Data from: Marine zooplankton, mini-barcodes, and DNA metabarcoding: The case for taxon-specific primers

<b>Abstract</b><b><br></b>DNA metabarcoding is an emerging tool for rapid species identification, with output data that can be applied to describe communities and provide biodiversity estimates. The approach utilizes high-throughput sequencing and target-specific markers to simultaneously identify multiple species present in taxonomically complex samples. Successful identification at species-level relies on genetic markers that cover a broad taxonomic range yet retain sufficient sequence divergence to resolve species; and on DNA reference libraries that link individual sequences to taxonomic descriptions. Here, we provide a versatile metabarcoding protocol for biomonitoring of bulk marine zooplankton samples targeting taxa with life-history stages important to commercial fisheries, such as prawns, shrimps, crabs, lobsters, and fish. Taxon-specific DNA mini-barcode primers were designed to amplify variable portions of the mitochondrial cytochrome c oxidase subunit I (COI) gene region and used together with primers already available in the literature. A series of tests were conducted on artificially assembled mock (with known species ratios) and coastal zooplankton communities to determine the efficiency of the selected protocol and primers. The use of a single primer pair versus primer cocktails (multiple primer sets) was assessed by evaluating species detection rates. Primer cocktails significantly increased the overall species detection in all samples. Taxon-specific primers increased the detection rate of target taxa when compared to using the universal primer set, highlighting the importance of accurate taxon-specific primer design for metabarcoding applications. The protocol developed, provides a rapid and cost-effective tool for biomonitoring of zooplankton communities in marine pelagic environments.<br>The data added to figshare includes the raw sequence data generated for each mock community using next-generation sequencing and Sanger sequences downloaded from GenBank to create the local reference library.