Data from: Effect of marker choice and thermal cycling protocol on zooplankton DNA metabarcoding studies

DNA metabarcoding is a promising approach for rapidly surveying
biodiversity and is likely to become an important tool for measuring
ecosystem responses to environmental change. Metabarcoding markers need
sufficient taxonomic coverage to detect groups of interest, sufficient
sequence divergence to resolve species, and will ideally indicate relative
abundance of taxa present. We characterized zooplankton assemblages with
three different metabarcoding markers (nuclear 18S rDNA, mitochondrial
COI, and mitochondrial 16S rDNA) to compare their performance in terms of
taxonomic coverage, taxonomic resolution, and correspondence between
morphology- and DNA-based identification. COI amplicons sequenced on
separate runs showed that operational taxonomic units representing
>0.1% of reads per sample were highly reproducible, although
slightly more taxa were detected using a lower annealing temperature.
Mitochondrial COI and nuclear 18S showed similar taxonomic coverage across
zooplankton phyla. However, mitochondrial COI resolved up to threefold
more taxa to species compared to 18S. All markers revealed similar
patterns of beta-diversity, although different taxa were identified as the
greatest contributors to these patterns for 18S. For calanoid copepod
families, all markers displayed a positive relationship between biomass
and sequence reads, although the relationship was typically strongest for
18S. The use of COI for metabarcoding has been questioned due to lack of
conserved primer-binding sites. However, our results show the taxonomic
coverage and resolution provided by degenerate COI primers, combined with
a comparatively well-developed reference sequence database, make them
valuable metabarcoding markers for biodiversity assessment.