DNA Extraction Protocols for Whole-Genome Sequencing in Marine Organisms

  • Marina Panova
  • Henrik Aronsson
  • R. Andrew Cameron
  • Peter Dahl
  • Anna Godhe
  • Ulrika Lind
  • Olga Ortega-Martinez
  • Ricardo Pereyra
  • Sylvie V. M. Tesson
  • Anna-Lisa Wrange
  • Anders Blomberg
  • Kerstin Johannesson
Part of the Methods in Molecular Biology book series (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.

Key words

Genomic DNA extraction Gastropod Littorina Isopod Idotea Barnacle Balanus Brittle star Amphiura Brown alga Fucus Diatom Skeletonema Marine yeast Debaryomyces 

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Copyright information

© Springer Science+Business Media New York 2016

Authors and Affiliations

  • Marina Panova
    • 1
  • Henrik Aronsson
    • 2
  • R. Andrew Cameron
    • 3
  • Peter Dahl
    • 4
  • Anna Godhe
    • 1
  • Ulrika Lind
    • 1
  • Olga Ortega-Martinez
    • 1
  • Ricardo Pereyra
    • 1
  • Sylvie V. M. Tesson
    • 1
  • Anna-Lisa Wrange
    • 1
  • Anders Blomberg
    • 1
  • Kerstin Johannesson
    • 1
  1. 1.Department of Marine SciencesUniversity of GothenburgStrömstadSweden
  2. 2.Department of Biological and Environmental SciencesUniversity of GothenburgGothenburgSweden
  3. 3.Division of Biology and Biological EngineeringCalifornia Institute of TechnologyPasadenaUSA
  4. 4.Department of Chemistry and Molecular BiologyUniversity of GothenburgGothenburgSweden

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