scholarly journals A DNA microarray for the authentication of giant tiger prawn (Penaeus monodon) and whiteleg shrimp (Penaeus (Litopenaeus) vannamei): a proof-of-principle

2021 ◽  
Author(s):  
Kristina Kappel ◽  
Joanna Fafińska ◽  
Markus Fischer ◽  
Jan Fritsche
Keyword(s):  
Dna Microarray ◽  
Dna Microarrays ◽  
Penaeus Monodon ◽  
Simple Alternative ◽  
Pcr Products ◽  
Tiger Prawn ◽  
Whiteleg Shrimp ◽  
Reference Specimens ◽  
Species Specific ◽  
Proof Of Principle

AbstractThis proof-of-principle study describes the development of a rapid and easy-to-use DNA microarray assay for the authentication of giant tiger prawns and whiteleg shrimp. Following DNA extraction and conventional end-point PCR of a 16S rDNA segment, the PCR products are hybridised to species-specific oligonucleotide probes on DNA microarrays located at the bottom of centrifuge tubes (ArrayTubes) and the resulting signal patterns are compared to those of reference specimens. A total of 21 species-specific probes were designed and signal patterns were recorded for 47 crustacean specimens belonging to 16 species of seven families. A hierarchical clustering of the signal patterns demonstrated the specificity of the DNA microarray for the two target species. The DNA microarray can easily be expanded to other important crustaceans. As the complete assay can be performed within half a day and does not require taxonomic expertise, it represents a rapid and simple alternative to tedious DNA barcoding and could be used by crustacean trading companies as well as food control authorities for authentication of crustacean commodities. Graphical abstract

Simultaneous detection ofAureliaandChrysaorascyphozoan jellyfish on a DNA microarray

2009 ◽  
Vol 90 (6) ◽  
pp. 1111-1117 ◽  
Author(s):  
Jang-Seu Ki ◽  
Dae-Sik Hwang ◽  
Jae-Seong Lee
Keyword(s):  
Dna Microarray ◽  
Simultaneous Detection ◽  
Dna Chip ◽  
Coi Gene ◽  
Low Density ◽  
Sequence Comparisons ◽  
Mitochondrial Coi ◽  
Pcr Products ◽  
Jellyfish Species ◽  
Species Specific

To demonstrate the effectiveness of microarrays for the detection of jellyfish, we developed a low density DNA chip based on the mitochondrial COI gene sequences of scyphozoans (jellyfish). We designed species-specific oligonucleotide probes by sequence comparisons between scyphozoans and other cnidarians such as hydrozoans and anthozoans. Each amine-labelled capture probe was arrayed onto a silylated slide. PCR products of the COI gene were hybridized to the DNA microarray that contained COI consensus sequences. We tested the ability of the DNA chip to discriminate between species from the generaAureliaandChrysaorabased on samples of both species from the polyp and ephyra stages. The array produced unique hybridization patterns for each of the two tested jellyfish species. Furthermore, we were able to simultaneously detect individual jellyfish species from mixtures of these two different species in the laboratory and from environmental samples. These results show that the low density DNA chip that we designed can be used as a technical platform for parallel molecular detection of various jellyfish species.

scholarly journals A Comparative Study of 5S rDNA Non-Transcribed Spacers in Elaeagnaceae Species

Plants ◽  
2020 ◽  
Vol 10 (1) ◽  
pp. 4
Author(s):  
Oleg S. Alexandrov ◽  
Olga V. Razumova ◽  
Gennady I. Karlov
Keyword(s):  
Polymerase Chain Reaction ◽  
Molecular Markers ◽  
Dna Markers ◽  
5S Rdna ◽  
Chain Reaction ◽  
Closely Related Species ◽  
Pcr Products ◽  
Polymerase Chain ◽  
Species Specific ◽  
Shepherdia Canadensis

5S rDNA is organized as a cluster of tandemly repeated monomers that consist of the conservative 120 bp coding part and non-transcribed spacers (NTSs) with different lengths and sequences among different species. The polymorphism in the 5S rDNA NTSs of closely related species is interesting for phylogenetic and evolutional investigations, as well as for the development of molecular markers. In this study, the 5S rDNA NTSs were amplified with universal 5S1/5S2 primers in some species of the Elaeagnaceae Adans. family. The polymerase chain reaction (PCR) products of five Elaeagnus species had similar lengths near 310 bp and were different from Shepherdia canadensis (L.) Nutt. and Sh. argentea (Pusch.) Nutt. samples (260 bp and 215 bp, respectively). The PCR products were cloned and sequenced. An analysis of the sequences revealed that intraspecific levels of NTS identity are high (approximately 95–96%) and similar in the Elaeagnus L. species. In Sh. argentea, this level was slightly lower due to the differences in the poly-T region. Moreover, the intergeneric and intervarietal NTS identity levels were studied and compared. Significant differences between species (except E. multiflora Thunb. and E. umbellata Thunb.) and genera were found. Herein, a range of the NTS features is discussed. This study is another step in the investigation of the molecular evolution of Elaeagnaceae and may be useful for the development of species-specific DNA markers in this family.

News & Notes: Virulence of Vibrio alginolyticus Isolated from Diseased Tiger Prawn, Penaeus monodon

1996 ◽  
Vol 32 (4) ◽  
pp. 229-231 ◽  
Author(s):  
Kuo-Kau Lee ◽  
Shu-Ru Yu ◽  
Ferng-Ruey Chen ◽  
Tun-I Yang ◽  
Ping-Chung Liu
Keyword(s):  
Penaeus Monodon ◽  
Vibrio Alginolyticus ◽  
Tiger Prawn

Species-specific duplex PCR for the detection of Pratylenchus penetrans

Nematology ◽  
2009 ◽  
Vol 11 (6) ◽  
pp. 847-857 ◽  
Author(s):  
Lieven Waeyenberge ◽  
Nicole Viaene ◽  
Maurice Moens
Keyword(s):  
Internal Control ◽  
Dna Sequences ◽  
Rrna Gene ◽  
Duplex Pcr ◽  
Specific Primers ◽  
5.8S Rrna Gene ◽  
5.8S Rrna ◽  
Wide Range ◽  
Pcr Products ◽  
Species Specific

Abstract ITS1, the 5.8S rRNA gene and ITS2 of the rDNA region were sequenced from 20 different Pratylenchus species. Additionally, the same region was sequenced from seven populations of P. penetrans. After purifying, cloning and sequencing the PCR products, all sequences were aligned in order to find unique sites suitable for the design of species-specific primers for P. penetrans. Since ITS regions showed variability between and even within populations of P. penetrans, only three small DNA sequences were suitable for the construction of three potentially useful species-specific primers. New species-specific primers were paired with existing universal ITS primers and tested in all possible primer combinations. The best performing primer set, supplemented with a universal 28S rDNA primer set that served as an internal control, was tested in duplex PCR. The ideal annealing temperature, Mg2+ concentration and primer ratios were then determined for the most promising primer set. The optimised duplex PCR was subsequently tested on a wide range of different Pratylenchus spp. and 25 P. penetrans populations originating from all over the world. To test the sensitivity, the duplex PCR was conducted on DNA extracted from a single P. penetrans nematode mixed with varying amounts of nematodes belonging to another Pratylenchus species. Results showed that a reliable and sensitive P. penetrans species-specific duplex PCR was constructed.

Four novel PYFs: members of NPY/PP peptide superfamily from the eyestalk of the giant tiger prawn Penaeus monodon

Peptides ◽  
2002 ◽  
Vol 23 (11) ◽  
pp. 1895-1906 ◽  
Author(s):  
Paisarn Sithigorngul ◽  
Jirasak Pupuem ◽  
Chatchadaporn Krungkasem ◽  
Siwaporn Longyant ◽  
Nanthika Panchan ◽  
...  
Keyword(s):  
Penaeus Monodon ◽  
Tiger Prawn
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