2023 Early Hearing Detection & Intervention Conference
March 5-7, 2023 • Cincinnati, OH
5/22/2018 | 10:00 AM - 10:15 AM | ENHANCING PREDICTABILITY OF PRIMER SPECIFICITY FOR EDNA DETECTION OF AQUATIC SPECIES | 420 B
ENHANCING PREDICTABILITY OF PRIMER SPECIFICITY FOR EDNA DETECTION OF AQUATIC SPECIES
Environmental DNA (eDNA) techniques have increased in popularity for single-species detection during the past decade owing to their high sensitivity relative to conventional survey methods. Using primers with high specificity can selectively magnify DNA signals collected from the environment, allowing the detection of rare or newly invasive species. However, the absence of guidelines for specific primer design may compromise the benefits of eDNA detection by incurring high costs and wasted effort during primer development. In this study, we investigated the relative importance of different primer properties (i.e. 3’ stability, guanine-cytosine content, dimer stability) and primer-template mismatch properties (i.e. total number, the type, and position of mismatches) in predicting primer specificity, using seven wetland fish species. Specificity was significantly increased if the 3’ end of the primers (the last five nucleotides) had fewer guanine/cytosine (i.e. was less stable) and more mismatches. Generally, all purine-purine and one of the pyrimidine-pyrimidine mismatches (cytosine-cytosine) have greater effects (except at the 3’ terminal) on primer specificity than other types of mismatches. Our study identifies primer properties that are critical for designing species-specific primers and should enable cost-effective and routine implementation of eDNA in species detection.
- Genetics
- Vision and Change
- Biodiversity
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Presenters/Authors
Ying Kin Ken So
(), School of Biological Sciences, the University of Hong Kong, Hong Kong, u3500795@hku.hk;
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Billy Hau
(), The University of Hong Kong, chhau@hku.hk;
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David Dudgeon
(), School of Biological Sciences, the University of Hong Kong, Hong Kong, ddudgeon@hku.hk;
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