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In silico assessment of primers for eDNA studies using PrimerTree and application to characterize the biodiversity surrounding the Cuyahoga River

https://doi.org/10.1038/srep22908
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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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ggplot2: Elegant Graphics for Data Analysis
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Introduction
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Surveillance of fish species composition using environmental DNA
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Barcoding diatoms: evaluation of the V4 subregion on the 18S rRNA gene, including new primers and protocols
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The extraction and purification of microbial DNA from sediments
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Choice of capture and extraction methods affect detection of freshwater biodiversity from environmental DNA
inferredcites →https://doi.org/10.1016/j.biocon.2014.11.029openalex-snapshot
Using eDNA to develop a national citizen science-based monitoring programme for the great crested newt (Triturus cristatus)
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Review and re-analysis of domain-specific 16S primers
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A novel method for determining microflora composition using dynamic phylogenetic analysis of 16S ribosomal RNA deep sequencing data
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Basic Local Alignment Search Tool
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Fast, scalable generation of high‐quality protein multiple sequence alignments using Clustal Omega
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Microbial community resemblance methods differ in their ability to detect biologically relevant patterns
inferredcites →https://doi.org/10.1038/nmeth.f.303openalex-snapshot
QIIME allows analysis of high-throughput community sequencing data
inferredcites →https://doi.org/10.1073/pnas.1406468111openalex-snapshot
Simultaneous assessment of the macrobiome and microbiome in a bulk sample of tropical arthropods through DNA metasystematics
inferredcites →https://doi.org/10.1086/678128openalex-snapshot
Utility of environmental DNA for monitoring rare and indicator macroinvertebrate species
inferredcites →https://doi.org/10.1093/bioinformatics/btg412openalex-snapshot
APE: Analyses of Phylogenetics and Evolution in R language
inferredcites →https://doi.org/10.1093/nar/gkl938openalex-snapshot
Power and limitations of the chloroplast trnL (UAA) intron for plant DNA barcoding
inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a025566openalex-snapshot
Reproducibility of ancient DNA sequences from extinct Pleistocene fauna
inferredcites →https://doi.org/10.1098/rsbl.2008.0118openalex-snapshot
Species detection using environmental DNA from water samples
inferredcites →https://doi.org/10.1111/1365-2664.12262openalex-snapshot
Environmental DNA surveillance for invertebrate species: advantages and technical limitations to detect invasive crayfish P rocambarus clarkiiin freshwater ponds
inferredcites →https://doi.org/10.1111/1365-2664.12306openalex-snapshot
REVIEW: The detection of aquatic animal species using environmental DNA – a review of eDNA as a survey tool in ecology
inferredcites →https://doi.org/10.1111/1755-0998.12159openalex-snapshot
Factors influencing detection of eDNA from a stream‐dwelling amphibian
inferredcites →https://doi.org/10.1111/1755-0998.12294openalex-snapshot
A metagenetic approach for revealing community structure of marine planktonic copepods
inferredcites →https://doi.org/10.1111/1755-0998.12355openalex-snapshot
Universal and blocking primer mismatches limit the use of high‐throughput DNA sequencing for the quantitative metabarcoding of arthropods
inferredcites →https://doi.org/10.1111/2041-210x.12206openalex-snapshot
Particle size distribution and optimal capture of aqueous macrobial eDNA
inferredcites →https://doi.org/10.1111/j.1365-294x.2011.05261.xopenalex-snapshot
Meta‐barcoding of ‘dirt’ DNA from soil reflects vertebrate biodiversity
inferredcites →https://doi.org/10.1111/j.1365-294x.2011.05297.xopenalex-snapshot
Metagenetic community analysis of microbial eukaryotes illuminates biogeographic patterns in deep‐sea and shallow water sediments
inferredcites →https://doi.org/10.1111/j.1365-294x.2011.05418.xopenalex-snapshot
Monitoring endangered freshwater biodiversity using environmental DNA
inferredcites →https://doi.org/10.1111/j.1365-294x.2012.05537.xopenalex-snapshot
New environmental metabarcodes for analysing soil DNA: potential for studying past and present ecosystems
inferredcites →https://doi.org/10.1111/j.1365-294x.2012.05542.xopenalex-snapshot
Environmental DNA
inferredcites →https://doi.org/10.1111/j.1529-8817.2007.00341.xopenalex-snapshot
UNIVERSAL PRIMERS AMPLIFY A 23S rDNA PLASTID MARKER IN EUKARYOTIC ALGAE AND CYANOBACTERIA1
inferredcites →https://doi.org/10.1111/j.1755-0998.2010.02920.xopenalex-snapshot
Taxon‐specific PCR for DNA barcoding arthropod prey in bat faeces
inferredcites →https://doi.org/10.1126/science.1093857openalex-snapshot
Environmental Genome Shotgun Sequencing of the Sargasso Sea
inferredcites →https://doi.org/10.1126/science.1107851openalex-snapshot
Comparative Metagenomics of Microbial Communities
inferredcites →https://doi.org/10.1128/aem.01541-09openalex-snapshot
Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities
inferredcites →https://doi.org/10.1186/1471-2105-13-134openalex-snapshot
Primer-BLAST: A tool to design target-specific primers for polymerase chain reaction
inferredcites →https://doi.org/10.1186/1471-2105-13-31openalex-snapshot
PANDAseq: paired-end assembler for illumina sequences
inferredcites →https://doi.org/10.1186/1471-2164-11-434openalex-snapshot
An In silico approach for the evaluation of DNA barcodes
inferredcites →https://doi.org/10.1186/1472-6785-12-28openalex-snapshot
Assessing biodiversity of a freshwater benthic macroinvertebrate community through non-destructive environmental barcoding of DNA from preservative ethanol
inferredcites →https://doi.org/10.1371/journal.pbio.0050077openalex-snapshot
The Sorcerer II Global Ocean Sampling Expedition: Northwest Atlantic through Eastern Tropical Pacific
inferredcites →https://doi.org/10.1371/journal.pone.0022746openalex-snapshot
Molecular Detection of Vertebrates in Stream Water: A Demonstration Using Rocky Mountain Tailed Frogs and Idaho Giant Salamanders
inferredcites →https://doi.org/10.1371/journal.pone.0058316openalex-snapshot
Validation of eDNA Surveillance Sensitivity for Detection of Asian Carps in Controlled and Field Experiments
inferredcites →https://doi.org/10.1371/journal.pone.0086175openalex-snapshot
Using Environmental DNA to Census Marine Fishes in a Large Mesocosm
inferredcites →https://doi.org/10.1371/journal.pone.0088786openalex-snapshot
Transport Distance of Invertebrate Environmental DNA in a Natural River
inferredcites →https://doi.org/10.1371/journal.pone.0117562openalex-snapshot
Metabarcoding Is Powerful yet Still Blind: A Comparative Analysis of Morphological and Molecular Surveys of Seagrass Communities
inferredcites →https://doi.org/10.1371/journal.pone.0130324openalex-snapshot
Can DNA-Based Ecosystem Assessments Quantify Species Abundance? Testing Primer Bias and Biomass—Sequence Relationships with an Innovative Metabarcoding Protocol
inferredcites →https://doi.org/10.4319/lom.2005.3.533openalex-snapshot
Isolation, amplification, and identification of ancient copepod DNA from lake sediments

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

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A comparative analysis of hybridisation capture and PCR-based eDNA metabarcoding for monitoring bryophytes in riparian ecosystems
inferred← citeshttps://doi.org/10.1002/aqc.3208openalex-snapshot
Taxonomic and geographical representation of freshwater environmental DNA research in aquatic conservation
inferred← citeshttps://doi.org/10.1002/ece3.4387openalex-snapshot
Toward an ecoregion scale evaluation of eDNA metabarcoding primers: A case study for the freshwater fish biodiversity of the Murray–Darling Basin (Australia)
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Environmental DNA metabarcoding primers for freshwater fish detection and quantification: In silico and in tanks
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A validation scale to determine the readiness of environmental DNA assays for routine species monitoring
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Comparing the performance of 12S mitochondrial primers for fish environmental DNA across ecosystems
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Targeted next‐generation sequencing of environmental DNA improves detection of invasive European green crab ( Carcinus maenas )
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Toward freshwater plant diversity surveys with eDNA barcoding and metabarcoding
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rCRUX : A rapid and versatile tool for generating metabarcoding reference libraries in R
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Validation of an eDNA ‐based workflow for monitoring inter‐ and intra‐specific CytB haplotype diversity of alpine amphibians
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Optimizing eDNA Replication for Standardized Application in Lotic Systems in Aotearoa, New Zealand
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Diet and Prey Selection of Migratory Shorebirds on Virginia Mudflats Revealed by Fecal DNA Metabarcoding
inferred← citeshttps://doi.org/10.1007/s00267-026-02551-9openalex-snapshot
A Review of Environmental DNA (eDNA)-Based Detection of Aquatic Denizens and Water‑Borne Pathogens in Wetlands: Recent Trends and Future Perspectives
inferred← citeshttps://doi.org/10.1007/s10530-021-02709-yopenalex-snapshot
Utilizing environmental DNA for wide-range distributions of reproductive area of an invasive terrestrial toad in Ishikari river basin in Japan
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Applications of environmental DNA (eDNA) in ecology and conservation: opportunities, challenges and prospects
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Highlighting the promise of qPCR-based environmental monitoring: response of the ribosomal RNA:DNA ratio of calanoid copepods to toxic cyanobacteria
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A review on the applications and recent advances in environmental DNA (eDNA) metagenomics
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Environmental DNA (eDNA): an eco-friendly approach for conservation of Indian freshwater diversity—a review
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Environmental DNA (eDNA): A Promising Biological Survey Tool for Aquatic Species Detection
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Metabarcoding markers and a reference database for neotropical mammals
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eDNA — Einführung in Methodik, Stand der Technik und Ausblick für alpine Gewässer
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14 Questions for Invasion in Ecological Networks
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Invasions Toolkit
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Environmental DNA metabarcoding for catchment-scale detection of aquatic plants, invasive species, and land-use indicators in a large river
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Applications of environmental DNA (eDNA) to detect subterranean and aquatic invasive species: A critical review on the challenges and limitations of eDNA metabarcoding
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Towards understanding the liver fluke transmission dynamics on farms: Detection of liver fluke transmitting snail and liver fluke-specific environmental DNA in water samples from an irrigated dairy farm in Southeast Australia
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The importance of nutrient ratios in determining elevations in geosmin synthase (geoA) and 2-MIB cyclase (mic) resulting in taste and odour events
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Extreme environmental conditions reduce coral reef fish biodiversity and productivity
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Demonstration of the potential of environmental DNA as a tool for the detection of avian species
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A novel metabarcoding diagnostic tool to explore protozoan haemoparasite diversity in mammals: a proof-of-concept study using canines from the tropics
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Diel and spatial variability in cyanobacterial composition, gene abundance, and toxin concentration: a pilot study
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A multiplex real-time PCR assay for detection of equid herpesvirus 1 and 4
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Evaluation of genetic markers for the metabarcoding of Australian marsupials from predator scats
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DNA metabarcoding potentially reveals multi-assemblage eutrophication responses in an eastern North American river
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High-throughput Identification of Eukaryotic Parasites and Arboviruses in Mosquitoes
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Utility of Occupancy Models with Environmental DNA (eDNA) from Olympic Coast National Marine Sanctuary
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A multiplex real-time PCR assay for detection of equine herpesvirus 1 and equine herpesvirus 4
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Environmental DNA reveals the structure of phytoplankton assemblages along a 2900-km transect in the Mississippi River
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Environmental DNA enables detection of terrestrial mammals from forest pond water
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Carrion fly‐derived DNA metabarcoding is an effective tool for mammal surveys: Evidence from a known tropical mammal community
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Measuring global fish species richness with eDNA metabarcoding
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Finding the perfect pairs: A matchmaking of plant markers and primers for multi‐marker eDNA metabarcoding
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Addressing false negatives and positives in eDNA studies
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Environmental DNA of aquatic macrophytes: The potential for reconstructing past and present vegetation and environments
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Uncovering the complete biodiversity structure in spatial networks: the example of riverine systems
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Improving herpetological surveys in eastern North America using the environmental DNA method
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The importance of molecular markers and primer design when characterizing biodiversity from environmental DNA
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PrimerEvalPy: a tool for in-silico evaluation of primers for targeting the microbiome
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Development of a novel mycobiome diagnostic for fungal infection
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Relative contributions of various endogenous and exogenous factors to the mosquito microbiota
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A high-throughput sequencing assay to comprehensively detect and characterize unicellular eukaryotes and helminths from biological and environmental samples
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High-throughput detection of eukaryotic parasites and arboviruses in mosquitoes
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Environmental DNA (eDNA) metabarcoding assays to detect invasive invertebrate species in the Great Lakes
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Dynamic microbial populations along the Cuyahoga River
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eDNA as a tool for non-invasive monitoring of the fauna of a turbid, well-mixed system, the Elbe estuary in Germany
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A workflow for the relative quantification of multiple fish species from oceanic water samples using environmental DNA (eDNA) to support large-scale fishery surveys
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Environmental DNA monitoring of waterfowl reveals community changes during migration
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Principle and application of co-occurrence networks for freshwater ecosystem assessment
inferred← citeshttps://doi.org/10.21203/rs.3.rs-9774605/v1openalex-snapshot
Waterborne eDNA reveals known and novel green plant diversity in two Texas rivers
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Development and Validation of an Environmental DNA Method for Detection of the Alligator Snapping Turtle (Macrochelys temminckii)
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VertU: universal multilocus primer sets for eDNA metabarcoding of vertebrate diversity, evaluated by both artificial and natural cases
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Environment DNA Reveals Fish Diversity in a Canyon River within the Upper Pearl River Drainage
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A Brief Review of Non-Avian Reptile Environmental DNA (eDNA), with a Case Study of Painted Turtle (Chrysemys picta) eDNA Under Field Conditions
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Metabarcoding of Environmental DNA Samples to Explore the Use of Uranium Mine Containment Ponds as a Water Source for Wildlife
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Artificial Intelligence-Assisted Environmental DNA Metabarcoding and High-Resolution Underwater Optical Imaging for Noninvasive and Innovative Marine Environmental Monitoring
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Are Genetic Reference Libraries Sufficient for Environmental DNA Metabarcoding of Mekong River Basin Fish?
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Seasonal Dynamics and Heavy Rain Effects on the Diversity of Microeukaryome in the Nakdonggang River
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An Overview of Ecological Indicators of Fish to Evaluate the Anthropogenic Pressures in Aquatic Ecosystems: From Traditional to Innovative DNA-Based Approaches
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A meta-barcoding census of freshwater planktonic protists in Appalachia – Natural Tunnel State Park, Virginia, USA
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Additional file 1 of Development of a novel mycobiome diagnostic for fungal infection
inferred← citeshttps://doi.org/10.6084/m9.figshare.25248928openalex-snapshot
Additional file 2 of Development of a novel mycobiome diagnostic for fungal infection
inferred← citeshttps://doi.org/10.6084/m9.figshare.26682601openalex-snapshot
Additional file 3 of Development of a novel mycobiome diagnostic for fungal infection
inferred← citeshttps://doi.org/10.6084/m9.figshare.26682604openalex-snapshot
Additional file 4 of Development of a novel mycobiome diagnostic for fungal infection
inferred← citeshttps://doi.org/10.6084/m9.figshare.26682607openalex-snapshot
Additional file 5 of Development of a novel mycobiome diagnostic for fungal infection
inferred← citeshttps://doi.org/10.6084/m9.figshare.26682610openalex-snapshot
Additional file 6 of Development of a novel mycobiome diagnostic for fungal infection
inferred← citeshttps://doi.org/10.6084/m9.figshare.26720172openalex-snapshot
Additional file 1 of PrimerEvalPy: a tool for in-silico evaluation of primers for targeting the microbiome
inferred← citeshttps://doi.org/10.6084/m9.figshare.26720175openalex-snapshot
Additional file 2 of PrimerEvalPy: a tool for in-silico evaluation of primers for targeting the microbiome
inferred← citeshttps://doi.org/10.6084/m9.figshare.26720178openalex-snapshot
Additional file 3 of PrimerEvalPy: a tool for in-silico evaluation of primers for targeting the microbiome
inferred← citeshttps://doi.org/10.6090/jarq.24j25openalex-snapshot
Development of Species-Specific Primers for Detecting Raccoon (Procyon lotor) eDNA from Field Water
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