scholarly journals Morphological and molecular identification of ectomycorrhizal fungi associated with Persian oak (Quercus brantii Lindl.) tree

2020 ◽  
Vol 66 (No. 6) ◽  
pp. 244-251
Author(s):  
Behnaz Yousefshahi ◽  
Masoud Bazgir ◽  
Samad Jamali ◽  
Fatemeh Valizadeh Kakhki
Keyword(s):  
Its Region ◽  
Molecular Techniques ◽  
Molecular Methods ◽  
Morphological Identification ◽  
Tree Roots ◽  
Microscopic Features ◽  
Zagros Zone ◽  
Oak Tree ◽  
Ecm Fungi ◽  
Quercus Brantii

Identification of ectomycorrhizal (ECM) fungi in different ecosystems has major significance. In this research, to identity ECM fungi, we used two methods including the morphological method and the molecular method that is more precise. Basidiocarp collection of fungi associated with oak tree (Quercus brantii Lindl.) roots was carried out in the spring season 2016 and was identified by morphological and molecular methods. We also checked macroscopic and microscopic features and measured each structure using BioloMICS Measures software. To verify the morphological identification, the internal transcribed spacer (ITS) region was amplified by PCR using the primer pair ITS1/ITS4, and the sequences were analyzed. According to the morphological observations, the identified species were Amanita crocea, Boletus comptus, Tricholoma giganteum, and Inocybe rimosa. Besides, based on molecular techniques by comparing sequences, we identified five species out of the eight ones as A. crocea and other species as T. giganteum, I. rimosa and B. comptus. Both morphological and molecular methods are necessary for identifying ECM fungi associated with tree roots in the Zagros zone in the west of Iran.

scholarly journals Genetic Diversity Within Colletotrichum acutatum sensu Simmonds

2001 ◽  
Vol 91 (6) ◽  
pp. 586-592 ◽  
Author(s):  
Stanley Freeman ◽  
Dror Minz ◽  
Marcel Maymon ◽  
Aida Zveibil
Keyword(s):  
Sequence Analysis ◽  
Its Region ◽  
Molecular Methods ◽  
Colletotrichum Acutatum ◽  
Morphological Identification ◽  
Chain Reaction ◽  
Subgroup Ii ◽  
Polymerase Chain ◽  
Percent Similarity ◽  
Species Specific

Isolates of Colletotrichum acutatum from several hosts were characterized by various molecular methods in comparison with morphological identification. Species-specific primer analysis was reliable for grouping C. acutatum isolates to their designated species. Arbitrarily primed polymerase chain reaction and A+T-rich DNA analyses identified four subgroups within C. acutatum. Subgroup I contained U.S. isolates from almond, apple, peach, and pecan, subgroup II contained isolates from anemone, olive, and strawberry, subgroup III contained isolates from almond (Israel) and strawberry (Spain), and subgroup IV contained a single isolate from anemone (the Netherlands). Likewise, sequence analysis of the internal transcribed spacer (ITS) 2 region alone or the complete ITS (ITS 1–5.8S-ITS 2) region grouped the isolates into the same four subgroups. Percent similarity of the complete ITS region within each cluster ranged from 99.6 to 100.0, 99.8 to 100.0, and 98.6% among subgroups I, II, and III, respectively. DNA sequence analysis of the ITS 2 region alone or the entire ITS 1-2 region was more informative than that of the ITS 1 region, which could only group the isolates into two main clusters. The molecular methods employed for studying genetic variation in populations of C. acutatum determined that this species is diverse, indicating that isolates within populations of each subgroup are not host specific.

scholarly journals Morphomolecular Identification of Trichoderma sp. and their Mycoparasitic Activity Against Soil Borne Pathogens

2020 ◽  
Vol 11 (6) ◽  
pp. 613-627
Author(s):  
Gyanendra Kumar ◽  
◽  
Anuradha Singh ◽  
Sonika Pandey ◽  
Jogender Singh ◽  
...  
Keyword(s):  
Sequence Data ◽  
Uttar Pradesh ◽  
Its Region ◽  
Morphological Identification ◽  
Single Spore ◽  
Trichoderma Species ◽  
Morphological Studies ◽  
Trichoderma Sp ◽  
Rdna Sequence Data ◽  
Microscopic Features

This study was carried out to identify and characterize Trichoderma species isolated from rhizospheric soil of Uttar Pradesh, India, by using single spore technique. Morphological, cultural and molecular characterization were done with sequence analysis of the internal transcribed spacer (ITS) region. The classes were compared with morphological identification and rDNA sequence data for every class of all Trichoderma strains were of the same identity. These strains belonged to T. harzianum (Th azad), T. viride (01PP), T. asperellum (Tasp/CSAU), T. Koningii [TK (CSAU)], T. atroviride (71L), T. longibrachiatum (21PP), T. virens [Tvi (CSAU)], T. reesei [Tr (CSAU)], T. aggressivum [T.agg(CSAU)], T. aureoviride [T. avi (CSAU)], T. citrinoviride [T. cvi (CSAU)], T. erinaceum [T. eri (CSAU)], T. koningiopsis [T. kop (CSAU)], T. tomentosum [T. tos (CSAU)], T. mintisporum [T. mip (CSAU)], T. pubscenes [T. sce (CSAU)], T. saturnisporum [T. ssp (CSAU)], T. spirale [T. sp. (CSAU)]. Morphological studies were based on the colony appearance, growth rate and microscopic features such as branching patterns of conidiophores, the arrangement of phialospores and their shape, size and color. The 5.8S-ITS regions of the Trichoderma strains were amplified using ITS1 and ITS4 primers. The rRNA based analysis is a central method used not only to explore microbial diversity but also to identify new strains. Validations of ITS marker with 18 Trichoderma sp. were done and their sequences were deposited at NCBI GenBank their permanent accession no. were allotted.

scholarly journals Molecular Depiction of Thirteen Indian Toxic Plants with ITS Markers

2020 ◽  
Vol 2 (2) ◽  
pp. 179-189
Author(s):  
Kiran Kumari ◽  
Saurabh Bhargava ◽  
Rajvinder Singh
Keyword(s):  
Plant Species ◽  
Forensic Toxicology ◽  
Its Region ◽  
Molecular Techniques ◽  
Reference Sequence ◽  
Morphological Identification ◽  
Molecular Technique ◽  
Accurate Identification ◽  
Universal Primer ◽  
Toxic Plants

Plant identification is an overwhelming task due to different biological attributes and great diversity in plant species. In the absence of physical markers, molecular techniques have become useful for the identification of species of origin of medicinal plant seeds, pastes, and formulations of suspected plants. The ITS region of nuclear rRNA was amplified from thirteen different toxic plant species by using universal primer ITS 1 & 4. Nucleotide sequences of all selected plants were submitted in NCBI and accession numbers were acquired. The results of this study give accurate identification of thirteen plant species and proved the ITS region of 18s-26s nuclear ribosome to be an important tool for phylogenetic analysis and species identification of plants. The sequence was aligned with top matched reference sequence and presented in Clustal Omega software for making a phylogenetic neighbour tree. The significance of these findings is paramount in forensic toxicology scenarios especially when fragmentary plant material is found in the stomach/intestine and its morphological identification becomes impossible. In these circumstances, the PCR based molecular technique surely plays a significant role in solving complicated forensic cases.

scholarly journals Biosorption potential and molecular characterization of metal resistant autochthonous microbes from tannery solid waste

2021 ◽  
Author(s):  
Hajira Younas ◽  
Aisha Nazir ◽  
Zakia Latif ◽  
Janice E Thies ◽  
Muhammad Shafiq ◽  
...  
Keyword(s):  
Solid Waste ◽  
Its Region ◽  
Metal Resistance ◽  
Molecular Techniques ◽  
Bacterial Strains ◽  
Fungal Strains ◽  
Resistant Strains ◽  
Tannery Solid Waste ◽  
Clean Metal

This study encompasses isolation and screening of heavy metal-resistant fungal and bacterial strains from tannery solid waste (TSW). Twelve fungal strains and twenty-five bacterial strains were isolated from TSW. The growth of fungal strains was observed against different heavy metals ranging from 10 mg L -1 to 1050 mg L -1 and the growth of bacteria was observed in metal concentrations ranging from 10 mg L -1 to 1200 mg L -1 . Five multi-metal resistant fungal isolates belonging to the genus Trichoderma and ten bacterial isolates belonging to the genus Bacillus showed good metal resistance and biosorption potential. They were identified through molecular techniques, fungi based on ITS region ribotyping, and bacteria based on 16S rRNA ribotyping. The fungal strains were characterized as T. hamatum (TSWF-06), T. harzianum (TSWF-11), T. lixii (TSWF-02) and T. pseudokoningii (TSWF-03, TSWF-10). The bacterial strains were characterized as Bacillus xiamenensis (TSW-02), B. velezensis (TSW-05), B. piscis (TSW-06), B. safensis (TSW-10), B. subtilis (TSW-14, TSW-15, TSW-17) B. licheniformis (TSW-19), B. cereus (TSW-20) and B. thuringiensis (TSW-22). The fungal strains namely, T. pseudokoningii (TSWF-03) and T. harzianum proved to be two multi-metal resistant strains with good biosorption efficiency. Unlike fungi, bacterial strains showed metal specific resistance. The strains Bacillus xiamenensis , B. subtilis (TSW-14) and B. subtilis (TSW-15) showed good biosorption efficiency against Cr, B. safensis against Cu, B. piscis and B. subtilis (TSW-17) against Pb and B. licheniformis and B. thuringiensis against Zn. The autochthonous fungal and bacterial strains can therefore be employed to clean metal contaminated environments.

scholarly journals Morphological and molecular identification of phytophthora species from maple trees in Serbia

Genetika ◽  
2014 ◽  
Vol 46 (2) ◽  
pp. 353-368 ◽  
Author(s):  
Ivan Milenkovic ◽  
Justyna Nowakowska ◽  
Tomasz Oszako ◽  
Katarina Mladenovic ◽  
Aleksandar Lucic ◽  
...  
Keyword(s):  
Molecular Identification ◽  
Genomic Dna ◽  
Its Region ◽  
Phytophthora Species ◽  
Morphological Identification ◽  
First Report ◽  
Phytophthora Spp ◽  
Isolated Species

The paper presents the results of the study performed with aims to determine the presence and diversity of Phytophthora species on maple trees in Serbia. Due to high aggressiveness and their multicyclic nature, presence of these pathogens is posing significant threat to forestry and biodiversity. In total, 29 samples of water, soil and tissues were taken from 10 different localities, and six different maple hosts were tested. After the isolation tests, 17 samples from five different maple hosts were positive for the presence of Phytophthora spp., and 31 isolates were obtained. After the detailed morphological and physiological classification, four distinct groups of isolates were separated. DNA was extracted from selected representative isolates and molecular identification with sequencing of ITS region was performed. Used ITS4 and ITS6 primers successfully amplified the genomic DNA of chosen isolates and morphological identification of obtained isolates was confirmed after the sequencing. Four different Phytophthora species were detected, including P. cactorum, P. gonapodyides, P. plurivora and P. lacustris. The most common isolated species was homothallic, and with very variable and semipapillate sporangia, P. plurivora with 22 obtained isolates. This is the first report of P. plurivora and P. gonapodyides on A. campestre, P. plurivora and P. lacustris on Acer heldreichii and first report of P. lacustris on A. pseudoplatanus and A. tataricum in Serbia.

scholarly journals An insight into biosecurity plant-disease diagnostics at MPI

2019 ◽  
Vol 72 ◽  
pp. 281
Author(s):  
Robert K. Taylor ◽  
Merje Toome-Heller ◽  
Wellcome W.H. Ho ◽  
Brett J.R. Alexander
Keyword(s):  
New Zealand ◽  
High Throughput Sequencing ◽  
Test Methods ◽  
Molecular Techniques ◽  
Morphological Identification ◽  
Sample Type ◽  
Emerging Pathogens ◽  
Post Entry ◽  
Biochemical Testing ◽  
Diagnostic Work

The Mycology and Bacteriology team of the Ministry for Primary Industries’ Plant Health and Environment Laboratory is responsible for the identification and verification of all suspected exotic, new, and emerging pathogens affecting plants and the environment in New Zealand. We work in an applied diagnostic environment where results can have significant implications for biosecurity. Sample submissions often result in detection of new to New Zealand fungi and bacteria on plants for which information on fungal and bacterial associations is generally sparse. The complexity of testing required is quite varied with samples being submitted from post entry quarantine (looking for a known pathogen using specific tests), border or surveillance (unknown pathogens requiring multiple tests), or a biosecurity response (scaling up to test large numbers, identification resolution required to strain level). Applied test methods depend largely on the sample type and consist of morphological identification, biochemical testing, pathogenicity testing, serological and molecular techniques, including high throughput sequencing. A profile of our diagnostic work and the most commonly detected taxa and host associations are presented.

Morphological and molecular characterization of adult worms of Leucochloridium paradoxum Carus, 1835 and L. perturbatum Pojmańska, 1969 (Digenea: Leucochloridiidae) from the great tit, Parus major L., 1758 and similarity with the sporocyst stages

2013 ◽  
Vol 88 (4) ◽  
pp. 506-510 ◽  
Author(s):  
I. Rząd ◽  
P. Hofsoe ◽  
R. Panicz ◽  
J.K. Nowakowski
Keyword(s):  
Parus Major ◽  
Morphological Characters ◽  
Great Tit ◽  
Molecular Techniques ◽  
Morphological Identification ◽  
The Baltic Sea ◽  
The Baltic ◽  
Morphological And Molecular Characterization ◽  
Sea Coast

AbstractUnlike the sporocyst stages, adult leucochloridiid digeneans are difficult to differentiate. Sporocyst broodsacs can be identified on the basis of their colour and banding pattern, but in the absence of broodsacs and when experimental infection cannot be performed, tentative morphological identification needs to be verified, and molecular techniques offer a tool to do this. In this study, adult leucochloridiid digeneans were collected from the great tit (Parus major) found dead at three localities at or near the Baltic Sea coast (Hel, Bukowo-Kopań and Szczecin) in northern Poland. On the basis of differences in their morphological characters, Hel specimens were tentatively assigned to Leucochloridium perturbatum, Bukowo-Kopań and Szczecin specimens being identified tentatively as L. paradoxum. Subsequent ribosomal DNA sequence analysis confirmed the identification of these leucochloridiid flukes. Nucleotide sequences discriminating between the two species were identical to those used by earlier authors as characteristic of two distinctly different sporocyst broodsacs representing L. perturbatum and L. paradoxum.

Idylla MSI test as a new tool for microsatellite instability detection in sebaceous tumours and keratoacanthomas

2021 ◽  
pp. jclinpath-2021-207606
Author(s):  
Loëtitia Favre ◽  
Ruiqian Chen ◽  
Yaëlle Bellahsen-Harrar ◽  
Nicolas Ortonne ◽  
Anaïs Pujals
Keyword(s):  
Lynch Syndrome ◽  
Microsatellite Instability ◽  
Sensitivity And Specificity ◽  
Molecular Techniques ◽  
Molecular Methods ◽  
Specific Method ◽  
Skin Tumours ◽  
Automated Method ◽  
Mmr Deficiency ◽  
Mmr Proteins

AimSebaceous tumours and keratoacanthomas can be associated with mismatch repair (MMR) deficiency and thus microsatellite instability (MSI). In such tumours, MSI phenotype could be an argument to search for an underlying Muir-Torre syndrome (MTS). MTS has been recognised as a variant of Lynch syndrome, characterised by a deficiency of the MMR proteins. In Lynch syndrome, the sensitivity and specificity of the techniques used to detect MSI is well described, which is not the case for skin tumours. In our hands, immunohistochemistry is a sensitive and specific method to detect MMR deficiency in those tumours. Contrasting with tumours of Lynch spectrum, sensitivity and specificity of molecular methods has not been extensively studied. This study aimed at evaluating two molecular methods to detect MSI phenotype in MTS associated tumours: a commonly used pentaplex PCR using Bethesda markers and the fully automated method using the Idylla MSI assay.MethodsA comparison between PCR, and Idylla was performed on 39 DNA extracted from cutaneous tumours. Immunohistochemistry was used as the gold standard to calculate sensitivity and specificity of both molecular techniques.ResultsConcordant results were found in 32 cases (82%) with pentaplex PCR and in 36 cases (92%) with Idylla. The sensitivity of pentaplex PCR to detect MSI phenotype was 76% whereas Idylla sensitivity was 90%.ConclusionIdylla is more performant than PCR, for the detection of MSI in MTS-associated tumours and is a reliable additional technique to help detecting MTS in these tumours.

Baorangia duplicatopora (Boletaceae, Boletales), a new bolete from tropical China

Phytotaxa ◽  
2021 ◽  
Vol 508 (1) ◽  
Author(s):  
XU ZHANG ◽  
ZHI-QUN LIANG ◽  
SHUAI JIANG ◽  
CHANG XU ◽  
XIN-HUA FU ◽  
...  
Keyword(s):  
New Species ◽  
Dna Sequences ◽  
Phylogenetic Analyses ◽  
Elongation Factor ◽  
Its Region ◽  
Tropical Region ◽  
Translation Elongation ◽  
Line Drawings ◽  
Microscopic Features ◽  
Tropical China

Baorangia duplicatopora is described as a new species from Hainan Province, a tropical region of China. It is morphologically characterized by large to very large basidiomata with a dull rose red, rose pink to purplish red pileus, compound pores, pileus context near hymenophore and stipe context staining blue when injured, a red stipe, and cheilocystidia wider than those of other Baorangia species. Phylogenetic analyses of DNA sequences from part of the 28S gene, the nuc rDNA internal transcribed spacer (ITS) region, and part of the translation elongation factor 1-α gene (TEF1) also confirmed that B. duplicatopora forms an independent lineage within Baorangia. Detailed descriptions, color photographs of fresh basidiomata, and line drawings of microscopic features of the new species are presented. A key to species of Baorangia in the world is also provided.

Characterization and pathogenicity of Diplodia, Lasiodiplodia and Neofusicoccum species causing Botryosphaeria canker and dieback of apple trees in central Chile

Plant Disease ◽  
2021 ◽  
Author(s):  
Gonzalo A. Díaz ◽  
Adrián Vinicio Valdez ◽  
Francois Halleen ◽  
Enrique Ferrada ◽  
Mauricio A. Lolas ◽  
...  
Keyword(s):  
Disease Incidence ◽  
Elongation Factor ◽  
Its Region ◽  
Morphological Identification ◽  
Apple Trees ◽  
Translation Elongation ◽  
Central Chile ◽  
Growing Seasons ◽  
First Time ◽  
Elongation Factor 1

In recent years, the number of apple trees affected by Botryosphaeria cankers and dieback has considerably increased in central Chile. This study aimed to identify the species of Botryosphaeriaceae associated with canker and dieback symptoms, estimate disease incidence and distributions, and study their pathogenicity and virulence on apple and other fruit crops. A field survey of 34 commercial orchards of apple (7-to 30-year-old) was conducted in 16 localities obtaining 270 symptomatic branches and trunks samples in 2017 and 2018 growing seasons. The incidence of Botryosphaeria canker and dieback ranged between 5 and 40%, and a total of 255 isolates of Botryosphaeriaceae spp. were obtained from 238 cankers. Morphological identification along with phylogenetics studies of the internal transcribed spacer (ITS) region (ITS1-5.8S-ITS2) of the rDNA, part of the translation elongation factor 1-α (tef1-α), and part of the beta tubulin (tub2) genes allowed to identify Diplodia mutila (n = 49 isolates), D. seriata (n = 136 isolates), Lasiodiplodia theobromae (n = 16 isolates) and Neofusicoccum arbuti (n= 54 isolates). L. theobromae was isolated mainly of apple dieback from northern localities. All pathogens tested were pathogenic, causing canker and dieback symptoms on lignified twigs of apple, pear, walnut, and green grapevine shoots in the field. Isolates of N. arbuti were the most virulent by reproducing more severe cankers on lignified tissues inoculated. This study reports D. mutila and L. theobromae for the first time associated with Botryosphaeria canker and dieback in Chile, and it is the first description of N. arbuti causing apple dieback worldwide.

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