Journal Article

Novel universal primers for metabarcoding environmental DNA surveys of marine mammals and other marine vertebrates

Carr, Ian, Goodman, Simon J., Galimberti, Andrea, Lombardi, Roberto, Bylemans, Jonas, Valsecchi, Elena, Galli, Paolo, Castellano, Laura

2020

Overview

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. 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. 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.

• Publisher: John Wiley & Sons, Inc,Wiley
• Subject: 12S / 16S / Aquariums / Aquatic mammals / Aquatic reptiles / Biodiversity / Caretta caretta / cetaceans / Deoxyribonucleic acid / Design / Diagnostic software / Diagnostic systems / DNA / DNA sequencing / Ecological research / Environmental DNA / Fish / Genomes / Introduced species / Invasive species / Invertebrates / Lepidochelys kempii / Lepidochelys olivacea / Loci / Marine mammals / Megafauna / Mitochondria / Performance evaluation / pinnipeds / Polls & surveys / Primers / rRNA 12S / rRNA 16S / Sea turtles / Species composition / Taxa / Taxonomy / Vertebrates