single column SPE and in some cases mechanical pre-treatment even improved the yield. Good quality tissue as obtained e.g. from commercial fishermen as frozen bulk material is more efficiently preserved by thawing in ethanol at room temperature than at 2-8°C. DNA from these and air dried tissues was very efficiently prepared by applying reverse SPE in 96-well format, allowing for fast processing of a multitude of samples for high throughput analysis.

Słowa kluczowe

EN

pike; Esox lucius; DNA extractions; solid-phase extraction

PL

szczupak; Esox lucius; ekstrakcja DNA; ekstrakcja do fazy stałej

• Wydawca: University of Warmia and Mazury in Olsztyn, Poland
• Czasopismo: Environmental Biotechnology
• Rocznik: 2012
• Tom: Vol. 8, No. 1
• Strony: 7--14
• Opis fizyczny: Bibliogr. 16 poz., rys., tab.

Twórcy

autor

Eschbach E.

• Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Department of Biology and Ecology of Fishes, Mueggelseedamm 310, 12587 Berlin, Germany, Phone: [phone],

Bibliografia

• Aguilar, A., J.D. Banks, K.F. Levine, R.K. Wayne. 2005. Population genetics of northern pike (Esox lucius) introduced into Lake Davis, California. Canadian Journal of Fisheries and Aquatic Sciences 62: 1589-1599.
• Altschul, S.F., T.L. Madden, A.A. Schäffer, J. Zhang, Z. Zhang, W. Miller, D.J. Lipman. 1997. Gapped BLAST and PSI-BLAST, a new generation of protein database search programs. Nucleic Acids Research 25: 3389-3402.
• Beacham, T.D., B. McIntosh, C. Wallace. 2010. A comparison of stock and individual identification for sockeye salmon (Oncorhynchus nerka) in British Columbia provided by microsatellites and single nucleotide polymorphisms. Canadian Journal of Fisheries and Aquatic Sciences 67: 1274-1290.
• De Bruyn, M., L.R. Parenti, G.R. Carvalho. 2011. Successful extraction of DNA from archived alcohol-fixed white-eye fish specimens using an ancient DNA protocol. Journal of Fish Biology 78: 2074-2079.
• Hansen, M.M. 2002. Estimating the long-term effects of stocking domesticated trout into wild brown trout (Salmo trutta) populations: an approach using microsatellite DNA analysis of historical and contemporary samples. Molecular Ecology 11: 1003-1015.
• Hansen, M.M., D.J. Fraser, K. Meier, K.D. Mensberg. 2009. Sixty years of anthropogenic pressure: a spatio-temporal genetic analysis of brown trout populations subject to stocking and population declines. Molecular Ecology 18: 2549-2562.
• Ishiguro, N.B., M. Miya, M. Nishida. 2003. Basal euteleostean relationships: a mitogenomic perspective on the phylogenetic reality of „Protacanthopterygii“. Molecular Phylogenetics and Evolution 27: 476-488.
• LaHood, E.S., J.J. Miller, C. Apland, M.J. Ford. 2008. A rapid, ethanol-free fish tissue collection method for molecular genetic analyses. Transactions of the American Fisheries Society 137: 1104-1107.
• Larsen, P.F., M.M. Hansen, E.E. Nielsen, L.F. Jensen, V. Loeschcke. 2005. Stocking impact and temporal stability of genetic composition in a brackish northern pike population (Esox lucius L.), assessed using microsatellite DNA analysis of historical and contemporary samples. Heredity 95: 136-143.
• Lucentini, L., S. Caporali, A. Palomba, H. Lancioni, F. Panara. 2006a. A comparison of conservative DNA extraction methods from fins and scales of freshwater fish: A useful tool for conservation genetics. Conservation Genetics 6: 1009-1012.
• Lucentini, L., A. Palomba, H. Lancioni, M. Natali, F. Panara. 2006b. A nondestructive, rapid, reliable and inexpensive method to sample, store and extract high-quality DNA from fish body mucus and buccal cells. Molecular Ecology Notes 6: 257-260.
• Miller, L.M., A.R. Kapuscinski. 1996. Microsatellite DNA markers reveal new levels of genetic variation in northern pike. Transactions of the American Fisheries Society 125: 971-977.
• Mirimin, L., D. O∂Keeffe, A. Ruggiero, M. Bolton-Warberg, S. Vartia, R. Fitzgerald. 2011. A quick, least-invasive, inexpensive and reliable method for sampling Gadus morhua postlarvae for genetic analysis. Journal of Fish Biology 79: 801-805.
• Quinn, T.P., T.R. Seamons. 2009. Tales from scales: old DNA yields insights into contemporary evolutionary processes affecting fishes. Molecular Ecology 18: 2545-2546.
• Reid, S.M., A. Kidd, C.C. Wilson. 2011. Validation of buccal swabs for noninvasive DNA sampling of small-bodied imperilled fishes. Journal of Applied Ichthyology 28: 290-292.
• Rozen, S., H.J. Skaletsky. 2000. Primer3 on the WWW for general users and for biologist programmers. In: Bioinformatics Methods and Protocols: Methods in Molecular Biology (ed. S. Krawetz, S. Misener), pp. 365-386. Humana Press, Totowa, New Jersey.