Quantitative PCR assays to detect whales, rockfish, and common murre environmental DNA in marine water samples of the Northeastern Pacific
Open Access
- 2 December 2020
- journal article
- research article
- Published by Public Library of Science (PLoS) in PLOS ONE
- Vol. 15 (12), e0242689
- https://doi.org/10.1371/journal.pone.0242689
Abstract
Monitoring aquatic species by identification of environmental DNA (eDNA) is becoming more common. To obtain quantitative eDNA datasets for individual species, organism-specific quantitative PCR (qPCR) assays are required. Here, we present detailed methodology of qPCR assay design and testing, including in silico, in vitro, and in vivo testing, and comment on the challenges associated with assay design and performance. We use the presented methodology to design assays for three important marine organisms common in the California Current Ecosystem (CCE): humpback whale (Megaptera novaeangliae), shortbelly rockfish (Sebastes jordani), and common murre (Uria aalge). All three assays have excellent sensitivity and high efficiencies ranging from 92% to 99%. However, specificities of the assays varied from species-specific in the case of common murre, genus-specific for the shortbelly rockfish assay, and broadly whale-specific for the humpback whale assay, which cross-amplified with other two other whale species, including one in a different family. All assays detected their associated targets in complex environmental water samples.Keywords
Funding Information
- National Aeronautics and Space Administration (NNX14AP62A)
This publication has 47 references indexed in Scilit:
- Analysis Tool Web Services from the EMBL-EBINucleic Acids Research, 2013
- Primer-BLAST: A tool to design target-specific primers for polymerase chain reactionBMC Bioinformatics, 2012
- Trophic Levels of North Pacific Humpback Whales (Megaptera novaeangliae) Through Analysis of Stable Isotopes: Implications on Prey and Resource QualityAquatic Mammals, 2011
- Multi-decadal oceanic ecological datasets and their application in marine policy and managementTrends in Ecology & Evolution, 2010
- An Overview of Marine Biodiversity in United States WatersPLOS ONE, 2010
- A new bioinformatics analysis tools framework at EMBL-EBINucleic Acids Research, 2010
- DNA extraction procedures meaningfully influence qPCR-based mtDNA copy number determinationMitochondrion, 2009
- Cetacean distributions relative to ocean processes in the northern California Current SystemDeep Sea Research Part II: Topical Studies in Oceanography, 2005
- A steady state model of particulate organic carbon flux below the mixed layer and application to the Joint Global Ocean Flux StudyJournal of Geophysical Research: Oceans, 2001
- Sequence logos: a new way to display consensus sequencesNucleic Acids Research, 1990