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AuthorBoughattas, Sonia
AuthorAlbatesh, Dana
AuthorAl-Khater, Albandari
AuthorGiraldes, Bruno W.
AuthorAlthani, Asma A.
AuthorBenslimane, Fatiha M.
Available date2022-01-17T06:56:22Z
Publication Date2021-12-07
Publication NameEcology and Evolution
Identifierhttp://dx.doi.org/10.1002/ece3.8447
CitationBoughattas, S., Albatesh, D., Al-Khater, A., Giraldes, B. W., Althani, A. A., & Benslimane, F. M. (2021). Whole genome sequencing of marine organisms by Oxford Nanopore Technologies: Assessment and optimization of HMW-DNA extraction protocols. Ecology and Evolution, 11, 18505– 18513. https://doi.org/10.1002/ece3.8447
URIhttps://www.scopus.com/inward/record.uri?partnerID=HzOxMe3b&scp=85120687096&origin=inward
URIhttp://hdl.handle.net/10576/25667
AbstractMarine habitats are Earth's largest aquatic ecosystems, yet little is known about marine organism's genomes. Molecular studies can unravel their genetics print, thus shedding light on specie's adaptation and speciation with precise authentication. However, extracting high molecular weight DNA from marine organisms and subsequent DNA library preparation for whole genome sequencing is challenging. The challenges can be explained by excessive metabolites secretion that co-precipitates with DNA and barricades their sequencing. In this work, we sought to resolve this issue by describing an optimized isolation method and comparing its performance with the most commonly reported protocols or commercial kits: SDS/phenol–chloroform method, Qiagen Genomic Tips kit, Qiagen DNeasy Plant mini kit, a modified protocol of Qiagen DNeasy Plant kit, Qiagen DNeasy Blood and Tissue kit, and Qiagen Qiamp DNA Stool mini kit. Our method proved to work significantly better for different marine species regardless of their shape, consistency, and sample preservation, improving Oxford Nanopore Technologies sequencing yield by 39 folds for Spirobranchus sp. and enabling generation of almost 10 GB data per flow cell/run for Chrysaora sp. and Palaemon sp. samples.
Languageen
PublisherWiley
SubjectDNA extraction
marine species
ONT sequencing
protocol optimization
whole genome sequencing
TitleWhole genome sequencing of marine organisms by Oxford Nanopore Technologies: Assessment and optimization of HMW-DNA extraction protocols
TypeArticle
Pagination1-9
Issue Number24
Volume Number11
dc.accessType Open Access


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