Characterization of Dryas octopetala ectomycorrhizas from limestone karst vegetation, western Ireland

2002 ◽  
Vol 80 (9) ◽  
pp. 970-982 ◽  
Author(s):  
Thomas J Harrington ◽  
Derek T Mitchell
Keyword(s):  
Rflp Analysis ◽  
Its Region ◽  
Fungal Species ◽  
Morphological Evidence ◽  
Soil Core ◽  
Cenococcum Geophilum ◽  
Dryas Octopetala ◽  
Pcr Rflp ◽  
Provisional Identification ◽  
Western Ireland

The principal ectomycorrhizas of Dryas octopetala L. from a treeless grass-heath in the Burren, western Ireland, were characterized using morphotyping and molecular methods (PCR-RFLP analysis of ITS-rDNA and sequencing of the ITS region). Twenty-one distinct morphotypes are described. Six of these (Cortinarius atrovirens Kalchbr., Cortinarius caesiocanescens (Mos.) Kühn. & Romagn., Cortinarius calochrous (Mos.) Nezd., Cortinarius odorifer Britz., Cortinarius mussivus Fr., and Tricholoma myomyces (Scop.) Quél.) were distinguished by tracing rhizomorph connections between mycorrhizas and basidiomes. The ectomycorrhizas of Cenococcum geophilum Fr., Craterellus lutescens (Pers.:Fr.) Fr., and Hebeloma sinapizans (Paulet:Fr.) Gill were identified based on molecular and morphological evidence. The ectomycorrhizas of Cortinarius brunneus (Pers.:Fr.) Fr., Cortinarius infractus (Pers.:Fr.) Fr., Hydnum repandum L., and Hebeloma circinans Quél. were distinguished provisionally, because they were consistently found in soil core samples containing basidiomes of a particular fungal species. The provisional identification of Lactarius sanguifluus (Paulet) Fr., and Russula delica Fr. ectomycorrhizas was also based on anatomical evidence, particularly the presence of lacticifers and cystidia, respectively. Six morphotypes could not be assigned to a specific fungal taxon and, therefore, were named "Dryadirhiza" + a characterizing epithet (D. aerea, D. cerina, D. fulgens, D. nigra, D. rugosa, and D. truncata). It is concluded that Dryas octopetala forms ectomycorrhizal associations in the Burren with woodland fungal species.Key words: ectomycorrhizas, Dryas octopetala, morphotyping, ITS-RFLP, mountain avens.

scholarly journals Genetic variation among pathogens causing "Helminthosporium" diseases of rice, maize and wheat

2002 ◽  
Vol 27 (6) ◽  
pp. 639-643 ◽  
Author(s):  
RITA C. B. WEIKERT-OLIVEIRA ◽  
M. APARECIDA DE RESENDE ◽  
HENRIQUE M. VALÉRIO ◽  
RACHEL B. CALIGIORNE ◽  
EDILSON PAIVA
Keyword(s):  
Triticum Aestivum ◽  
Genetic Variation ◽  
Climatic Factors ◽  
Rapd Analysis ◽  
Its Region ◽  
Restriction Enzymes ◽  
Fungal Species ◽  
High Similarity ◽  
Pcr Rflp ◽  
Upgma Phenogram

Twenty isolates of four fungal species, agents of "Helminthosporium" diseases in cereals, were collected from different regions: nine Bipolarisoryzae isolated from rice (Oryza sativa), seven B.sorokiniana from wheat (Triticum aestivum), two B. maydis, and two Exserohilumturcicum from maize (Zea mays). The strains were compared by PCR-RFLP and RAPD analysis. Size polymorphism among the isolates in the ITS region comprising the 5.8 S rDNA indicated genetic differences among the isolates, while a UPGMA phenogram constructed after the digestion of this region with restriction enzymes showed inter- and intra-specific polymorphism. The RAPD profiles indicated an expressive level of polymorphism among different species, compared with a low level of polymorphism among isolates of the same species. A UPGMA phenogram grouped the isolates according to the species and their host plant. RAPD profiles did not reveal polymorphism that directly correlated climatic factors with geographic source of the isolates of B. sorokiniana, and B. oryzae. Teleomorphic species revealed high similarity with their correspondent anamorphs.

Steinernema apuliae sp. n. (Rhabditida: Steinernematidae): a new entomopathogenic nematode from southern Italy

Zootaxa ◽  
2004 ◽  
Vol 460 (1) ◽  
pp. 1 ◽  
Author(s):  
ORESTE TRIGGIANI ◽  
ZDENEK MRÁ»EK ◽  
ALEX REID
Keyword(s):  
First Generation ◽  
Southern Italy ◽  
Entomopathogenic Nematode ◽  
Rflp Analysis ◽  
Tail Length ◽  
Its Region ◽  
The Body ◽  
Steinernema Glaseri ◽  
Pcr Rflp ◽  
H 41

Steinernema apuliae sp. n. has been found in soil samples collected along a saltpan border habitat in southern Italy characterized by a salted silt soil. This species belongs to the long-IJ nematode group represented by Steinernema glaseri (Steiner, 1929) and Steinernema arenarium (Artyukhovsky, 1967) among others. However, it differs from these taxa in some morphometric values such as V%, H%. Females possess asymmetrical, oblique slit vulva, slant vagina and small flap in the vulval opening. These characteristics are more distinct in second generation females which is different from most other steinernematids; the vulva position is behind the mid-body about 57% to 61% of the body length. First-generation females have a conical-like tip bearing 2 to 3 papilla-like protuberances. Male mucron is absent in both generations. Lightly brown spicules have bluntly pointed tip and elongated manubrium. Third-stage infective juveniles are on average over 1000 m long; the position of the excretory pore is posterior (D% 66) and the hyaline layer is less than half the tail length (H% 41 42). Lateral fields are formed by 8 equally distributed ridges. S. apuliae differs from S. glaseri and S. arenarium and is separated by PCR-RFLP analysis of the ITS region. There were no positive cross-breedings among these species.

scholarly journals Determination of Types of Enterocytozoon bieneusiStrains Isolated from Patients with Intestinal Microsporidiosis

1998 ◽  
Vol 36 (7) ◽  
pp. 1882-1885 ◽  
Author(s):  
Olivier Liguory ◽  
Felicia David ◽  
Claudine Sarfati ◽  
Francis Derouin ◽  
Jean-Michel Molina
Keyword(s):  
Rflp Analysis ◽  
Its Region ◽  
Restriction Enzymes ◽  
Epidemiological Studies ◽  
Enterocytozoon Bieneusi ◽  
Type I ◽  
Pcr Rflp ◽  
Intestinal Microsporidiosis ◽  
Rflp Typing

To determine the types of Enterocytozoon bieneusistrains associated with intestinal microsporidiosis, we developed a rapid and efficient approach for typing parasites obtained from stool specimens by PCR-restriction fragment length polymorphism (PCR-RFLP). Typing was based on DNA polymorphism of the ribosomal DNA internal transcribed spacer (ITS) region of E. bieneusi. RFLPs generated with two restriction enzymes (NlaIII andFnu4HI) in PCR-amplified ITS products were used to classify strains into different lineages. This approach was successfully used to differentiate 78 strains that had been obtained from the stools of 65 patients with intestinal microsporidiosis. Among the 78 strains, we found four genetically unrelated lineages, showing the genetic diversity of E. bieneusi. Type I strains of E. bieneusi were found in a majority of the samples, accounting for 51 (78%) of the 65 microsporidiosis cases. In contrast, type II, III, and IV strains were found in only 8 (12%), 3 (5%), and 3 (5%) cases, respectively. All strains of E. bieneusi we have tested so far fall into one of four different lineages, and this study shows that human intestinal microsporidiosis is most often associated with type I strains. PCR-RFLP analysis of the ITS region of E. bieneusishould be useful for epidemiological studies.

scholarly journals Characterization of Ascaris from Ecuador and Zanzibar

2014 ◽  
Vol 89 (4) ◽  
pp. 512-515 ◽  
Author(s):  
A.M. Sparks ◽  
M. Betson ◽  
G. Oviedo ◽  
C. Sandoval ◽  
P.J. Cooper ◽  
...  
Keyword(s):  
Fragment Length Polymorphism ◽  
Rflp Analysis ◽  
Its Region ◽  
Restriction Enzymes ◽  
Zoonotic Transmission ◽  
Pcr Rflp ◽  
Double Digestion ◽  
Polymerase Chain ◽  
Shed Light

AbstractTo shed light on the epidemiology of ascariasis in Ecuador and Zanzibar, 177 adult worms retrieved by chemo-expulsion from either people or pigs were collected, measured and subjected to polymerase chain reaction–restriction fragment length polymorphism (PCR-RFLP) analysis of the ribosomal internal transcribed spacer (ITS) region. Upon double digestion with RsaI and HaeIII, PCR-RFLP analysis revealed the presence of A. lumbricoides in people and A. suum in pigs in Ecuador. In contrast, while there are no pigs on Zanzibar, of the 56 worms obtained from people, one was genotyped as A. suum. No additional genetic variation was detected upon further PCR-RFLP analysis with several other restriction enzymes. Upon measurement, worm mass and length differed by location and by species, A. suum being lighter and longer. While there is no evidence to suggest zoonotic transmission in Ecuador, an enduring historical signature of previous zoonotic transmission remains on Zanzibar.

scholarly journals An RFLP-Based Technique for Identifying Fungi in the Sooty Blotch and Flyspeck Complex on Apple

Plant Disease ◽  
2008 ◽  
Vol 92 (5) ◽  
pp. 794-799 ◽  
Author(s):  
K. B. Duttweiler ◽  
G. Y. Sun ◽  
J. C. Batzer ◽  
T. C. Harrington ◽  
M. L. Gleason
Keyword(s):  
Agar Plate ◽  
Pcr Amplification ◽  
Rflp Analysis ◽  
Its Region ◽  
Morphological Description ◽  
Sooty Blotch ◽  
Pcr Rflp ◽  
Sooty Blotch And Flyspeck ◽  
Rflp Assay

A restriction fragment length polymorphism (RFLP)-based technique was developed to identify members of the sooty blotch and flyspeck (SBFS) disease complex on apple because these fungi are difficult to identify using agar-plate isolation and morphological description. The method includes polymerase chain reaction (PCR) amplification of the internal transcribed spacer (ITS) region of ribosomal DNA (rDNA) using a fungal-specific forward primer (ITS1-F) and an SBFS-specific reverse primer (Myc1-R), followed by digestion of the PCR product by the HaeIII restriction enzyme. When applied to previously identified isolates of 24 SBFS-causing species in nine genera, the PCR-RFLP assay produced 14 unique banding patterns. Different genera never shared the same RFLP pattern. To evaluate performance in vivo, the technique was applied to DNA extracted directly from SBFS colonies on apple fruit from three Iowa orchards. The primers amplified the rDNA of only SBFS fungi, with the exception of a Cladosporium sp.; however, its RFLP banding pattern was distinct from those of SBFS fungi. The majority (60%) of SBFS colonies in the in vivo trial were identified to genus by RFLP analysis. The PCR-RFLP assay greatly streamlined the identification process by minimizing the need for culturing, indicating its value as a tool for field studies of the SBFS complex.

scholarly journals Genetic Sequence Variation in the ITS Region of Nine Rubus Genotypes

HortScience ◽  
2004 ◽  
Vol 39 (4) ◽  
pp. 754A-754 ◽  
Author(s):  
Eric Stafne* ◽  
John Clark ◽  
Allen Szalanski
Keyword(s):  
Genetic Variation ◽  
Rflp Analysis ◽  
Small Variation ◽  
Its Region ◽  
Genetic Distances ◽  
Nuclear Ribosomal Dna ◽  
Internal Transcribed Spacer Region ◽  
Pcr Rflp ◽  
Restriction Sites ◽  
Polymerase Chain

In this study, the nuclear ribosomal DNA internal transcribed spacer region (ITS) of six Rubus cultivars were sequenced, then compared with sequences of three Rubus species in Genbank. DNA sequencing revealed little genetic variation among blackberry cultivars, but ably revealed distinctions between blackberry and red raspberry genotypes. Analysis by maximum-parsimony and pairwise genetic distances confirmed the small variation among blackberry cultivars. The resulting sequences were analyzed for useful restriction sites and polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) analysis was conducted on a total of six cultivars to establish genetic variation. Digests were difficult to interpret due to heterogeneity at restriction sites.

PCR-RFLP Analysis of the Internal Transcribed Spacer (ITS) Region for Identification of 3 Clam Species

2001 ◽  
Vol 66 (5) ◽  
pp. 657-661 ◽  
Author(s):  
A. Fernandez ◽  
T. Garcia ◽  
L. Asensio ◽  
M.A. Rodriguez ◽  
I. Gonzalez ◽  
...  
Keyword(s):  
Internal Transcribed Spacer ◽  
Rflp Analysis ◽  
Its Region ◽  
Pcr Rflp

scholarly journals Phenotypical and Molecular Characterization of Microsporum canis Strains in North-Tunisia

2014 ◽  
Vol 63 (3) ◽  
pp. 307-315
Author(s):  
CYRINE DHIEB ◽  
BADIÂA ESSGHAIER ◽  
DALINDA EL EUCH ◽  
NAJLA SADFI-ZOUAOUI
Keyword(s):  
Carbon Sources ◽  
Rflp Analysis ◽  
Its Region ◽  
Enzymatic Digestion ◽  
Morphological Characterization ◽  
Restriction Pattern ◽  
Microsporum Canis ◽  
Biochemical Tests ◽  
Pcr Rflp ◽  
Tunisian Patients

In this study, 40 Microsporum canis isolates were obtained from different patients from the Mycology Unit of the Hospital La Rabta (Tunis) during a 3 month period. The phenotypic identification was done by morphological characterization and biochemical tests. Molecular analysis was performed by amplification of the ITS region of rDNA, the amplified region was subjected to enzymatic digestion and sequenced to evaluate phylogenetic relationships. The morphological analysis showed a considerable diversity of colonies as well as different morphologies of conidia and we have noted variability in the assimilation of the nitrogen and carbon sources. The PCR-RFLP results showed only one restriction pattern for each enzyme. The phylogenetic tree proves that all the strains from Tunisian patients are clonal and related with other strains from different origins. The classical methods used in the mycological laboratories are time-consuming, the PCR-RFLP analysis of the ITS is a reliable tool for the identification of M. canis strains. M. canis from infected Tunisian patients are clonal, although the isolates had different phenotypic characteristics.

scholarly journals Autoscreening of Restriction Endonucleases for PCR-Restriction Fragment Length Polymorphism Identification of Fungal Species, with Pleurotus spp. as an Example

2007 ◽  
Vol 73 (24) ◽  
pp. 7947-7958 ◽  
Author(s):  
Zhi-Hui Yang ◽  
Ji-Xiang Huang ◽  
Yi-Jian Yao
Keyword(s):  
Fragment Length Polymorphism ◽  
Rflp Analysis ◽  
Restriction Enzymes ◽  
Fungal Species ◽  
Restriction Endonucleases ◽  
Its Sequences ◽  
Pcr Rflp ◽  
Average Coefficient ◽  
Identification Of Species ◽  
Restriction Fragment Length

ABSTRACT A molecular method based on PCR-restriction fragment length polymorphism (RFLP) analysis of internal transcribed spacer (ITS) ribosomal DNA sequences was designed to rapidly identify fungal species, with members of the genus Pleurotus as an example. Based on the results of phylogenetic analysis of ITS sequences from Pleurotus, a PCR-RFLP endonuclease autoscreening (PRE Auto) program was developed to screen restriction endonucleases for discriminating multiple sequences from different species. The PRE Auto program analyzes the endonuclease recognition sites and calculates the sizes of the fragments in the sequences that are imported into the program in groups according to species recognition. Every restriction endonuclease is scored through the calculation of the average coefficient for the sequence groups and the average coefficient for the sequences within a group, and then virtual electrophoresis maps for the selected restriction enzymes, based on the results of the scoring system, are displayed for the rapid determination of the candidate endonucleases. A total of 85 haplotypes representing 151 ITS sequences were used for the analysis, and 2,992 restriction endonucleases were screened to find the candidates for the identification of species. This method was verified by an experiment with 28 samples representing 12 species of Pleurotus. The results of the digestion by the restriction enzymes showed the same patterns of DNA fragments anticipated by the PRE Auto program, apart from those for four misidentified samples. ITS sequences from 14 samples (of which nine sequences were obtained in this study), including four originally misidentified samples, confirmed the species identities revealed by the PCR-RFLP analysis. The method developed here can be used for the identification of species of other living microorganisms.

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