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 Relationships of Local Durian Species based on Morphological Characteristics and PCR-RFLP Analysis of the Ribosomal Internal Transcribed Spacer (ITS) DNA

2016 ◽  
Vol 8 (3) ◽  
pp. 362
Author(s):  
Fidia Fibriana ◽  
Lutfia Nur Hadiyanti
Keyword(s):  
Phylogenetic Relationships ◽  
Internal Transcribed Spacer ◽  
Morphological Characteristics ◽  
Biology Education ◽  
Rflp Analysis ◽  
Restriction Pattern ◽  
Internal Transcribed Spacers ◽  
Central Java ◽  
Pcr Rflp ◽  
Pcr Products

<p>In this study, twenty local durian accessions obtained from Central Java in situ collection were characterized using the morphological characteristics and the restriction patterns which generated from the region spanning the internal transcribed spacers ITS LEU and ITS 4. Morphological characteristics of durian leaf, stem, tree, and fruit showed variations for the different accessions, whereas polymerase chain reaction (PCR) products of ribosomal DNA region showed a low length of variation. The size of the PCR products and the restriction analyses with the restriction endonucleases Bsp1431yielded a restriction pattern for each accessions. The results of this study can be utilized by local durian farmers as a preliminary reference for durian propagation. The data obtained need to be supported by further research using the other molecular markers to obtain more accurate data. The clear identity of durian species can help the management of propagation systems by farmers to get superior local durian.</p><p><strong>How to Cite</strong></p><p>Fibriana, F., &amp; Hadiyanti, L. N. (2016). Phylogenetic Relationships of Local Durian Species based on Morphological Characteristics and PCR-RFLP Analysis of the Ribosomal Internal Transcribed Spacer (ITS) DNA. <em>Biosaintifika: Journal of Biology &amp; Biology Education</em>, 8(3), 362-370. </p>

scholarly journals The use of PCR-RFLP to genetically distinguish the morphologically close species: Ceriodaphnia dubia Richard, 1894 and Ceriodaphnia silvestrii Daday, 1902 (Crustacea Cladocera)

2010 ◽  
Vol 70 (1) ◽  
pp. 121-124 ◽  
Author(s):  
MJ. Abreu ◽  
MJ. Santos-Wisniewski ◽  
O. Rocha ◽  
TC. Orlando
Keyword(s):  
Exotic Species ◽  
Native Species ◽  
Rflp Analysis ◽  
Ceriodaphnia Dubia ◽  
Molecular Techniques ◽  
Rrna Genes ◽  
Its2 Region ◽  
State Of Water ◽  
Pcr Rflp ◽  
Rna Genes

The cladocerans are important components of planktonic and benthic freshwater and good indicators of the trophic state of water bodies. The morphological taxonomy of many species of Cladocera is considered complex with minor differences separating some species. Nowadays, molecular techniques provide a powerful tool to identify and classify different taxonomical levels, using mainly ribosomal RNA genes (rRNA) as molecular markers. In the present work we performed PCR-RFLP to separate Ceriodaphnia dubia, an exotic species in Brazil and the native species Ceriodaphnia silvestrii, widely distributed in Brazilian freshwater. The RFLP analysis of the ITS1-5.8S-ITS2 region of rRNA genes showed to be different between C. dubia and C. silvestrii when using enzymes EcoRI, ApaI and SalI. Thus, the ITS1-5.8S-ITS2 region proved to be a useful molecular marker to differentiate the studied Ceriodaphnia species, which makes the task easier of telling apart species that are morphologically very similar. Also, this methodology might be interesting in determining the distribution of the exotic species C. dubia in Brazilian freshwaters, particularly in cases when C. dubia occurs in the absence of C. silvestrii, a particularly difficult task for ecologists who are not taxonomy specialists.

scholarly journals Genotypic characterisation of the Erwinia genus by PCR-RFLP analysis of rpoS gene

2017 ◽  
Vol 38 (SI 2 - 6th Conf EFPP 2002) ◽  
pp. 288-290 ◽  
Author(s):  
M. Waleron ◽  
K. Waleron ◽  
E. Łojkowska
Keyword(s):  
Restriction Analysis ◽  
Wide Spectrum ◽  
Rflp Analysis ◽  
Pcr Primers ◽  
High Variability ◽  
Rpos Gene ◽  
Pcr Rflp ◽  
Identification Of Species ◽  
Genetic Profiles ◽  
Erwinia Species

Genotypic characterisation of the members of the genus Erwinia, based on the PCR-RFLP analysis of a fragment of the rpoS gene was done. PCR primers deduced from described rpoS gene sequences of E. carotovora allowed the amplification of about 880 bp DNA fragments from all tested Erwinia species. The rpoS fragments, amplified from 20 species of the studied Erwinia genus, were compared by RFLP analysis with 4 enzymes (AluI, Hin6I, HinfI, and Tru1I). Restriction analysis allowed drawing 63 common profiles of RFLP products for all tested Erwinia. From 1 to 3 specific RFLP profiles were identified among most of the species tested. However, in two cases: E. chrysanthemi and E. c. subsp. carotovora 15 and 20 specific RFLP groups were detected, respectively. High variability of genetic profiles of the E. chrysanthemi and E. c. subsp. carotovora can be explained by the wide spectrum of plants, which they infect. The results indicated that rpoS PCR-RFLP analysis is a useful tool for identification of species and subspecies belonging to the former Erwinia genus, as well as for differentiation of strains within E. c. subsp. carotovora and E. chrysanthemi.

scholarly journals Identification of Trichophyton mentagrophytes strains isolated from patients with dermatophytosis

2019 ◽  
pp. 01-07
Author(s):  
Imen Dhib ◽  
Yaacoub A ◽  
Ben Said M ◽  
Fathallah A ◽  
Zemni R
Keyword(s):  
Rflp Analysis ◽  
Trichophyton Mentagrophytes ◽  
Molecular Techniques ◽  
The Body ◽  
Its2 Region ◽  
Direct Microscopic Examination ◽  
Pcr Rflp ◽  
Tunisian Patients ◽  
Mycological Examination

According to epidemiological, clinical and mycological criteria, it has long been admitted that the Trichophyton mentagrophytes species includes two varieties: a zoophilic variety (var. mentagrophytes) and an anthropophilic variety (var. interdigital) that involve the upper and the lower part of the body respectively. The further application of molecular techniques to the characterization of dermatophyte strains showed that this classification is unreliable. The aim of our study was to assess the usefulness of PCR-RFLP (restriction fragment length polymorphism) and sequencing in the characterization of T. mentagrophytes strains taken from Tunisian patients. The study was carried out in 2008 in the laboratory of Parasitology-Mycology of Farhat Hatched hospital, Sousse, Tunisia. A total of 133 strains were isolated from 133 patients addressed to the laboratory for dermatological lesions very evocative of dermatomycosis. Eighty strains were isolated from lesions located on the lower part of the body (onychomycosis, tinea pedis) and 53 strains from the upper part of the body (tinea capitis, tinea corporis). All strains were submitted to mycological examination (direct microscopic examination, and culture on Sabered medium) and further investigated by using RFLP analysis of the PCR amplified ITS1-5.8 s and ITS2 region of the ribosomal DNA and the MvaI restriction enzyme. In addition, 20 strains were further submitted to a sequencing of the ITS1-5.8 s and ITS2 region. On the basis of mycological criteria all strains were diagnosed as T. mentagrophytes. All strains produced the same RFLP pattern and were identified as T. mentagrophytes interdigital regardless of the location of lesions. Out of the 20 sequenced strains, five were found anthropophilic and 15 were zoophilic. In conclusion, all strains provisionally diagnosed as T. mentagrophytes on the basis of mycological criteria were shown to belong to T. interdigital by using PCR-RFLP and sequencing irrespective of the site of lesions. The predominance of zoophilic strains needs further investigation. Keywords: Dermatophytes; Trichophyton mentagrophytes; PCR-RFLP; Sequencing; Phenotypic features

New records of Drosera tokaiensis subsp. hyugaensis (Droseraceae) from Kochi Prefecture, Japan

Botany ◽  
2012 ◽  
Vol 90 (8) ◽  
pp. 763-769
Author(s):  
Hiroshi Hayakawa ◽  
Hidenori Hamachi ◽  
Kohei Ogawa ◽  
Yukio Minaniya ◽  
Jun Yokoyama ◽  
...  
Keyword(s):  
Internal Transcribed Spacer ◽  
Nuclear Dna ◽  
New Records ◽  
Parental Species ◽  
Pollen Grains ◽  
Rflp Analysis ◽  
Drosera Rotundifolia ◽  
Pcr Rflp ◽  
Its Regions ◽  
Kochi Prefecture

Drosera tokaiensis subsp. hyugaensis (3x), a hybrid between Drosera spatulata (4x) and Drosera rotundifolia (2x), was found in Kochi Prefecture, Japan. Results of PCR–RFLP analysis of the internal transcribed spacer (ITS) regions of nuclear DNA showed that the hybrid individuals had the combined patterns of both parental species. Moreover, the chloroplast DNA of all hybrid individuals was identical to that of D. spatulata, suggesting that the hybrids were generated as a result of the transfer of pollen grains from D. rotundifolia to D. spatulata. Drosera tokaiensis subsp. hyugaensis was reported from Miyazaki and Kochi prefectures only. Drosera tokaiensis subsp. tokaiensis (6x), which is an allopolyploid species of D. tokaiensis subsp. hyugaensis, grows mainly in the Tokai and Kinki districts and is not distributed with D. tokaiensis subsp. hyugaensis in Miyazaki and Kochi prefectures. These findings indicate that the hybridization between D. spatulata and D. rotundifolia occurred independently and repeatedly in various areas of Japan.

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
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