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DNA Extraction Protocols for Whole-Genome Sequencing in Marine Organisms

Panova, Marina and Aronsson, Henrik and Cameron, R. Andrew and Dahl, Peter and Godhe, Anna and Lind, Ulrika and Ortega-Martinez, Olga and Pereyra, Ricardo and Tesson, Sylvie V. M. and Wrange, Anna-Lisa and Blomberg, Anders and Johannesson, Kerstin (2016) DNA Extraction Protocols for Whole-Genome Sequencing in Marine Organisms. In: Marine Genomics. Methods in Molecular Biology. No.1452. Springer , New York, NY, pp. 13-44. ISBN 978-1-4939-3772-1. http://resolver.caltech.edu/CaltechAUTHORS:20160801-153255845

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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.


Item Type:Book Section
Related URLs:
URLURL TypeDescription
http://dx.doi.org/10.1007/978-1-4939-3774-5_2DOIArticle
http://link.springer.com/protocol/10.1007%2F978-1-4939-3774-5_2PublisherArticle
ORCID:
AuthorORCID
Cameron, R. Andrew0000-0003-3947-6041
Additional Information:© 2016 Springer.
Subject Keywords:Genomic DNA extraction Gastropod Littorina Isopod Idotea Barnacle Balanus Brittle star Amphiura Brown alga Fucus Diatom Skeletonema Marine yeast Debaryomyces
Record Number:CaltechAUTHORS:20160801-153255845
Persistent URL:http://resolver.caltech.edu/CaltechAUTHORS:20160801-153255845
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:69365
Collection:CaltechAUTHORS
Deposited By: Tony Diaz
Deposited On:01 Aug 2016 23:24
Last Modified:01 Aug 2016 23:24

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