DNA Extraction protocols for whole-genome sequencing in marine organisms
Panova, M.; Aronsson, H.; Cameron, R.A.; Dahl, P.; Godhe, A.; Lind, U.; Ortega-Martinez, O.; Pereyra, R.; Tesson, S.V.M.; Wrange, A-L.; Blomberg, A.; Johannesson, K. (2016). DNA Extraction protocols for whole-genome sequencing in marine organisms, in: Bourlat, S.J. (Ed.) Marine genomics: methods and protocols. Methods in Molecular Biology, 1452: pp. 13-44. https://dx.doi.org/10.1007/978-1-4939-3774-5_2
In: Bourlat, S.J. (Ed.) (2016). Marine genomics: methods and protocols. Methods in Molecular Biology, 1452. Humana Press/Springer Science+Business Media, Inc: New York. ISBN 978-1-4939-3772-1. 253 pp. https://dx.doi.org/10.1007/978-1-4939-3774-5, more
In: Methods in Molecular Biology. Humana Press. ISSN 1064-3745, more
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| Keywords |
Arthropods > Crustacea > Cirripedia > Thoracica > Balanidae > Balanus
Eukaryotes > Fungi > Eumycota > Ascomycotina > Endomycetales > Debaryomyces
Amphiura (Amphiura) Forbes, 1843 [WoRMS]; Fucus Linnaeus, 1753 [WoRMS]; Idotea Fabricius, 1798 [WoRMS]; Littorina A. Férussac, 1822 [WoRMS]; Skeletonema R.K. Greville, 1865 [WoRMS]
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| Author keywords |
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| Authors | | Top |
- Panova, M.
- Aronsson, H.
- Cameron, R.A.
- Dahl, P.
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- Godhe, A.
- Lind, U.
- Ortega-Martinez, O.
- Pereyra, R.
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- Tesson, S.V.M.
- Wrange, A-L.
- Blomberg, A.
- Johannesson, K.
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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. |
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