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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.
PLoS One. 2015; 10(2):e0117803.Plos

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.

Authors+Show Affiliations

Environmental Laboratory, United States Army Engineer Research and Development Center, Vicksburg, Mississippi, United States of America.Environmental Laboratory, United States Army Engineer Research and Development Center, Vicksburg, Mississippi, United States of America.Environmental Laboratory, United States Army Engineer Research and Development Center, Vicksburg, Mississippi, United States of America.Environmental Laboratory, United States Army Engineer Research and Development Center, Vicksburg, Mississippi, United States of America.United States Army Corps of Engineers, Rock Island, Illinois, United States of America.Environmental Laboratory, United States Army Engineer Research and Development Center, Vicksburg, Mississippi, United States of America.

Pub Type(s)

Journal Article
Research Support, Non-U.S. Gov't

Language

eng

PubMed ID

25706532

Citation

Farrington, Heather L., et al. "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." PloS One, vol. 10, no. 2, 2015, pp. e0117803.
Farrington HL, Edwards CE, Guan X, et al. 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. PLoS ONE. 2015;10(2):e0117803.
Farrington, H. L., Edwards, C. E., Guan, X., Carr, M. R., Baerwaldt, K., & Lance, R. F. (2015). 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. PloS One, 10(2), e0117803. https://doi.org/10.1371/journal.pone.0117803
Farrington HL, et al. 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. PLoS ONE. 2015;10(2):e0117803. PubMed PMID: 25706532.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - 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. AU - Farrington,Heather L, AU - Edwards,Christine E, AU - Guan,Xin, AU - Carr,Matthew R, AU - Baerwaldt,Kelly, AU - Lance,Richard F, Y1 - 2015/02/23/ PY - 2014/10/06/received PY - 2015/01/01/accepted PY - 2015/2/24/entrez PY - 2015/2/24/pubmed PY - 2016/1/12/medline SP - e0117803 EP - e0117803 JF - PloS one JO - PLoS ONE VL - 10 IS - 2 N2 - 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. SN - 1932-6203 UR - https://www.unboundmedicine.com/medline/citation/25706532/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_ L2 - http://dx.plos.org/10.1371/journal.pone.0117803 DB - PRIME DP - Unbound Medicine ER -