Variation in the ribosomal ITS-sequence of the lichens Buellia Frigida and Xanthoria Elegans from the Vestfold Hills, Eastern Antarctica

2001 ◽  
Vol 33 (2) ◽  
pp. 151-159 ◽  
Author(s):  
P. S. Dyer ◽  
G. J. Murtagh
Keyword(s):  
Genetic Variation ◽  
Its Region ◽  
Nucleotide Position ◽  
Maritime Antarctica ◽  
Specific Primers ◽  
Region Sequence ◽  
Distinct Cluster ◽  
Continental Antarctica ◽  
Buellia Frigida ◽  
Vestfold Hills

AbstractThalli of the lichens Buellia frigida and Xanthoria elegans were collected from five different locations each 5-15 km apart in the Vestfold Hills, Princess Elizabeth Land, eastern Antarctica. A further collection was made from Mawson Station, Mac Robertson Land, eastern Antarctica, 660 km away. DNA was extracted from whole thalli and the ribosomal ITS region amplified by PCR using fungal specific primers. Resulting products were sequenced to gain an indication of whether or not variation was present within populations of lichen-forming fungi from continental Antarctica, and therefore of the availability of genetic resources to react to pressures such as climate change. Three genotypes of B. frigida and two of X. elegans were detected in the Vestfold Hill collections. However, these differed by only one nucleotide position suggesting the presence of relatively little genetic variation, if the ITS region is indicative of the overall genome. Buellia frigida collected from Mawson Station had an identical ITS region sequence to the most common Vestfold Hills genotype, indicating that this species may have a low level of genetic variation across much of eastern Antarctica. In contrast, X. elegans collected from Mawson showed considerable genetic variation from the Vestfolds thalli, differing at 14·2% of nucleotide positions and had an identical ITS region sequence to an isolate from maritime Antarctica 4960 km away. Samples from the Vestfold Hills formed a distinct cluster in a phylogenetic analysis of ITS sequences from a worldwide collection of X. elegans isolates.

Fungal composition of lichen thalli assessed by single strand conformation polymorphism

2010 ◽  
Vol 42 (4) ◽  
pp. 461-473 ◽  
Author(s):  
Lucia MUGGIA ◽  
Martin GRUBE
Keyword(s):  
Direct Sequencing ◽  
Its Region ◽  
Single Strand Conformation Polymorphism ◽  
Morphological Characters ◽  
Single Strand ◽  
Specific Primers ◽  
Lichenicolous Fungi ◽  
Large Numbers ◽  
Total Dna ◽  
Conformation Polymorphism

AbstractFungi that are unrelated to the mycobiont species frequently colonize lichens. Some of these fungal colonists are described lichenicolous fungi, lichen parasites and pathogens that produce recognizable morphological characters, while others apparently produce no noticeable structures. Here we apply the single strand conformation polymorphism (SSCP) technique to directly assess the abundance of different fungi in lichens. Twenty-eight lichen thalli were chosen, some with and some without externally visible symptoms of parasite infection, and these were subjected to total DNA extraction. PCR was conducted with fungal-specific primers for the ITS region of ribosomal DNA. Single strands of the products were separated on native acrylamide gels. The majority of lichen specimens, both infected and those without symptoms, displayed more than one band in the stained gels. In one case, 14 bands were detected using SSCP. Some of these bands apparently represent other neighbouring lichens in the habitat, but many are apparently non-lichen-forming. Since few lichen-associated fungi have been cultured and sequenced, it is difficult to know if SSCP bands represent obligate lichenicolous fungi, other asymptomatic lichen parasites, or fungi not obligately associated with lichens, but our results indicate that large numbers of non-lichen-forming fungi commonly co-occur with lichens in nature. For specimens of the filamentous lichens Cystocoleus ebeneus and Racodium rupestre we used cloned sequences to compare the number of sequences obtained by the SSCP method to the number obtained by direct sequencing of thallus extracts, and we generally found that more sequences could be detected by SSCP than could be seen by direct sequencing.

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.

scholarly journals RIP mutated ITS genes in populations of Ophiocordyceps sinensis and their implications for molecular systematics

IMA Fungus ◽  
2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Yi Li ◽  
Lan Jiang ◽  
Ke Wang ◽  
Hai-Jun Wu ◽  
Rui-Heng Yang ◽  
...  
Keyword(s):  
Evolutionary History ◽  
Large Scale ◽  
Its Region ◽  
Wide Distribution ◽  
Specific Primers ◽  
Ophiocordyceps Sinensis ◽  
Single Genome ◽  
History Of ◽  
Geographic Populations ◽  
Internal Transcribed Spacer Sequences

Abstract Different hypotheses have been proposed to interpret the observed unusual ITS (internal transcribed spacer) sequences in Ophiocordyceps sinensis. The coexistence of diverged ITS paralogs in a single genome was previously shown by amplifying the ITS region from mono-ascospore isolates using specific primers designed for different ITS paralog groups. Among those paralogs, are AT-biased ITS sequences which were hypothesized to result from repeat-induced point mutation (RIP). This is a process that detects and mutates repetitive DNA and frequently leads to epigenetic silencing, and these mutations have been interpreted as pseudogenes. Here we investigate the occurrence and frequency of ITS pseudogenes in populations of O. sinensis using large-scale sampling, and discusses the implications of ITS pseudogenes for fungal phylogenetic and evolutionary studies. Our results demonstrate a wide distribution of ITS pseudogenes amongst different geographic populations, and indicate how ITS pseudogenes can contribute to the reconstruction of the evolutionary history of the species.

First Report of Leaf Smut of Tomatillo Caused by Entyloma austral

2010 ◽  
Vol 11 (1) ◽  
pp. 58 ◽  
Author(s):  
Steven T. Koike ◽  
Dean A. Glawe ◽  
Tess Barlow
Keyword(s):  
Its Region ◽  
First Record ◽  
Causal Agent ◽  
First Report ◽  
Region Sequence ◽  
Leaf Smut

The causal agent was identified as Entyloma australe Speg. based on host and on pathogen morphology and ITS region sequence. The size, shape, and color of teliospores and the production of fascicles of conidiophores fit the descriptions for E. australe. This appears to be the only Entyloma species occurring on Physalis. This report appears to be the first record of E. australe on P. philadelphica. Accepted for publication 11 November 2009. Published 16 February 2010.

Sabbea gen. nov., a new diatom genus (Bacillariophyta) from continental Antarctica

Phytotaxa ◽  
2019 ◽  
Vol 418 (1) ◽  
pp. 42-56 ◽  
Author(s):  
JORDAN BISHOP ◽  
KATEŘINA KOPALOVÁ ◽  
JOSHUA P. DARLING ◽  
NICHOLAS O. SCHULTE ◽  
TYLER J. KOHLER ◽  
...  
Keyword(s):  
New Genus ◽  
Morphological Characteristics ◽  
Sensu Stricto ◽  
Morphological Features ◽  
Marine Diatom ◽  
Continental Antarctica ◽  
Diatom Genus ◽  
Antarctic Continent ◽  
Vestfold Hills ◽  
The Antarctic

The non-marine diatom flora of the Antarctic Continent includes several endemic taxa recorded over the past 100 years. One of these taxa, Navicula adminensis D.Roberts & McMinn, was described from the Vestfold Hills, East Antarctica. Detailed light and scanning electron microscopy observations have shown that based on its morphological features, the species does not belong to the genus Navicula sensu stricto. To determine the most closely related genera to N. adminensis, the morphological features of Adlafia, Kobayasiella, Envekadea, Stenoneis, Berkeleya, Climaconeis, and Parlibellus were compared with those of N. adminensis. Although each of these genera shows one or more similar features, none of them accommodates the salient morphological characteristics of N. adminensis. Therefore, a new genus, Sabbea gen. nov., is herein described, and Navicula adminensis is formally transferred to the new genus as Sabbea adminensis comb. nov. The genus Sabbea is characterized by uniseriate striae composed of small, rounded areolae occluded externally by individual hymenes, a rather simple raphe structure with straight, short proximal ends and short terminal raphe fissures, open girdle bands with double perforation and a very shallow mantle.

scholarly journals Detection of Pythium ultimum Using Polymerase Chain Reaction with Species-Specific Primers

Plant Disease ◽  
1997 ◽  
Vol 81 (10) ◽  
pp. 1155-1160 ◽  
Author(s):  
K. Kageyama ◽  
A. Ohyama ◽  
M. Hyakumachi
Keyword(s):  
Polymerase Chain Reaction ◽  
Internal Transcribed Spacer ◽  
Pcr Amplification ◽  
Its Region ◽  
Pythium Ultimum ◽  
Pythium Species ◽  
Chain Reaction ◽  
Specific Primers ◽  
Polymerase Chain ◽  
Species Specific

This study was conducted to sequence the rDNA internal transcribed spacer (ITS) region of Pythium ultimum and Pythium group HS, design species-specific primers for polymerase chain reaction (PCR), and detect P. ultimum from diseased seedlings using PCR. The sequence of the ITS region of P. ultimum was identical with that of Pythium group HS. The results support the reports that the HS group is an asexual strain of P. ultimum. Using PCR, the primer pair K1+K3, designed on portions of the sequence of the ITS region, amplified isolates of P. ultimum and the HS group but not isolates of 20 other Pythium species. DNA extracts from damped-off seedlings were not amplified, but a 10-fold dilution of the extracts with Tris-EDTA (TE) buffer diluted the inhibitors and allowed PCR amplification. The primer pair used detected P. ultimum from a single diseased seedling.

scholarly journals Implementation of Sanger DNA Sequencing Technologies in Tracing the Phylogeny of Meliola mangiferae

2017 ◽  
pp. 6-9
Author(s):  
Rafiq Ahmad Dar ◽  
Akhila Nand Rai
Keyword(s):  
Genetic Variance ◽  
Random Amplified Polymorphic Dna ◽  
Its Region ◽  
Fungal Species ◽  
Distinct Region ◽  
Specific Primers ◽  
Closely Related Species ◽  
Sequencing Technologies ◽  
Leaf Surfaces ◽  
Specific Band

During the summer 2014, dark black symptoms beneath the leaf surfaces were observed on the Populas alba L species in the south Kashmir. In the later stages of development the infection subtends the whole surface resulting in leaf collapse. Fungal isolates were recovered directly from the structures present on the lesions. Purified DNA from each isolate was amplified using the random amplified polymorphic DNA technique recruiting the ITSI (TCCGTAGGTGAACCTGCGG) and ITS4 (TCCTCCGC TTATTGATATGC) specific primers. Amplification products visualized on agarose gel showed specific band pattern for each isolate. The mycotaxonomic characterization and phylogenetic interpretations showed the emergence of fungal species, Meliola sp. KY623717 with genetic variance of 2% in Internal Transcribed Spacer (ITS) region of rDNA from closely related species under geographically distinct region.

scholarly journals Application of High Resolution Melt analysis (HRM) for screening haplotype variation in a non-model plant genus: Cyclopia (Honeybush)

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e9187
Author(s):  
Nicholas C. Galuszynski ◽  
Alastair J. Potts
Keyword(s):  
Genetic Variation ◽  
High Resolution ◽  
Cape Floristic Region ◽  
Model Systems ◽  
High Resolution Melt ◽  
Specific Primers ◽  
Screening Process ◽  
High Resolution Melt Analysis ◽  
Haplotype Variation ◽  
Pcr Products

Aim This study has three broad aims: to (a) develop genus-specific primers for High Resolution Melt analysis (HRM) of members of Cyclopia Vent., (b) test the haplotype discrimination of HRM compared to Sanger sequencing, and (c) provide an example of using HRM to detect novel haplotype variation in wild C. subternata Vogel. populations. Location The Cape Floristic Region (CFR), located along the southern Cape of South Africa. Methods Polymorphic loci were detected through a screening process of sequencing 12 non-coding chloroplast DNA segments across 14 Cyclopia species. Twelve genus-specific primer combinations were designed around variable cpDNA loci, four of which failed to amplify under PCR; the eight remaining were applied to test the specificity, sensitivity and accuracy of HRM. The three top performing HRM Primer combinations were then applied to detect novel haplotypes in wild C. subternata populations, and phylogeographic patterns of C. subternata were explored. Results We present a framework for applying HRM to non-model systems. HRM accuracy varied across the PCR products screened using the genus-specific primers developed, ranging between 56 and 100%. The nucleotide variation failing to produce distinct melt curves is discussed. The top three performing regions, having 100% specificity (i.e. different haplotypes were never grouped into the same cluster, no false negatives), were able to detect novel haplotypes in wild C. subternata populations with high accuracy (96%). Sensitivity below 100% (i.e. a single haplotype being clustered into multiple unique groups during HRM curve analysis, false positives) was resolved through sequence confirmation of each cluster resulting in a final accuracy of 100%. Phylogeographic analyses revealed that wild C. subternata populations tend to exhibit phylogeographic structuring across mountain ranges (accounting for 73.8% of genetic variation base on an AMOVA), and genetic differentiation between populations increases with distance (p < 0.05 for IBD analyses). Conclusions After screening for regions with high HRM clustering specificity—akin to the screening process associated with most PCR based markers—the technology was found to be a high throughput tool for detecting genetic variation in non-model plants.

scholarly journals Characterizing the ribosomal tandem repeat and its utility as a DNA barcode in lichen-forming fungi

2019 ◽  
Author(s):  
Michael Bradshaw ◽  
Felix Grewe ◽  
Anne Thomas ◽  
Cody H. Harrison ◽  
Hanna Lindgren ◽  
...  
Keyword(s):  
Species Complex ◽  
High Throughput Sequencing ◽  
Sequence Data ◽  
Dna Barcode ◽  
Intergenic Spacer ◽  
Its Region ◽  
Nuclear Ribosomal Dna ◽  
Nucleotide Position ◽  
Ribosomal Operon ◽  
Intragenomic Variation

Abstract Background: Regions within the nuclear ribosomal operon are a major tool for inferring evolutionary relationships and investigating diversity in fungi. In spite of the prevalent use of ribosomal markers in fungal research, central features of nuclear ribosomal DNA (nrDNA) evolution are poorly characterized for fungi in general, including lichenized fungi. The internal transcribed spacer (ITS) region of the nrDNA has been adopted as the primary DNA barcode identification marker for fungi. However, little is known about intragenomic variation in the nrDNA in symbiotic fungi. In order to better understand evolution of nrDNA and the utility of the ITS region for barcode identification of lichen-forming fungal species, we generated nearly complete nuclear ribosomal operon sequences from nine species in the Rhizoplaca melanophthalma species complex using short reads from high-throughput sequencing. Results: We estimated copy numbers for the nrDNA operon, ranging from nine to 48 copies for members of thiscomplex, and found low levels of intragenomic variation in the standard barcode region (ITS). Monophyly of currently described species in this complex was supported in phylogenetic inferences based on the ITS, 28S, IGS, and some intronic regions; however, a phylogenetic inference based on the 18S provided much lower resolution. Phylogenetic analysis of concatenated ITS and intergenic spacer sequence data generated from 496 specimens collected worldwide revealed previously unrecognized lineages in the nrDNA phylogeny. Conclusions: The results from our study support the general assumption that the ITS region of the nrDNA is an effective barcoding marker for fungi. For the R. melanophthalma group, the limited amount of potential intragenomic variability in the ITS region did not correspond to fixed diagnostic nucleotide position characters separating taxa within this species complex. Previously unrecognized lineages inferred from ITS sequence data may represent undescribed species-level lineages or reflect uncharacterized aspects of nrDNA evolution in the R. melanophthalma species complex.

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