Valsecchi, E, Bylemans, J, Goodman, SJ orcid.org/0000-0003-4118-8575 et al. (5 more authors) (2020) Novel universal primers for metabarcoding environmental DNA surveys of marine mammals and other marine vertebrates. Environmental DNA, 2 (4). pp. 460-476. ISSN 2637-4943
Abstract
Metabarcoding studies using environmental DNA (eDNA) and high‐throughput sequencing (HTS) are rapidly becoming an important tool for assessing and monitoring marine biodiversity, detecting invasive species, and supporting basic ecological research. Several barcode loci targeting teleost fish and elasmobranchs have previously been developed, but to date primer sets focusing on other marine megafauna, such as marine mammals, have received less attention. Similarly, there have been few attempts to identify potentially “universal” barcode loci which may be informative across multiple marine vertebrate orders. Here we describe the design and validation of two new sets of primers targeting hypervariable regions of the vertebrate mitochondrial 12S and 16S rRNA genes, which have conserved priming sites across virtually all cetaceans, pinnipeds, elasmobranchs, boney fish, sea turtles, and birds, and amplify fragments with consistently high levels of taxonomically diagnostic sequence variation. “In silico” validation using the OBITOOLS software showed our new barcode loci outperformed most existing vertebrate barcode loci for taxon detection and resolution. We also evaluated sequence diversity and taxonomic resolution of the new barcode loci in 680 complete marine mammal mitochondrial genomes demonstrating that they are effective at resolving amplicons for most taxa to the species level. Finally, we evaluated the performance of the primer sets with eDNA samples from aquarium communities with known species composition. These new primers will potentially allow surveys of complete marine vertebrate communities in single HTS metabarcoding assessments, simplifying workflows, reducing costs, and increasing accessibility to a wider range of investigators.
Metadata
Item Type: | Article |
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Authors/Creators: |
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Copyright, Publisher and Additional Information: | © 2020 The Authors. Environmental DNA published by John Wiley & Sons Ltd. This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/. |
Keywords: | 12S; 16S; cetaceans; fish; pinnipeds; sea turtles |
Dates: |
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Institution: | The University of Leeds |
Academic Units: | The University of Leeds > Faculty of Biological Sciences (Leeds) > School of Biology (Leeds) |
Depositing User: | Symplectic Publications |
Date Deposited: | 22 Jul 2020 12:43 |
Last Modified: | 25 Jun 2023 22:21 |
Status: | Published |
Publisher: | Wiley |
Identification Number: | 10.1002/edn3.72 |
Open Archives Initiative ID (OAI ID): | oai:eprints.whiterose.ac.uk:163577 |