Characterizing the spatial and temporal occurrence patterns of the endangered botiid loach Parabotia curtus by environmental DNA analysis using a newly developed species-specific primer set

Environmental DNA (eDNA) method used by many ecologists as effective investigation tool can detect endangered species, rare species, and invasive species. In case of invasive species, eDNA method help to monitor the target species when the species was hard to detect through the traditional survey such as the early stage of invasion, low abundance, and larva or juvenile stage. The bryozoan, Bugulina californica, was known as a marine fouling invasive species in Korea since its first reported in 1978. This species expanded nationwide, and damages to ascidian aquaculture through attached on the ship hulls and artificial facilities. To monitor the distribution and biomass of invasive bryozoan, B. californica, the qPCR analysis of environmental DNA was performed on seawater samples from 12 harbors. In this study, we designed species-specific markers which can calculate the detected DNA copies of B. californica, and the presence and monitoring of this species can be more accurately estimated by environmental DNA analysis than by traditional survey, in which it is difficult to identify the species. Real-time PCR analysis using environmental DNA is an effective monitoring method that can determine both the distribution and the monthly change in biomass of B. californica in Korea.

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Species-specific detection of the endangered piscivorous cyprinid fish Opsariichthys uncirostris uncirostris, three-lips, using environmental DNA analysis

Ecological Research ◽

10.1007/s11284-018-1612-2 ◽

2018 ◽

Vol 33 (5) ◽

pp. 1075-1078 ◽

Cited By ~ 4

Author(s):

Hiroki Yamanaka ◽

Daiki Takao ◽

Atsushi Maruyama ◽

Akio Imamura

Keyword(s):

Dna Analysis ◽

Environmental Dna ◽

Cyprinid Fish ◽

Specific Detection ◽

Species Specific

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Environmental DNA and Specific Primers for Detecting the Invasive Species Ectopleura crocea (Hydrozoa: Anthoathecata) in Seawater Samples

Sustainability ◽

10.3390/su12062360 ◽

2020 ◽

Vol 12 (6) ◽

pp. 2360 ◽

Cited By ~ 1

Author(s):

Philjae Kim ◽

Tae Joong Yoon ◽

Sook Shin

Keyword(s):

Invasive Species ◽

Survey Methods ◽

Environmental Dna ◽

Visual Assessment ◽

Molecular Techniques ◽

Mitochondrial Cytochrome ◽

Specific Primer ◽

Specific Primers ◽

Seawater Samples ◽

Species Specific

In marine environments, environmental DNA (eDNA) can be effectively detected and possibly quantified when combined with molecular techniques, as demonstrated by several recent studies. In this study, we developed a species-specific primer set and a probe to detect the distribution and biomass of an invasive hydrozoan in South Korea, Ectopleura crocea. These molecular markers were designed to amplify a 187 bp region based on mitochondrial cytochrome c oxidase subunit I (COI) of E. crocea and were tested on seawater samples from 35 Korean harbors in 2017. Of the 35 sites we investigated, only nine harbors returned positive detections when using traditional survey methods, while surveys based on the use of eDNA techniques detected E. crocea DNA in all seawater samples. These results suggest that eDNA surveys based on molecular techniques are more effective at identifying species distribution and estimating biomass than traditional surveys based on visual assessment of morphology.

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The Use of Real-Time Polymerase Chain Reaction Combined with Specific-Species Primer for Analysis of Dog Meat DNA in Meatball

Indonesian Journal of Chemistry ◽

10.22146/ijc.48930 ◽

2020 ◽

Vol 21 (1) ◽

pp. 225

Author(s):

Abdul Rohman ◽

Wiranti Sri Rahayu ◽

Sudjadi Sudjadi ◽

Sudibyo Martono

Keyword(s):

Polymerase Chain Reaction ◽

Real Time ◽

Real Time Pcr ◽

Dna Analysis ◽

Limit Of Detection ◽

Specific Primer ◽

Chain Reaction ◽

Relative Standard ◽

Polymerase Chain ◽

Species Specific

The presence of dog meat is a crucial issue because dog meat is non-halal meat for Muslims. The objective of this study was to design and validate species-specific primer for the identification of dog meat DNA in meatball using real-time polymerase chain reaction (real-time PCR). The specific primer targeting mitochondrial cytochrome c oxidase subunit 1 (CO1) was validated. The specific primers used were designed using Integrated DNA Technologies (IDT) software and subjected to NCBI BLAST procedure. The candidate primers were tested for specificity study using several DNAs from fresh meat of pork, chicken, beef, lamb, and rat. The method was also validated by determining several parameters of linearity, sensitivity, precision, and efficiency. The results showed that primer could amplify specifically DNA target at an optimized annealing temperature of 56.6 °C. The limit of detection (LoD) obtained was 5 ng DNA, corresponding to 2.5% of dog meat in a meatball. The repeatability evaluation, expressed with relative standard deviation (RSD), and efficiency value was in the acceptable range (RSD < 25% and efficiency (90–105%). This method was successfully used for the analysis of marketed samples. Real-time PCR can be used as a standard method in halal authentication analysis through DNA analysis.

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