scholarly journals DNA barcoding of Thrixspermum longipilosum based on Internal Transcribed Spacer 2 (ITS2) region

2021 ◽  
Vol 743 (1) ◽  
pp. 012092
Author(s):  
S Rohimah ◽  
T Ratnasari ◽  
M Su’udi
Keyword(s):  
Dna Barcoding ◽  
Internal Transcribed Spacer ◽  
Its2 Region ◽  
Internal Transcribed Spacer 2

What Else Is in Salviae officinalis folium? Comprehensive Species Identification of Plant Raw Material by DNA Metabarcoding

Planta Medica ◽  
2017 ◽  
Vol 84 (06/07) ◽  
pp. 428-433 ◽  
Author(s):  
Corinna Schmiderer ◽  
Brigitte Lukas ◽  
Joana Ruzicka ◽  
Johannes Novak
Keyword(s):  
Next Generation Sequencing ◽  
Dna Barcoding ◽  
Species Identification ◽  
Internal Transcribed Spacer ◽  
Raw Material ◽  
Next Generation ◽  
Additional Species ◽  
Internal Transcribed Spacer 2 ◽  
Dna Metabarcoding ◽  
Generation Sequencing

AbstractQuality control of drugs consists of identifying the raw material to avoid unwanted admixtures or exchange of material as well as looking for abiotic and biotic contaminations. So far, identity and microbial contamination are analyzed by separate processes and separate methods. Species identification by their DNA (“DNA barcoding”) has the potential to supplement existing methods of identification. The introduction of next-generation sequencing methods offers completely new approaches like the identification of whole communities in one analysis, termed “DNA metabarcoding”. Here we present a next-generation sequencing assessment to identify plants and fungi of two commercial sage samples (Salvia officinalis) using the standard DNA barcoding region “internal transcribed spacer” consisting of internal transcribed spacer 1 and internal transcribed spacer 2, respectively. The main species in both samples was identified as S. officinalis. The spectrum of accompanying plant and fungal species, however, was completely different between the samples. Additionally, the composition between internal transcribed spacer 1 and internal transcribed spacer 2 within the samples was different and demonstrated the influence of primer selection and therefore the need for harmonization. This next-generation sequencing approach does not result in quantitative species composition but gives deeper insight into the composition of additional species. Therefore, it would allow for a better knowledge-based risk assessment than any other method available. However, the method is only economically feasible in routine analysis if a high sample throughput can be guaranteed.

scholarly journals Evaluation of internal transcribed spacer 2-RFLP analysis for the identification of dermatophytes

2010 ◽  
Vol 59 (1) ◽  
pp. 48-54 ◽  
Author(s):  
Thierry De Baere ◽  
Richard Summerbell ◽  
Bart Theelen ◽  
Teun Boekhout ◽  
Mario Vaneechoutte
Keyword(s):  
Internal Transcribed Spacer ◽  
Rflp Analysis ◽  
Its2 Region ◽  
Restriction Digestion ◽  
Internal Transcribed Spacer 2 ◽  
Pcr Rflp ◽  
Identification Technique ◽  
Identification Of Species ◽  
Length Determination ◽  
Taxonomic Approach

A total of 95 isolates, belonging to 33 species of five dermatophyte genera, i.e. Arthroderma (15 species), Chrysosporium (two), Epidermophyton (one), Microsporum (three) and Trichophyton (12), were studied using internal transcribed spacer 2 (ITS2)-PCR-RFLP analysis (ITS2-RFLP), consisting of amplification of the ITS2 region, restriction digestion with BstUI (CG/CG) and restriction fragment length determination by capillary electrophoresis. ITS2-RFLP analysis proved to be most useful for identification of species of the genera Arthroderma, Chrysosporium and Epidermophyton, but could not distinguish between several Trichophyton species. The identification results are in agreement with established and recent taxonomical insights into the dermatophytes; for example, highly related species also had closely related and sometimes difficult-to-discriminate ITS2-RFLP patterns. In some cases, several ITS2-RFLP groups could be distinguished within species, again mostly in agreement with the taxonomic delineations of subspecies and/or genomovars, confirming the relevance of ITS2-RFLP analysis as an identification technique and as a useful taxonomic approach.

scholarly journals Phylogenetic reconstruction of endophytic fungal isolates using internal transcribed spacer 2 (ITS2) region

2014 ◽  
Vol 10 (6) ◽  
pp. 320-328 ◽  
Author(s):  
Kathamuthu GokulRaj ◽  
◽  
Natesan Sundaresan ◽  
Enthai Jagan Ganeshan ◽  
Pandi Rajapriya ◽  
...  
Keyword(s):  
Internal Transcribed Spacer ◽  
Phylogenetic Reconstruction ◽  
Its2 Region ◽  
Internal Transcribed Spacer 2 ◽  
Fungal Isolates

scholarly journals Shark Species on Export Products from East Java and Bali by Dna Barcoding Based on Internal Transcribed Spacer-2 (Its-2) Locus in Mitochondrial

2017 ◽  
Vol 3 (6) ◽  
pp. 105
Author(s):  
Eduardus Bimo Aksono
Keyword(s):  
Dna Barcoding ◽  
Internal Transcribed Spacer ◽  
Iucn Red List ◽  
The Body ◽  
Shark Species ◽  
Universal Primer ◽  
Internal Transcribed Spacer 2 ◽  
The Government ◽  
Data Deficient ◽  
The Right

DNA barcoding method is the mitochondrial marker for all animal species, and it is claimed as distinguishing feature from one species to another Species identification in shark products is often difficult to perform as they have morphological similarities with many other species and it is even more difficult as they are parts separated from the body for the storage. This research is aimed to know which species of sharks identified in the export products from East Java and Bali by DNA barcoding method. The samples of sharks (meat, fins, skin and bones) used were 90 samples acquired in Surabaya from the export products of East Java and Bali from 2015 to 2017. The DNA barcoding method uses universal primer through nested PCR (Polymerase Chain Reaction) process which is able to amplify the DNA until around 1,340 bp based on Internal Transcribed Spacer-2 (ITS-2) locus of mitochondria. Based on the result of phylogenetic analysis and the classification list by IUCN, from 90 samples of sharks acquired from export products in East Java and Bali, species identified were: 1.11% Daenia sp categorized as NE (not evaluated); 4.44% Sphyrna zygaena categorized as NT (not Threatened); 3.33% Sphyrna lewini categorized as NT (not Threatened); 10% Rhizoprionodon taylori categorized as LC (least concern); 24% Charcarhinus brevipinna categorized as NT (not Threatened); 2.22% Charcarhinus obscurus categorized as NT (not Threatened); 3.33% Charcarhinus falciformis categorized as LC (least concern); 1.11% Charcarhinus plumbeus categorized as NT (not Threatened); 27.78% Charcarhinus longimanus categorized as VU (vulnerable); 1.11% Neutrygon kuhlii categorized as NE (not evaluated); 1.11% Charcarhinus Taurus categorized as VU (vulnerable); 3.33% Rhizoprionodon longurio categorized as DD (data deficient); 1.11% Rhizoprionodon porosus categorized as DD (data deficient); 1.11% Eusphyra blochii categorized as NT (not Threatened); 4.44% Chiloscyllium griseum categorized as DD (data deficient); 5.56% Rhizoprionodon oligolinx categorized as LC (least concern); 1.11% Prionace glauca categorized as NT (not Threatened); 1.11% Rhizoprionodon lalandii categorized as DD (data deficient). Generally all species found in this research were special fish from Indo-Australian archipelago and included in IUCN red list. The government policy to prohibit export of these species was the right decision to prevent the species extinction. Keywords : ITS-2; Shark; Export Products; Java and Bali

scholarly journals Barcoding theDendrobium(Orchidaceae) Species and Analysis of the Intragenomic Variation Based on the Internal Transcribed Spacer 2

2017 ◽  
Vol 2017 ◽  
pp. 1-10 ◽  
Author(s):  
Xiaoyue Wang ◽  
Xiaochen Chen ◽  
Pei Yang ◽  
Lili Wang ◽  
Jianping Han
Keyword(s):  
Internal Transcribed Spacer ◽  
Phylogenetic Trees ◽  
Growth Conditions ◽  
Genetic Distances ◽  
Species Level ◽  
Its2 Region ◽  
High Demand ◽  
Internal Transcribed Spacer 2 ◽  
Multiple Copies ◽  
Intragenomic Variation

Many species belonging to the genusDendrobiumare of great commercial value. However, their difficult growth conditions and high demand have caused many of these species to become endangered. Indeed, counterfeitDendrobiumproducts are common, especially in medicinal markets. This study aims to assess the suitability of the internal transcribed spacer 2 (ITS2) region as a marker for identifyingDendrobiumand to evaluate its intragenomic variation inDendrobiumspecies. In total, 29,624 ITS2 copies from 18 species were obtained using 454 pyrosequencing to evaluate intragenomic variation. In addition, 513 ITS2 sequences from 26Dendrobiumspecies were used to assess its identification suitability. The highest intragenomic genetic distance was observed inDendrobium chrysotoxum(0.081). The average intraspecific genetic distances of each species ranged from 0 to 0.032. Phylogenetic trees based on ITS2 sequences showed that mostDendrobiumspecies are monophyletic. The intragenomic and intraspecies divergence analysis showed that greater intragenomic divergence is mostly correlated with larger intraspecific variation. As a major ITS2 variant becomes more common in genome, there are fewer intraspecific variable sites in ITS2 sequences at the species level. The results demonstrated that the intragenomic multiple copies of ITS2 did not affect species identification.

scholarly journals Identification of plant materials containing ephedrine alkaloids based on DNA barcoding and TaqMan real-time PCR assay

2021 ◽  
Vol 43 (11) ◽  
Author(s):  
Yaqin Zheng ◽  
Han Gao ◽  
Ming Song ◽  
Yunhan Lin ◽  
Jiajia Fan ◽  
...  
Keyword(s):  
Real Time ◽  
Dna Barcoding ◽  
Real Time Pcr ◽  
Sequence Comparison ◽  
Internal Transcribed Spacer ◽  
Its2 Region ◽  
Neighbor Joining ◽  
Pcr Assay ◽  
Plant Materials ◽  
Target Dna

AbstractAn intentional or inadvertent mixing of plant materials containing ephedrine alkaloids, especially Ephedra, is illegal. In order to better detect plant materials containing ephedrine alkaloids in export and smuggling, DNA barcoding combined with a TaqMan real-time PCR-based assay were used in this study. We collected 201 samples from 18 species belonging to four genera distributed in three families to amplify two barcoding markers, internal transcribed spacer 2 (ITS2) and psbA-trnH. 175 ITS2 sequences and 136 psbA-trnH sequences were obtained. Alignments and the neighbor-joining tree indicated that ITS2 showed a better discrimination of species than psbA-trnH. In addition, based on the sequence comparison of the ITS2 region from 18 species, three sets of primer/probes were designed using the real-time PCR assay platform. A sensitivity test showed the above primer/probe sets were specific and sensitive (as little as 0.0050 ng/μL target DNA) to identify species containing ephedrine alkaloids. Hence, the combination of novel DNA barcoding and the TaqMan real-time PCR-based technique are promising tools for the identification of plant materials containing ephedrine alkaloids. It is beneficial to standardize market circulation and detection of plant materials containing ephedrine alkaloids.

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