Toward a global reference database of COI barcodes for marine zooplankton

Abstract

Characterization of species diversity of zooplankton is key to understanding, assessing, and predicting the function and future of pelagic ecosystems throughout the global ocean. The marine zooplankton assemblage, including only metazoans, is highly diverse and taxonomically complex, with an estimated ~28,000 species of 41 major taxonomic groups. This review provides a comprehensive summary of DNA sequences for the barcode region of mitochondrial cytochrome oxidase I (COI) for identified specimens. The foundation of this summary is the MetaZooGene Barcode Atlas and Database (MZGdb), a new open-access data and metadata portal that is linked to NCBI GenBank and BOLD data repositories. The MZGdb provides enhanced quality control and tools for assembling COI reference sequence databases that are specific to selected taxonomic groups and/or ocean regions, with associated metadata (e.g., collection georeferencing, verification of species identification, molecular protocols), and tools for statistical analysis, mapping, and visualization. To date, over 150,000 COI sequences for ~ 5600 described species of marine metazoan plankton (including holo- and meroplankton) are available via the MZGdb portal. This review uses the MZGdb as a resource for summaries of COI barcode data and metadata for important taxonomic groups of marine zooplankton and selected regions, including the North Atlantic, Arctic, North Pacific, and Southern Oceans. The MZGdb is designed to provide a foundation for analysis of species diversity of marine zooplankton based on DNA barcoding and metabarcoding for assessment of marine ecosystems and rapid detection of the impacts of climate change.

From Phenotypes to Genotypes and Back: Toward an Integrated Evaluation of Biodiversity in Calanoid Copepods

“…Next, as a template for PCR, the extracted DNA was used to amplify the mitochondrial gene cytochrome c oxidase subunit I (COI) 710 bp, in a final volume of 25 µL, using C-1000 TouchTM Thermal Cycler. Primers pairs used for amplification and for the following sequence analysis were the universal COI primers (forward LCO1490: 5'-ggtcaacaaatcataaagatattgg-3' and reverse HC02198: 5'-taaacttcagggtgaccaaaaaatca-3') (Folmer et al, 1994), considered a reference standard for marine zooplankton (Bucklin et al, 2010a(Bucklin et al, , 2011(Bucklin et al, , 2021. The PCR thermal conditions included an initial denaturation step at 95 • C for 5 min, followed by forty cycles at 95 • C (denaturation for 5 min), 45 • C (annealing for 1 min), and 72 • C (extension for 1 min), then a final extension step at 72 • C for 7 min.…”

“…Currently, ∼5,700 holoplankton species are described, but it is estimated that ∼1,600 more species are yet to be discovered and described (Bucklin et al, 2010b(Bucklin et al, , 2021. Among holoplanktonic organisms, copepods often dominate marine zooplankton assemblages, both in terms of abundance (Humes, 1994) and diversity (Uttieri, 2018;Laakmann et al, 2020;Bucklin et al, 2021;Walter and Boxshall, 2021). The morphological identification and the molecular taxonomy of these microscopic crustaceans are very difficult to address.…”

“…DNA barcoding, based on the sequencing of highly conserved DNA regions with little intraspecific variations of the mitochondrial cytochrome c oxidase I (COI) gene, is a precise and reliable identification tool (Tautz et al, 2002). Despite calanoid copepods are one of the best studied groups of marine zooplankton by using such an approach (Bucklin et al, 2010a,b;Laakmann et al, 2013Laakmann et al, , 2020Blanco-Bercial et al, 2014) molecular barcoding is still restricted to few copepod families, mainly from the order Calanoida (42%) (Bucklin et al, 2021), and only 104 calanoid species (26%) presently have COI barcodes. 1 Such gap calls for an effort, coupling traditional taxonomy (phenotypic-based) with molecular taxonomy (genotypic-based).…”

Framing Cutting-Edge Integrative Deep-Sea Biodiversity Monitoring via Environmental DNA and Optoacoustic Augmented Infrastructures

“…These inventories are exclusively based on records of collected organisms. In parallel, genetic and genomic databases have been implemented, that are either inclusive as in the case of GenBank (Clark et al, 2016) or BOLD (Ratnasingham and Hebert, 2013), or restricted to selected groups of organisms, such as MZGdb (Bucklin et al, 2021), PR2 (Guillou et al, 2013) and PLANiTS (Banchi et al, 2020).…”

“…However, such reference databases are still far from complete, especially for deep-sea communities (Weigand et al, 2019). Additionally, misidentifications of reference sequences have been frequently reported, highlighting the need of refinement and curation of these databases to reduce false negatives, and conflicts in taxonomic assignment (Stefanni et al, 2018;Schroeder et al, 2020;Bucklin et al, 2021).…”