Mitochondrial genome sequencing and development of genetic markers for the detection of DNA of invasive bighead and silver carp (Hypophthalmichthys nobilis and H. molitrix) in environmental water samples from the United States.

Heather L. Farrington,Christine E. Edwards,Kelly Baerwaldt,Matthew R. Carr,Richard F. Lance,Xin Guan,Tom Gilbert

doi:10.1371/journal.pone.0117803

Heather L. Farrington, Christine E. Edwards + Show 5 more

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https://doi.org/10.1371/journal.pone.0117803

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Abstract

Invasive Asian bighead and silver carp (Hypophthalmichthys nobilis and H. molitrix) pose a substantial threat to North American aquatic ecosystems. Recently, environmental DNA (eDNA), genetic material shed by organisms into their environment that can be detected by non-invasive sampling strategies and genetic assays, has gained recognition as a tool for tracking the invasion front of these species toward the Great Lakes. The goal of this study was to develop new species-specific conventional PCR (cPCR) and quantitative (qPCR) markers for detection of these species in North American surface waters. We first generated complete mitochondrial genome sequences from 33 bighead and 29 silver carp individuals collected throughout their introduced range. These sequences were aligned with those from other common and closely related fish species from the Illinois River watershed to identify and design new species-specific markers for the detection of bighead and silver carp DNA in environmental water samples. We then tested these genetic markers in the laboratory for species-specificity and sensitivity. Newly developed markers performed well in field trials, did not have any false positive detections, and many markers had much higher detection rates and sensitivity compared to the markers currently used in eDNA surveillance programs. We also explored the use of multiple genetic markers to determine whether it would improve detection rates, results of which showed that using multiple highly sensitive markers should maximize detection rates in environmental samples. The new markers developed in this study greatly expand the number of species-specific genetic markers available to track the invasion front of bighead and silver carp and will improve the resolution of these assays. Additionally, the use of the qPCR markers developed in this study may reduce sample processing time and cost of eDNA monitoring for these species.

Highlights

Invasive aquatic nuisance species pose a major threat to aquatic ecosystems worldwide
bighead carp (BHC) and silver carp (SC) have been found in 23 states, and they have rapidly expanded their population sizes, with BHC and SC representing over 60% of the biomass in some portions of their North American range [3]
We explored whether using combinations of multiple markers would improve the sensitivity and detection rates in environmental DNA (eDNA) monitoring programs for SC and BHC

Summary

Introduction

Invasive aquatic nuisance species pose a major threat to aquatic ecosystems worldwide. It is impossible to fully predict the potential effects of self-sustaining populations of BHC or SC in the Great Lakes, there is concern that these species have the potential to dramatically alter the ecosystem, leading to negative effects on populations of native fishes and many threatened or endangered plant/animal species [6]. The impact of this invasion on Great Lakes commercial and recreational fisheries is of particular concern

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