Optimising DNA extraction from a critically endangered marine alga
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TECHNICAL NOTE
Optimising DNA extraction from a critically endangered marine alga M. A. Coleman1,2 · K. E. Weigner1 · B. P. Kelaher1
Received: 5 October 2016 / Accepted: 7 July 2017 © Springer Science+Business Media B.V. 2017
Abstract Prior to conducting genetic studies on critically endangered species, it is desirable to optimise DNA extraction to limit destructive sampling and reduce impacts on populations. We optimized DNA extraction for the critically endangered marine alga, Nereia lophocladia. Only gentle cryogenic homogenization using a mortar and pestle, followed by brief incubation in lysis buffer, produced high molecular weight DNA. However, this DNA still required post hoc cleanup to be of sufficient quantity for PCR and next generation sequencing. Importantly, sufficient DNA can be obtained from as little as 25 mg of algal material while still allowing contingencies for losses associated with cleanup. Optimisation of DNA extraction for this critically endangered species is paving the way for genomic studies to inform management strategies and conservation. Keywords Seaweed · Threatened · Rare · Brown alga Genetic studies of endangered, vulnerable and threatened species are critical for understanding and reviewing conservation status and for informing management (Kramer and Havens 2009). For many such species, however, genetic studies are hindered by inability to collect samples Electronic supplementary material The online version of this article (doi:10.1007/s12686-017-0810-5) contains supplementary material, which is available to authorized users. * M. A. Coleman [email protected] 1
National Marine Science Centre, Southern Cross University, P. O. Box 4321, Coffs Harbour, NSW, Australia
2
Department of Primary Industries, National Marine Science Centre, 2 Bay Drive, Coffs Harbour, NSW 2450, Australia
from protected populations and the need to avoid destructive or invasive sampling (Taberlet et al. 1999). Optimising methodology, including DNA extraction, is therefore vital to limit collection of material required for meaningful analyses. This is particularly important for species where DNA extraction is challenging (Wilson et al. 2016) and for genomic studies that utilize NGS technologies where DNA quality and quantity is paramount (Russello et al. 2015). Genetic research to inform protection of algae lags behind other taxa (Brodie et al. 2009). The marine brown alga, Nereia lophocladia (J.Agardh) is listed as critically endangered under Part 7A of the Fisheries Management Act 1994 (FSC 2008) in New South Wales (NSW) Australia. This species was thought to be extinct because surveys within its only known location failed to find it over a 13 year period (Yee and Finley 2015). The rediscovery of this critically endangered species in 2015 (Yee and Finley 2015) warrants prompt reassessment of its population biology to prioritize management actions. In particular, the NSW Government has placed high priority on obtaining and analysing “genetic material from remnant populations to
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