DOI: 10.5061/dryad.0sc0s
title: Data from: Benchmarking DNA metabarcoding for biodiversity-based monitoring and assessment

description: Characterization of biodiversity has been extensively used to confidently
 monitor and assess environmental status. Yet, visual morphology,
 traditionally and widely used for species identification in coastal and
 marine ecosystem communities, is tedious and entails limitations.
 Metabarcoding coupled with high-throughput sequencing represents an
 alternative to rapidly, accurately and cost-effectively analyze thousands
 of environmental samples simultaneously, and this method is increasingly
 used to characterize the metazoan taxonomic composition of a wide variety
 of environments. However, a comprehensive study benchmarking visual and
 metabarcoding-based taxonomic inferences that validates this technique for
 environmental monitoring is still lacking. Here we compare taxonomic
 inferences of benthic macroinvertebrate samples of known taxonomic
 composition obtained using alternative metabarcoding protocols based on a
 combination of different DNA sources, barcodes of the mitochondrial
 cytochrome oxidase I gene and amplification conditions. Our results
 highlight the influence of the metabarcoding protocol in the obtained
 taxonomic composition and suggest the better performance of an alternative
 313 bp length barcode to the traditionally 658 bp length one used for
 metazoan metabarcoding. Additionally, we show that a biotic index inferred
 from the list of macroinvertebrate taxa obtained using DNA-based taxonomic
 assignments is comparable to that inferred using morphological
 identification. Thus, our analyses prove metabarcoding valid for
 environmental status assessment and will contribute to accelerating the
 implementation of this technique to regular monitoring programs.
description: Taxonomic assignments
 using mlCOI barcodeThe file contains the
 taxonomic assignments for reads obtained using mlCOI barcode across all
 stations for each sample source, DNA type (Extracellular, Bulk or Pooled
 DNA) and PCR annealing temperature (46 °C, 50 °C or, TD). Ecological Group
 (EG) for each taxa according AMBI is detailed and number of reads
 transformed into relative proportions shown. Presence/absence of taxa
 found using traditional identification at each station is represented by
 x.Taxonomic_assignments_mlCOI.docTaxonomic assignments using folCOI barcodeThe file contains the taxonomic assignments for reads obtained using folCOI barcode across all stations for each sample source, DNA type (Extracellular, Bulk or Pooled DNA) and PCR annealing temperature (46 °C, 50 °C or, TD). Ecological Group (EG) for each taxa according AMBI is detailed and number of reads transformed into relative proportions shown. Presence/absence of taxa found using traditional identification at each station is represented by x.Taxonomic_assignments_folCOI.docUnique Sequences mlCOI barcodeFollowing Illumina MiSeq sequencing of the mlCOI barcode of 114 samples, 130,670 unique metazoan sequences were identified. The zip file contains a fasta file with all the unique sequences and a table showing the distribution of sequencing reads for all unique sequences across the 114 samples for each DNA type (extracellular (ext), Bulk or Pooled DNA) and PCR annealing temperature (46 °C, 50 °C or, TD).UniqueSequences_mlCOI.zipUnique Sequences folCOI barcodeFollowing Illumina MiSeq sequencing of the folCOI barcode of 110 samples, 652,356 unique metazoan sequences were identified. The zip file contains a fasta file with all the unique sequences and a table showing the distribution of sequencing reads for all unique sequences across the 110 samples for each DNA type (extracellular (ext), Bulk or Pooled DNA) and PCR annealing temperature (46, 50 or TD).UniqueSequences_folCOI.zip