Development of species‐specific primers for rapid identification by PCR of the ecologically important pathogen Fusarium keratoplasticum from isolated and environmental samples

2021 ◽  
Author(s):  
Alexandra F. Agee ◽  
Michelle M. Barthet
Keyword(s):  
Environmental Samples ◽  
Rapid Identification ◽  
Specific Primers ◽  
Species Specific

scholarly journals Development of specific markers for the detection of Tolypella canadensis eDNA in water samples

2021 ◽  
Vol 4 ◽  
Author(s):  
Christina Wiebe ◽  
Petra Nowak ◽  
Hendrik Schubert
Keyword(s):  
Rare Species ◽  
Environmental Samples ◽  
Large Scale ◽  
Morphological Characters ◽  
Its2 Region ◽  
Specific Marker ◽  
Specific Primers ◽  
Species Specific ◽  
Taxonomic Groups ◽  
Scale Integration

Assessing the biodiversity of an ecosystem plays a major role in ecosystem management. However, proper determination on species-level is often tricky when morphological features are scarce and especially rare species require huge sampling efforts to be detected in the aquatic realm. As an alternative to conventional methods, environmental samples can be examined via the eDNA method, allowing for large-scale integration as well as taxa resolution independent from expression of morphological characters. However, to apply this technique genetic markers that are specific to a species or at least a genus are required. Such markers until now have been successfully developed only for a few well studied taxonomic groups like, e.g., fishes and amphibians, but are still missing for others, especially plants and algae (e.g. Bista et al. 2017). This project focusses on the development of species-specific markers for the macrophytic green algae Tolypella canadensis (Characeae, Charophyta), a rare alga preferring deep water and known so far mainly from remote places. Tolypella canadensis is a circumpolar species and prefers oligotrophic lakes, where it grows in depths up to 13 m (Langangen 2002; Romanov and Kopyrina 2016). In addition, proper determination of Tolypella-species is a field of a few specialists, further complicating monitoring or even detection of this rare species. The design of the species-specific primers was based on reference nucleotide sequences of the chloroplast genes rbcL, psbC and atpB and of the ribosomal internal transcribed spacer regions ITS1 and ITS2, obtained from GenBank (Perez et al. 2017). To determine the specificity of the newly designed primers, DNA isolates obtained from T. canadensis specimens collected from the Torneträsk (Sweden, 2018) and other charophyte species were prepared in different proportions. The sensitivity of the primers was experimentally assayed by using serial dilutions of T. canadensis DNA. Additionally, a mock test comprised of a sample with the DNA of several charophyte species was conducted and finally, the markers were tested on environmental samples from the Torneträsk. Tolypella canadensis-specific primers of the ITS2 region yielded positive PCR amplifications of one single band when T. canadensis was present in a sample. Cross-amplification was not found during the mock test; other charophyte species did not yield positive amplification. The eDNA samples from the Torneträsk validated the performance of the ITS2 marker. The T. canadensis-specific marker designed in this project was proven to be sensitive and accurate. It could be recommended as a useful tool to detect the presence of T. canadensis DNA, even at low concentration and in complex samples containing other charophyte species.

scholarly journals Rapid identification of the invasive fall armyworm Spodoptera frugiperda (Lepidoptera, Noctuidae) using species-specific primers in multiplex PCR

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Cheng-Lung Tsai ◽  
I.-Hsuan Chu ◽  
Ming-Hsun Chou ◽  
Theeraphap Chareonviriyaphap ◽  
Ming-Yao Chiang ◽  
...  
Keyword(s):  
Spodoptera Frugiperda ◽  
Egg Production ◽  
Mainland China ◽  
Fall Armyworm ◽  
The United States ◽  
Rapid Identification ◽  
Economic Losses ◽  
Specific Primers ◽  
Wide Range ◽  
Species Specific

Abstract The fall armyworm (FAW), Spodoptera frugiperda (Smith), is a major pest native to the Americas. A recent invasion of FAWs from Africa eastward to South Asia, the Indochina Peninsula, and mainland China has received much attention due to the considerable economic losses in agriculture. FAWs can rapidly colonise a new area, likely due to the wide range of host plants, good flying capability, and high egg production. Therefore, a convenient, quick, and accurate tool for FAW identification is urgently required to establish a FAW invasion management strategy. In this study, FAW-specific primers were designed to recognise FAWs on the basis of internal transcribed spacer 1 (ITS1). The results revealed the accurate FAW recognition of the three congeneric species and eight common corn lepidopteran pests, especially at their larval stage. Furthermore, species-specific primers have confirmed their efficacy by using 69 FAW specimens from Taiwan, Thailand, and the United States, with a 96% success rate, excluding 3 decayed specimens. By using the simple, reliable, and convenient FAW-specific primers, a pest management programme can be developed not only to reduce sequencing costs and experimental time from 2 days to 4 h, but eradicate the FAW as soon as it enters a new area.

Development of species-specific primers for rapid identification of Debaryomyces hansenii

2015 ◽  
Vol 193 ◽  
pp. 109-113 ◽  
Author(s):  
Petra Wrent ◽  
Eva-María Rivas ◽  
Elena Gil de Prado ◽  
José M. Peinado ◽  
María-Isabel de Silóniz
Keyword(s):  
Debaryomyces Hansenii ◽  
Rapid Identification ◽  
Specific Primers ◽  
Species Specific

Rapid identification of Saccharomonospora strains by multiplex PCR using species-specific primers within the 16S rRNA gene

1996 ◽  
Vol 27 (1) ◽  
pp. 89-95 ◽  
Author(s):  
Jung-Hoon Yoon ◽  
Sung Taik Lee ◽  
Yong Kook Shin ◽  
Sam-Bong Kim ◽  
Hong-Joong Kim ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Multiplex Pcr ◽  
Rapid Identification ◽  
Rrna Gene ◽  
Specific Primers ◽  
Species Specific ◽  
The 16S Rrna Gene

scholarly journals Rapid identification of the species of theBacteroides fragilisgroup by multiplex PCR assays using group- and species-specific primers

2003 ◽  
Vol 222 (1) ◽  
pp. 9-16 ◽  
Author(s):  
Chengxu Liu ◽  
Yuli Song ◽  
Maureen McTeague ◽  
Ann W. Vu ◽  
Hannah Wexler ◽  
...  
Keyword(s):  
Multiplex Pcr ◽  
Rapid Identification ◽  
Specific Primers ◽  
Pcr Assays ◽  
Species Specific

scholarly journals HIDE AND SEEK: MOLECULAR BARCODING CLARIFIES THE DISTRIBUTION OF TWO CRYPTIC DUCKWEED SPECIES ACROSS ALBERTA

Botany ◽  
2021 ◽  
Author(s):  
Kanishka M. Senevirathna ◽  
Varina E. Crisfield ◽  
Theresa M. Burg ◽  
Robert A. Laird
Keyword(s):  
Cryptic Species ◽  
Dna Barcoding ◽  
Molecular Identification ◽  
Lemna Minor ◽  
Rapid Identification ◽  
Specific Primers ◽  
Molecular Barcoding ◽  
Geographic Ranges ◽  
Global Biodiversity ◽  
Species Specific

Regional and global biodiversity may be underestimated due to the presence of cryptic species: species that are morphologically similar, but genetically distinct. Here we focus on two cryptic duckweed species, Lemna minor and L. turionifera, which have overlapping geographic ranges and are easily mistaken for one another. We developed species-specific primers based on DNA barcoding sequences to facilitate the rapid identification of these two monomorphic duckweeds, allowing us to investigate their presence and distribution in Alberta, Canada. While current reports indicate the presence of L. turionifera (and the morphologically distinct L. trisulca) in Alberta, our data indicate that L. minor is also present, predominantly in the southern part of the province. Thus, this paper (1) contributes to the accuracy and completeness of a regional flora, and (2) provides useful and flexible tools for the rapid molecular identification of cryptic Lemna species, species of wide interest in such diverse fields as biotechnology, toxicology, bioremediation, and ecology.

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