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Metabarcoding marine sediments: preparation of amplicon libraries

Fonseca, V. G. & Lallias, D.
Vollständiger Titel: 
Metabarcoding marine sediments: preparation of amplicon libraries
ZFMK-Autorinnen / ZFMK-Autoren: 
Org. Einordnung: 
Publiziert in: 
Methods in Molecular Biology
Beitrag zu Sammelwerk
DOI Name: 
Metabarcoding; Marine eukaryotes; Environmental DNA; High-throughput sequencing; NGS; Molecular biodiversity; Illumina
Bibliographische Angaben: 
Fonseca, V. G. & Lallias, D. (2016): Metabarcoding marine sediments: preparation of amplicon libraries. In: Bourlat, S. J. (ed.): Marine Genomics - Methods and protocols. - Springer (New York). pp. 183-196. https://doi.org/10.1007/978-1-4939-3774-5_12

The accurate assessment of community composition and ultimately species identification is of utmost importance in any ecological and evolutionary study. Advances in sequencing technologies have allowed the unraveling of levels of biodiversity never imagined before when applied to large-scale environmental DNA studies (also termed metabarcoding/metagenetics/metasystematics/environmental barcoding). Here, we describe a detailed protocol to assess eukaryotic biodiversity in marine sediments, identifying key steps that should not be neglected when preparing Next-Generation Sequencing (NGS) amplicon libraries: DNA extraction, multiple PCR amplification of DNA barcode markers with index/ tag-primers, and final Illumina MiSeq sequencing library preparation.