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 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 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 The new Internal Transcribed Spacer 2 diagnostic tool clarifies the taxonomic position and geographic distribution of the North American malaria vector Anopheles punctipennis

2021 ◽  
Vol 20 (1) ◽  
Author(s):  
James M. Hodge ◽  
Andrey A. Yurchenko ◽  
Dmitriy A. Karagodin ◽  
Reem A. Masri ◽  
Ryan C. Smith ◽  
...  
Keyword(s):  
Malaria Vector ◽  
Internal Transcribed Spacer ◽  
Single Species ◽  
Its2 Sequence ◽  
Pathogen Transmission ◽  
Molecular Diagnostic ◽  
Diagnostic Tools ◽  
Sequence Length ◽  
Phylogenetic Position ◽  
Internal Transcribed Spacer 2

Abstract Background The malaria mosquito Anopheles punctipennis, a widely distributed species in North America, is capable of transmitting human malaria and is actively involved in the transmission of the ungulate malaria parasite Plasmodium odocoilei. However, molecular diagnostic tools based on Internal Transcribed Spacer 2 (ITS2) of ribosomal DNA are lacking for this species. Anopheles punctipennis is a former member of the Anopheles maculipennis complex but its systematic position remains unclear. Methods In this study, ITS2 sequences were obtained from 276 An. punctipennis specimens collected in the eastern and midwestern United States and a simple and robust Restriction Fragment Length Polymorphism approach for species identification was developed. The maximum-likelihood phylogenetic tree was constructed based on ITS2 sequences available through this study and from GenBank for 20 species of Anopheles. Results The analysis demonstrated a consistent ITS2 sequence length and showed no indications of intragenomic variation among the samples based on ITS2, suggesting that An. punctipennis represents a single species in the studied geographic locations. In this study, An. punctipennis was found in urban, rural, and forest settings, suggesting its potential broad role in pathogen transmission. Phylogeny based on ITS2 sequence comparison demonstrated the close relationship of this species with other members of the Maculipennis group. Conclusions This study developed molecular tools based on ITS2 sequences for the malaria vector An. punctipennis and clarified the phylogenetic position of the species within the Maculipennis group.

scholarly journals Rhizospheric Microbiome Profiling of Capsicum annuum L. Cultivated in Amended Soils by 16S and Internal Transcribed Spacer 2 rRNA Amplicon Metagenome Sequencing

2017 ◽  
Vol 5 (30) ◽  
Author(s):  
Ali Asaff-Torres ◽  
Mariana Armendáriz-Ruiz ◽  
Manuel Kirchmayr ◽  
Raúl Rodríguez-Heredia ◽  
Marcos Orozco ◽  
...  
Keyword(s):  
Capsicum Annuum ◽  
Internal Transcribed Spacer ◽  
Root Exudate ◽  
Microbial Consortium ◽  
Amended Soils ◽  
Internal Transcribed Spacer 2 ◽  
Capsicum Annuum L ◽  
Metagenome Sequencing ◽  
Microbiome Profiling

ABSTRACT Rhizospheric microbiomes of Capsicum annuum L. cultivated either conventionally or amended with a synthetic microbial consortium or a root exudate inductor, were characterized by 16S/internal transcribed spacer 2 (ITS2) rRNA amplicon metagenome sequencing. The most abundant taxa found, although differently represented in each treatment, were Gammaproteobacteria, Alphaproteobacteria, Actinobacteria, and Bacilli, as well as Chytridiomycetes and Mortierellomycotina.

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