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Critical analysis of DNA extraction techniques: yield, quality, time, cost, and plastic usage
  • Jessica Gordon,
  • Michelle Taylor
Jessica Gordon
University of Essex Department of Biological Sciences

Corresponding Author:[email protected]

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Michelle Taylor
University of Essex Department of Biological Sciences
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Abstract

Using non model-organisms is becoming increasingly common in NGS. Different NGS techniques have different demands of DNA extraction; abundant DNA, “clean” HMW DNA, to be cheap, to be quick, and increasingly considered, to use minimal plastics. Here we compare five DNA extraction methods: a phenol-based extraction, salting-out protocol, and three commercially available kits from Qiagen: Blood and Tissue Kit, Plant Mini kit, and PowerSoil Pro kit. These protocols were tested across non-model organisms: deep-sea octocorals and scleractinians. We included four individuals from each of the octocorals, Acanella arbuscula, Paragoria sp., and Pennatula sp., as well as four individuals from each of the scleractinian corals, Madrepora oculata, Lophelia pertusa, and Desmophyllum dianthus. DNA yield and quality were measured and compared across methods. Phenol yielded the most DNA per mg of tissue across all corals except Acanella and Madrepora- where salting-out yielded the most DNA. The Qiagen Plant Mini kit produced the highest ratio of HMW DNA to degraded DNA in all corals tested. The purity of DNA (measured by absorbance) was equal across methods. The amount of plastic used for each protocol was also measured with kit DNA extractions using significantly more plastics than non-kit protocols. We also make recommendations on how to reduce future plastic usage. Overall, it was found that recovering HMW DNA across extraction methods was genus specific, and the method used by researchers should take into account their specific research needs.