title: Metabarcoding Marine Sediments: Preparation of Amplicon Libraries.
abstract: 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.
authors.affiliation: Zoological Research Museum Alexander Koenig (ZFMK), Centre for Molecular Biodiversity Research, Adenauerallee 160, 53113, Bonn, Germany. vfonseca@uni-bonn.de.
authors.forename: Vera G
authors.initials: VG
authors.lastname: Fonseca
authors.affiliation: Institut National de la Recherche Agronomique (INRA), Unité Génétique en Aquaculture, Centre de Jouy-en-Josas, Domaine de Vilvert, 78350, Jouy-en-Josas, France.
authors.forename: Delphine
authors.initials: D
authors.lastname: Lallias
mesh_terms: D044822:Biodiversity; D058893:DNA Barcoding, Taxonomic / Q000379:methods*; D017931:DNA Primers / Q000235:genetics; D019015:Geologic Sediments / Q000032:analysis*; D059014:High-Throughput Nucleotide Sequencing; D016133:Polymerase Chain Reaction
chemical_list: D017931:DNA Primers
keywords: Environmental DNA; High-throughput sequencing; Illumina; Marine eukaryotes; Metabarcoding; Molecular biodiversity; NGS