USGS Science⌕ Search
Home/Archive/USGS

USGS · 70210779

Development of a quantitative PCR assay for detecting Egeria densa in environmental DNA samples

Dorothy M. Chase·Lauren M Kuehne·Julian D. Olden·Carl O. Ostberg
View original source ↗Export metadata ↓

Abstract

Brazilian elodea ( Egeria densa ) is an invasive freshwater plant that demonstrates widespread ecological impacts in freshwater ecosystems and causes substantial economic damage. Here, we developed an environmental DNA assay for detection of E. densa to provide resource managers with a tool for early detection, identification, and monitoring of invasive populations.

Explore related subjects

Conservation Genetics ResourcesArticle

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

Dorothy M. Chase, Lauren M Kuehne, Julian D. Olden, Carl O. Ostberg. 2020-06-02. Development of a quantitative PCR assay for detecting Egeria densa in environmental DNA samples. https://doi.org/10.1007/s12686-020-01152-w

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related USGS reports

USGS2025

Quantitative PCR detection of endangered diamond darter Crystallaria Cincotta in environmental DNA: Employing locked nucleic acids and blocking probe for specificity

This study presents a quantitative PCR (qPCR) assay for the detection of the endangered diamond darter Crystallaria cincotta from environmental DNA (eDNA) in water samples. The assay design is based on an alignment of mitochondrial cytochrome b DNA sequences from 58 individuals representing 25 percid species. Leveraging genetic differences, a species-specific qPCR assay was designed, incorporating alocked nucleic acid (LNA)-enriched probe and a secondary blocking probe to enhance specificity. The assay targets a 93-base pair fragment that includes a diagnostic single nucleotide polymorphism in the probe region; combined with multiple primer mismatches, this provides specificity for distinguishing C. cincotta from other sympatric percid species. Specificity was validated by testing genomic DNA from 16 percid species and synthetic templates, confirming no cross-reactivity. Performance metrics, including the standard curve, qPCR efficiency, limit of detection, and limit of quantification, are reported. The qPCR assay exhibited sufficient sensitivity to detect C. cincotta eDNA in environmental water samples collected from occupied riverine habitats. This study illustrates the effectiveness of LNA-enriched and blocking probes in developing species-specific qPCR assays for eDNA applications, demonstrating their utility in accurately distinguishing closely related species within diverse fish communities.

Conservation Genetics Resources↗
USGS2025

A single nucleotide polymorphism panel for identifying North American species and hybrids in the genus Morone

Four species of the fish genus Morone exist in North America and are often the focus of management actions, including propagation and stocking of their hybrids. We have developed an amplicon-based single nucleotide polymorphism (SNP) genotyping panel that provides the ability to distinguish all four species and the commonly stocked M. chrysops x M. saxatilis hybrid using a set of 47 SNPs. This resource provides a means of cost effective, high confidence genetic species identification that may aid management and conservation efforts for North American Morone species.

North America↗
USGS2025

Development of species-specific primers for the identification of Atlantic and shortnose sturgeons

Atlantic ( Acipenser oxyrinchus oxyrinchus ) and shortnose sturgeon ( Acipenser brevirostrum ) are broadly distributed along the Atlantic Coast of North America, where they use rivers, estuaries, and coastal habitats. In order to support management under the U.S. Endangered Species Act, it is important to understand when and where these fish occur. However, this presents a challenge as the two taxa are sometimes misidentified and some life stages (e.g., eggs) are challenging to identify with confidence. In this study, we used cytochrome b sequences to develop molecular primers to confirm the identity of shortnose and Atlantic sturgeon samples. We tested these primers using reference DNA samples for these two species. The results suggested that the primers were able to positively identify and distinguish Atlantic and shortnose sturgeon. The accuracy of the Atlantic sturgeon primers was 95.34%, whereas the accuracy of the shortnose sturgeon primers was 90.7%. Even though there were some individuals that were not positively identified as their corresponding species (false negatives), we did not observe any false positives. Our paper does not aim to develop eDNA markers; rather, the objective of our study was to create species-specific, unlabeled, and cost-effective primers which can be amplified using conventional PCR. The amplification product can be observed in a 2% agarose gel run through electrophoresis. This entire procedure is relatively inexpensive and involves basic instruments found in most conservation genetics laboratories.

Conservation Genetics Resources↗