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DNA Extraction Protocols for Whole-Genome Sequencing in Marine Organisms

Panova, M; Aronsson, H; Cameron, RA; Dahl, P; Godhe, A; Lind, U; Ortega-Martinez, O; Pereyra, R; Tesson, Sylvie LU and Wrange, A-L, et al. (2016) In Marine Genomics - Methods and Protocols 1452. p.13-44
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... (More)
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. (Less)
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organization
publishing date
type
Chapter in Book/Report/Conference proceeding
publication status
published
subject
in
Marine Genomics - Methods and Protocols
editor
Bourlat, Sarah and
volume
1452
pages
13 - 44
publisher
Humana Press
external identifiers
  • scopus:84982747287
ISSN
1064-3745
ISBN
978-1-4939-3772-1
978-1-4939-3774-5
DOI
10.1007/978-1-4939-3774-5
language
English
LU publication?
yes
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2c561405-5a04-4e22-a376-9b481fd63966
date added to LUP
2016-07-25 15:35:55
date last changed
2017-04-30 17:28:49
@inbook{2c561405-5a04-4e22-a376-9b481fd63966,
  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.},
  author       = {Panova, M and Aronsson, H and Cameron, RA and Dahl, P and Godhe, A and Lind, U and Ortega-Martinez, O and Pereyra, R and Tesson, Sylvie and Wrange, A-L and Blomberg, A and Johannesson, K},
  editor       = {Bourlat, Sarah},
  isbn         = {978-1-4939-3772-1},
  issn         = {1064-3745},
  language     = {eng},
  pages        = {13--44},
  publisher    = {Humana Press},
  series       = {Marine Genomics - Methods and Protocols},
  title        = {DNA Extraction Protocols for Whole-Genome Sequencing in Marine Organisms},
  url          = {http://dx.doi.org/10.1007/978-1-4939-3774-5},
  volume       = {1452},
  year         = {2016},
}