Typing Tuber ectomycorrhizae by polymerase chain amplification of the internal transcribed spacer of rDNA and the sequence characterized amplified region markers

1997 ◽  
Vol 43 (8) ◽  
pp. 723-728 ◽  
Author(s):  
Delphine Gandeboeuf ◽  
Chantal Dupré ◽  
Gérard Chevalier ◽  
Paul Nicolas ◽  
Patricia Roeckel-Drevet

Identification of some economically important Tuber species using classical morphological characteristics is sometimes difficult. We report here the molecular characterization of a species coming from China, Tuber indicum, mistaken with Tuber melanosporum species. Using restriction analysis of the amplified internal transcribed spacer (ITS) of rDNA, ITS sequence analysis, and sequence characterized amplified region markers, with DNA from fruit bodies or mycorrhizae, genetic variation was found between these two species, allowing to differentiate and characterize them.Key words: molecular identification, Tuber, internal transcribed spacer, sequence characterized amplified region.

2012 ◽  
Vol 11 (101) ◽  
pp. 16635-16639
Author(s):  
Maria do Carmo Catanho Pereira de Lyra ◽  
◽  
Maria Luiza Ribeiro Bastos da Silva ◽  
Vanildo Alberto Leal Bezerra Cavalcanti ◽  
Adália Cavalcanti Espírito Santo Mergulhão

2021 ◽  
Author(s):  
Diego Cunha Zied ◽  
Wagner G. Vieira Junior ◽  
Douglas M. M. Soares ◽  
Cassius V. Stevani ◽  
Eustáquio S. Dias ◽  
...  

Abstract The mushroom Agaricus subrufescens has been synonymous with Agaricus blazei and Agaricus brasiliensis during the last decades and there has been much discussion with regards to the origin, distribution, and nomenclature of this mushroom. Therefore, we conducted a genetic and morphological characterization of the mycelium and mushroom of four commercial strains currently cultivated in Brazil (ABL CS7, ABL 18/01, ABL 98/11, and ABL 16/01) together with an assessment of their agronomic behavior and compared these results with those of other strains used during the last 15 years. All the A. subrufescens strains characterized here are phylogenetically related to the Americas/Europe specimens, bearing an internal transcribed spacer region of type A (ABL 16/01) or both types A and B (ABL 18/01, ABL 98/11, and ABL CS7). We did not find any correlation between the morphological characteristics of the mycelial colonies and the agronomic behavior of the strains. Strains ABL 98/11 and ABL 16/01 produced the best yields and morphological characteristics for the mushrooms, indicating their high weight, which enhances the commercialization of the mushroom and justifies their longstanding commercial use over the last 15 years.


Plant Disease ◽  
2013 ◽  
Vol 97 (1) ◽  
pp. 138-138 ◽  
Author(s):  
B. Z. Fu ◽  
M. Yang ◽  
G. Y. Li ◽  
J. R. Wu ◽  
J. Z. Zhang ◽  
...  

Chinese bean tree, Catalpa fargesii f. duciouxii (Dode) Gilmour, is an ornamental arbor plant. Its roots, leaves, and flowers have long been used for medicinal purposes in China. During July 2010, severe outbreaks of leaf spot disease on this plant occurred in Kunming, Yunnan Province. The disease incidence was greater than 90%. The symptoms on leaves began as dark brown lesions surrounded by chlorotic halos, and later became larger, round or irregular spots with gray to off-white centers surrounded by dark brown margins. Leaf tissues (3 × 3 mm), cut from the margins of lesions, were surface disinfected in 0.1% HgCl2 solution for 3 min, rinsed three times in sterile water, plated on potato dextrose agar (PDA), and incubated at 28°C. The same fungus was consistently isolated from the diseased leaves. Colonies of white-to-dark gray mycelia formed on PDA, and were slightly brown on the underside of the colony. The hyphae were achromatic, branching, septate, and 4.59 (±1.38) μm in diameter on average. Perithecia were brown to black, globose in shape, and 275.9 to 379.3 × 245.3 to 344.8 μm. Asci that formed after 3 to 4 weeks in culture were eight-spored, clavate to cylindrical. The ascospores were fusiform, slightly curved, unicellular and hyaline, and 13.05 to 24.03 × 10.68 to 16.02 μm. PCR amplification was carried out by utilizing universal rDNA-ITS primer pair ITS4/ITS5 (2). Sequencing of the PCR products of DQ1 (GenBank Accession No. JN165746) revealed 99% similarity (100% coverage) with Colletotrichum gloeosporioides isolates (GenBank Accession No. FJ456938.1, No. EU326190.1, No. DQ682572.1, and No. AY423474.1). Phylogenetic analyses (MEGA 4.1) using the neighbor-joining (NJ) algorithm placed the isolate in a well-supported cluster (>90% bootstrap value based on 1,000 replicates) with other C. gloeosporioides isolates. The pathogen was identified as C. gloeosporioides (Penz.) Penz. & Sacc. (teleomorph Glomerella cingulata (Stoneman) Spauld & H. Schrenk) based on the morphological characteristics and rDNA-ITS sequence analysis (1). To confirm pathogenicity, Koch's postulates were performed on detached leaves of C. fargesii f. duciouxii, inoculated with a solution of 1.0 × 106 conidia per ml. Symptoms similar to the original ones started to appear after 10 days, while untreated leaves remained healthy. The inoculation assay used three leaves for untreated and six leaves for treated. The experiments were repeated once. C. gloeosporioides was consistently reisolated from the diseased tissue. C. gloeosporioides is distributed worldwide causing anthracnose on a wide variety of plants (3). To the best of our knowledge, this is the first report of C. gloeosporioides causing leaf spots on C. fargesii f. duciouxii in China. References: (1) B. C. Sutton. Page 1 in: Colletotrichum: Biology, Pathology and Control. CAB International. Wallingford, UK, 1992. (2) T. J. White et al. Page 315 in: PCR Protocols: A Guide to Methods and Applications. Academic Press, San Diego, 1990. (3) J. Yan et al. Plant Dis. 95:880, 2011.


2001 ◽  
Vol 91 (6) ◽  
pp. 527-533 ◽  
Author(s):  
K. Nielsen ◽  
A. F. Justesen ◽  
D. Funck Jensen ◽  
D. S. Yohalem

Fifty-one isolates representing the four Botrytis spp. associated with onion neck rot were clustered by unweighted pair group method with arithmetic mean based on universal-primed polymerase chain reaction (UP-PCR) fingerprints. Bootstrap analysis of the consensus phenogram clearly demonstrated five strong clusters among the four Botrytis spp.: B. cinerea (C), B. squamosa (S), B. byssoidea (B), and B. aclada (AI and AII). Subdivision of the 30 B. aclada isolates, AI (14) and AII (16), from Europe, Egypt, North America, and Japan was further supported by restriction analysis of the internal transcribed spacer of the ribosomal genes and spore size measurements. Gene diversities (H) among AI and AII isolates were very low (0.007 and 0.043, respectively). A likelihood ratio chi-square test (G2) of Nei's coefficient of genetic differentiation (GST) showed that both B. aclada subgroups, AI and AII, were significantly different from B. byssoidea (P < 0.001), and that B. aclada subgroups AI and AII were significantly different from each other (P < 0.001). No UP-PCR alleles were shared by AI and B. byssoidea isolates, whereas 10 and 12 alleles were shared by AI:AII and AII:B. byssoidea, respectively. The hypothesis that AII may be a hybrid between AI and B. byssoidea is discussed.


Author(s):  
Seo Hee Lee ◽  
Thuong T. T. Nguyen ◽  
Hyang Burm Lee

The order Mucorales, the largest in number of species within the Mucoromycotina, comprises typically fast-growing saprotrophic fungi. During a study of the fungal diversity of undiscovered taxa in Korea, two novel mucoralean strains, CNUFC-GWD3-9 and CNUFC-EGF1-4, were isolated from specific habitats including freshwater and fecal samples, respectively, in Korea. On the basis of their morphological characteristics and sequence analyses of internal transcribed spacer (ITS) and large subunit (LSU) of 28S ribosomal DNA regions, the CNUFC-GWD3-9 and CNUFC-EGF1-4 isolates were confirmed to be Gilbertella persicaria and Pilobolus crystallinus, respectively. It is ecologically, pathologically and mycologically significant to find such rare zygomycetous fungi in such specific habitats.&nbsp;


2020 ◽  
Vol 18 (2) ◽  
pp. e1003
Author(s):  
Eleonora Rodríguez-Polanco ◽  
Juan G. Morales ◽  
Melissa Muñoz-Agudelo ◽  
José D. Segura ◽  
Martha L. Carrero

Aim of study: To characterize isolates of Phytophthora sp. causing black pod rot (BPR) of cacao (Theobroma cacao L.).Area of study: Eight cocoa-growing regions in Colombia.Material and methods: Sixty isolates of Phytophthora sp. were obtained from tissues of cacao pods showing symptoms of BPR. Isolates were characterized using the morphology of sporangia and chlamydospores, molecular sequencing of regions of nuclear DNA (rDNA-ITS) and mitochondrial (COX) and virulence in different genotypes of cocoa pods.Main results: A high phenotypic variability between the isolates was determined, being the pedicel length and the length/width ratio (L/W) the most stable characters for species identification. Short pedicels with an average of 3.13 μm ± 0.28 and a length/width ratio of sporangia (L/W) with an average of 1.55 μm ± 0.11 were established as the most consistent morphological characteristics within palmivora species.Research highlights: Phytophthora pamivora was the only species associated to BPR, identified using morphology together with sequence analyses.


Author(s):  
Arístides López ◽  
Fermin Acosta ◽  
Dilcia Sambrano ◽  
Musharaf Tarajia ◽  
Sophia Navajas ◽  
...  

Mycobacterium tuberculosis (MTB) stands out as the main causative agent of pulmonary tuberculosis (TB). However, nontuberculous mycobacteria (NTM) species also have the potential to infect and cause TB in susceptible individuals. The objective of this study was to identify NTM species that cause public health problems in remote areas. The study was carried out using 105 sputum smears obtained from patients from the Guna Yala Region of Panama with clinical signs suggestive of TB. DNA was extracted from sputum smears. Nontuberculous mycobacteria and MTB were characterized using polymerase chain reaction restriction analysis (hsp65, rpob) and an evaluation of 24-mycobacterial interspersed repetitive units–variable number of tandem repeats loci. Twenty-six Mycobacterium species were characterized; 19 (18%) were identified as MTB, and 7 (6.7%) were identified as NTM (four M. avium complex, two M. haemophilum, one M. tusciae). These results suggest that at least one in five cases of pulmonary TB among this population is caused by an NTM. Thus, identifying the bacteria causing pulmonary disease is key even in remote regions of the world where standard diagnosis and culture are not available. Strengthening the laboratory capacity within the Guna Yala Region is needed to identify NTM infections promptly.


Plant Disease ◽  
2021 ◽  
Author(s):  
Caiyun Xiao ◽  
Rongyu Li ◽  
Xingchen Song ◽  
Xujun Tian ◽  
Qijun Zhao

In recent years, soft rot is one of the most serious diseases in the production of Dendrobium officinale. In this study, we took the diseased plants of Dendrobium officinale in Guizhou as samples, through Koch's rule and sequence analysis of rDNA internal transcribed spacer (rDNA-ITS), calmodulin (cmdA), the second largest subunit of RNA polymerase Ⅱ (RPB2), elongation factor EF-1 α and β-tubulin (β-Tub), it was determined that the pathogen of Dendrobium officinale soft rot was sorghum accessory cocci. This is our first report on the soft rot of Dendrobium officinale caused by Epicoccum sorghinum in China. The morphological characteristics of the pathogen shown in the study will have a certain reference value for the prevention and control of the soft rot of Dendrobium officinale in the future.


Phytotaxa ◽  
2019 ◽  
Vol 414 (6) ◽  
pp. 280-288 ◽  
Author(s):  
YAN-HONG MU ◽  
FANG WU ◽  
HAI-SHENG YUAN

A new hydnaceous fungus, Phellodon subconfluens, from northeast China, is described and illustrated based on morphological characteristics and rDNA ITS sequences. The new species is characterized by circular to flabelliform basidiocarps, a greyish buff, brownish orange to reddish brown and obscurely zonate pileal surface with white, incurved margins, a monomitic hyphal system with simple-septate, generative hyphae, and broadly ellipsoid to subglobose, thin-walled basidiospores with echinulate ornamentation. Molecular analysis confirms the phylogenetic position of the new species in Phellodon. The discriminating characters of the new species and closely related species are discussed.


2006 ◽  
Vol 52 (6) ◽  
pp. 570-574
Author(s):  
Ching-Fu Lee ◽  
Daniel Yuen Teh Liu ◽  
Ming Tsong Lai ◽  
Tzong-Hsiung Hseu

Strain W-10, originally identified as Trichoderma koningii, and its supposed mutant G-39, published for production and gene expression of cellulase and xylanase, demonstrated morphological characteristics distinct from those of T. koningii, respectively. To clarify the identification derived from morphological characteristics, several methods were used, including electrophoretic karyotyping, internal transcribed spacer (ITS) analysis of rDNA, and polymerase chain reaction (PCR) fingerprinting using the universal primer L45. All the molecular characteristics showed that strains G-39 and W-10 were identical to T. reesei and T. longibrachiatum, respectively. The results strongly supported that T. koningii G-39 and W-10 should be reassigned as T. reesei and T. longibrachiatum, respectively. Strain G-39 should be considered a mutant from T. reesei QM9414 whose spores were contaminated with those of strain W-10 during a laboratory operation. According to this, we declare that T. koningii G-39 and W-10 must be renamed as T. reesei and T. longibrachiatum, respectively.Key words: PCR fingerprinting, electrophoretic karyotypes, ITS, Trichoderma.


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