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DNA Extraction Protocols for Whole-Genome Sequencing in Marine Organisms

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Book cover Marine Genomics

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1452))

Abstract

The marine environment harbors a large proportion of the total biodiversity on this planet, including the majority of the earths’ different phyla and classes. Studying the genomes of marine organisms can bring interesting insights into genome evolution. Today, almost all marine organismal groups are understudied with respect to their genomes. One potential reason is that extraction of high-quality DNA in sufficient amounts is challenging for many marine species. This is due to high polysaccharide content, polyphenols and other secondary metabolites that will inhibit downstream DNA library preparations. Consequently, protocols developed for vertebrates and plants do not always perform well for invertebrates and algae. In addition, many marine species have large population sizes and, as a consequence, highly variable genomes. Thus, to facilitate the sequence read assembly process during genome sequencing, it is desirable to obtain enough DNA from a single individual, which is a challenge in many species of invertebrates and algae. Here, we present DNA extraction protocols for seven marine species (four invertebrates, two algae, and a marine yeast), optimized to provide sufficient DNA quality and yield for de novo genome sequencing projects.

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Acknowledgments

This work was funded by the Swedish Research Councils (VR and Formas) through the Linnaeus Centre for Marine Evolutionary Biology at University of Gothenburg. We thank Mikael Dahl, Sonja Leidenberger, and Pierre De Wit for sharing their experience on other DNA extraction protocols for Idotea balthica and Natalia Mikhailova for sharing her experience on DNA extraction methods for Littorina saxatilis.

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Authors and Affiliations

  1. Department of Marine Sciences, University of Gothenburg, Strömstad, Sweden

    Marina Panova, Anna Godhe, Ulrika Lind, Olga Ortega-Martinez, Ricardo Pereyra, Sylvie V. M. Tesson, Anna-Lisa Wrange, Anders Blomberg & Kerstin Johannesson

  2. Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden

    Henrik Aronsson

  3. Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA

    R. Andrew Cameron

  4. Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden

    Peter Dahl

Authors
  1. Marina Panova
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  2. Henrik Aronsson
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  3. R. Andrew Cameron
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  4. Peter Dahl
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  5. Anna Godhe
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  6. Ulrika Lind
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  7. Olga Ortega-Martinez
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  8. Ricardo Pereyra
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  9. Sylvie V. M. Tesson
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  10. Anna-Lisa Wrange
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  11. Anders Blomberg
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  12. Kerstin Johannesson
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Corresponding author

Correspondence to Marina Panova .

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Editors and Affiliations

  1. Department of Marine Sciences, University of Gothenburg, Gothenburg, Sweden

    Sarah J. Bourlat

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© 2016 Springer Science+Business Media New York

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Panova, M. et al. (2016). DNA Extraction Protocols for Whole-Genome Sequencing in Marine Organisms. In: Bourlat, S. (eds) Marine Genomics. Methods in Molecular Biology, vol 1452. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-3774-5_2

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  • DOI: https://doi.org/10.1007/978-1-4939-3774-5_2

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-3772-1

  • Online ISBN: 978-1-4939-3774-5

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