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DNA Extraction Techniques for Genomic Analyses of Macroalgae

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Seaweed Phylogeography

Abstract

Extracting high-quality DNA in large quantities from Phaeophyceae (brown), Rhodophyta (red), and Chlorophyta (green) macroalgae presents a substantial obstacle for modern molecular studies. Macroalgal tissues are rich in polysaccharides and polyphenols that are known to interfere with downstream molecular techniques. These compounds are released during DNA extraction procedures and often persist despite purification attempts. A wide range of DNA extraction and purification methods have been developed in attempts to overcome these challenges. Here, we review methods of macroalgal DNA extraction, including commercial kits. We discuss each method’s merits and limitations, and examine its potential use in both traditional and high-throughput molecular approaches. Finally, we present our own findings from a range of DNA extraction, purification, and sequencing trials based on the commercially available MoBio PowerPlant® Pro and PowerPlant® Clean kits, carried out on a number of Phaeophyceae species. We found that DNA yield and quality can be improved by lengthy soaking of tissue in extraction buffers, altering the homogenization procedures and modifying solutions used. The DNA extraction protocol presented here can be scaled up for high-throughput analyses and preliminary results suggest suitability for next-generation sequencing.

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Acknowledgments

We are very grateful to the technical support team of Mo Bio Laboratories incorporated, Niccy Aitken (Australian National University), Duckahul Park (Landcare Research, New Zealand), and Leon Smith (Australian National University) for providing technical advice and assistance. Likewise, we would like to thank Jon Waters (University of Otago) for advice and comments on this work. LJW was funded by a scholarship from the North Australian Marine Research Association and an Australian Research Council Linkage grant led by Graham Edgar (University of Tasmania) (ARC LP100200122), XW was funded by a Capacity-Building scholarship from the Australian Biological Resources Study, TK was funded by the Department of Zoology at the University of Otago, and CIF was funded by an Australian Research Council DECRA grant (DE140101715).

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Authors and Affiliations

  1. Fenner School of Environment and Society, Australian National University, Daley Road, Acton, ACT, 2601, Australia

    Laura J. Wilson, Xénia A. Weber & Ceridwen I. Fraser

  2. Department of Zoology, University of Otago, 340 Great King Street, Dunedin, 9016, New Zealand

    Tania M. King

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  1. Laura J. Wilson
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  2. Xénia A. Weber
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  3. Tania M. King
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  4. Ceridwen I. Fraser
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Correspondence to Ceridwen I. Fraser .

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Editors and Affiliations

  1. Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China

    Zi-Min Hu

  2. Fenner School of Environment and Society, Australian National University, Canberra, Aust Capital Terr, Australia

    Ceridwen Fraser

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Wilson, L.J., Weber, X.A., King, T.M., Fraser, C.I. (2016). DNA Extraction Techniques for Genomic Analyses of Macroalgae. In: Hu, ZM., Fraser, C. (eds) Seaweed Phylogeography. Springer, Dordrecht. https://doi.org/10.1007/978-94-017-7534-2_15

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