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

Citation

Clarke, LJ and Beard, JM and Swadling, KM and Deagle, BE, Effect of marker choice and thermal cycling protocol on zooplankton DNA metabarcoding studies, Ecology and Evolution, 7, (3) pp. 873-883. ISSN 2045-7758 (2017) [Refereed Article]


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Copyright Statement

Copyright 2017 The Authors. Licensed under Creative Commons Attribution 4.0 International (CC BY 4.0) https://creativecommons.org/licenses/by/4.0/

DOI: doi:10.1002/ece3.2667

Abstract

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.

Item Details

Item Type:Refereed Article
Keywords:cytochrome oxidase subunit I, environmental DNA, metabarcoding, mitochondrial 16S ribosomal DNA, nuclear 18S rDNA, zooplankton
Research Division:Biological Sciences
Research Group:Genetics
Research Field:Population, Ecological and Evolutionary Genetics
Objective Division:Environment
Objective Group:Flora, Fauna and Biodiversity
Objective Field:Sparseland, Permanent Grassland and Arid Zone Flora, Fauna and Biodiversity
Author:Clarke, LJ (Dr Laurence Clarke)
Author:Beard, JM (Mr Jason Beard)
Author:Swadling, KM (Dr Kerrie Swadling)
Author:Deagle, BE (Dr Bruce Deagle)
ID Code:114582
Year Published:2017
Web of Science® Times Cited:1
Deposited By:CRC-Antarctic Climate & Ecosystems
Deposited On:2017-02-20
Last Modified:2017-11-15
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