scholarly journals Towards Genomic Criteria for Delineating Fungal Species

2020 ◽  
Vol 6 (4) ◽  
pp. 246
Author(s):  
Cene Gostinčar
Keyword(s):  
Fungal Species ◽  
Species Delineation ◽  
Genomic Distance ◽  
Phylogenetic Species Concept ◽  
Additional Tool ◽  
Fungal Genomics ◽  
Powerful Approach ◽  
Species Similarity ◽  
Traditional Approaches ◽  
Methodological Guidelines

The discussion of fungal species delineation has yet to reach a consensus, despite the advancements in technology, which helped modernise traditional approaches. In particular, the phylogenetic species concept was one of the tools that has been used with considerable success across the fungal kingdom. The fast rise of fungal genomics provides an unprecedented opportunity to expand measuring the relatedness of fungal strains to the level of whole genomes. However, the use of genomic information in taxonomy has only just begun, and few methodological guidelines have been suggested so far. Here, a simple approach of computationally measuring genomic distances and their use as a standard for species delineation is investigated. A fixed threshold genomic distance calculated by the quick and easy-to-use tools Mash and Dashing proved to be an unexpectedly widely applicable and robust criterion for determining whether two genomes belong to the same or to different species. The accuracy of species delineation in an uncurated dataset of GenBank fungal genomes was close to 90%—and exceeded 90% with minimal curation. As expected, the discriminative power of this approach was lower at higher taxonomic ranks, but still significantly larger than zero. Simple instructions for calculation of a genomic distance between two genomes and species similarity thresholds at different k-mer sizes are suggested. The calculation of genomic distance is identified as a powerful approach for delineating fungal species and is proposed—not as the only criterion—but as an additional tool in the versatile toolbox of fungal taxonomy.

Subspecies definitions and legislation: from eastern wallaroo (Osphranter robustus robustus) to euro (Osphranter robustus erubescens)

2019 ◽  
Vol 41 (1) ◽  
pp. 65 ◽  
Author(s):  
Barry J. Richardson
Keyword(s):  
Species Concept ◽  
Genetic Data ◽  
Ecological Approach ◽  
Phylogenetic Species ◽  
Management Decisions ◽  
Evolutionary Trajectory ◽  
Genetic Studies ◽  
Phylogenetic Species Concept ◽  
Population Structuring ◽  
Traditional Approaches

As a consequence of genetic studies of population structuring, the usefulness of subspecies has been questioned, with opinions divided. The situation is further confused by the use of varying species and subspecies concepts. Most alternatives require each taxon to be following an independent evolutionary trajectory. These include traditional approaches and the more recent phylogenetic species concept. The latter has led to large increases in the apparent number of taxa in some groups, though strong objections have been raised to this approach. An alternative, the ecological species concept, has been opposed by phylogeneticists. These two approaches are compared using morphological and genetic data from common wallaroo (Osphranter robustus) populations. The different taxonomies that might result (many species, one species with two subspecies, one species with no subspecies) can have significant consequences for legislative and management decisions. The ecological approach is considered preferable for subspecies and the present taxonomy is maintained. A potential location of the boundary between the wallaroo subspecies is proposed. How the use of the different subspecies definitions would affect legislative decisions is explored.

scholarly journals RELATe enables genome-scale engineering in fungal genomics

2020 ◽  
Vol 6 (38) ◽  
pp. eabb8783
Author(s):  
Zhongming Li ◽  
Kwang Sik Kim
Keyword(s):  
High Throughput Screening ◽  
Traditional Approach ◽  
Central Nervous System Infection ◽  
Cost Effective ◽  
Fungal Species ◽  
Model Organisms ◽  
Simple Method ◽  
Guide Rna ◽  
Fungal Genomics ◽  
Genome Scale

CRISPR-Cas9–based screening with single-guide RNA (sgRNA) libraries has emerged as a revolutionary tool for comprehensive analysis of genetic elements. However, genome-scale sgRNA libraries are currently available only in a few model organisms. The traditional approach is to synthesize thousands to tens of thousands of sgRNAs, which is laborious and expensive. We have developed a simple method, RELATe (restriction/ligation coupled with Agrobacterium-mediated transformation), to generate sgRNA libraries from 10 μg of genomic DNA, targeting over 98% of the protein-coding genes in the human fungal pathogen Cryptococcus neoformans. Functional screens identified 142 potential C. neoformans genes contributing to blood-brain barrier penetration. We selected two cryptococcal genes, SFP1 and WDR1, for a proof-of-concept demonstration that RELATe-identified genes are relevant to C. neoformans central nervous system infection. Our RELATe method can be used in many other fungal species and is powerful and cost-effective for genome-wide high-throughput screening for elucidating functional genomics.

scholarly journals rDNA based analysis of autochtonous fungal species from Serbia

Genetika ◽  
2014 ◽  
Vol 46 (1) ◽  
pp. 33-42
Author(s):  
Eleonora Capelja ◽  
Nevena Stevic ◽  
Vladislava Galovic ◽  
Milana Novakovic ◽  
Maja Karaman
Keyword(s):  
Phylogenetic Tree ◽  
Molecular Data ◽  
Fungal Species ◽  
Its Sequences ◽  
Local Alignment ◽  
Phylogenetic Species Concept ◽  
Morphological Approach ◽  
Search Tool ◽  
Morphological And Molecular Data

Determination of fungal species by traditional morphological approach can often be problematic. In the phylum Basidiomycota, sporocarps of different species can share very similar morphoanatomical characteristics. Using molecular markers and phylogenetic species concept this problem can be reduced. In this study identification of six autochtonous fungal species, collected from several locations in Serbia (Tara, Kopaonik, Stara planina) was done by comparison between morphological and molecular data of fungal species, as well as information obtained from phylogenetic tree. ITS sequences amplified from 11 specimens of two genera of ph. Basidiomycota: Marasmius and Ganoderma, were compared with ITS sequences from database using basic local alignment search tool (BLAST). Phylogenetic tree was constructed using Neighbor joining method based on differences between analyzed ITS sequences. Our results showed that within genera Marasmius and Ganoderma morphological and molecular determinations are usually in accordance, but for proper species delimitation both approaches should be used.

scholarly journals Climate-Fungal Pathogen Modeling Predicts Loss of Up to One-Third of Tea Growing Areas

2021 ◽  
Vol 11 ◽  
Author(s):  
Saowaluck Tibpromma ◽  
Yang Dong ◽  
Sailesh Ranjitkar ◽  
Douglas A. Schaefer ◽  
Samantha C. Karunarathna ◽  
...  
Keyword(s):  
Climate Change ◽  
Land Use ◽  
Plant Pathology ◽  
Fungal Pathogen ◽  
Fungal Pathogens ◽  
Fungal Species ◽  
Climatic Conditions ◽  
Colletotrichum Acutatum ◽  
Fungal Genomics ◽  
Climatic Scenarios

Climate change will affect numerous crops in the future; however, perennial crops, such as tea, are particularly vulnerable. Climate change will also strongly influence fungal pathogens. Here, we predict how future climatic conditions will impact tea and its associated pathogens. We collected data on the three most important fungal pathogens of tea (Colletotrichum acutatum, Co. camelliae, and Exobasidium vexans) and then modeled distributions of tea and these fungal pathogens using current and projected climates. The models show that baseline tea-growing areas will become unsuitable for Camellia sinensis var. sinensis (15 to 32% loss) and C. sinensis var. assamica (32 to 34% loss) by 2050. Although new areas will become more suitable for tea cultivation, existing and potentially new fungal pathogens will present challenges in these areas, and they are already under other land-use regimes. In addition, future climatic scenarios suitable range of fungal species and tea suitable cultivation (respectively in CSS and CSA) growing areas are Co. acutatum (44.30%; 31.05%), Co. camelliae (13.10%; 10.70%), and E. vexans (10.20%; 11.90%). Protecting global tea cultivation requires innovative approaches that consider fungal genomics as part and parcel of plant pathology.

The Potentials of Scanning Microscopy

1968 ◽  
Vol 26 ◽  
pp. 352-353
Author(s):  
A. V. Crewe
Keyword(s):  
Salient Feature ◽  
Secondary Emission ◽  
Resolving Power ◽  
X Rays ◽  
Scanning Microscope ◽  
Forming Process ◽  
Additional Tool ◽  
Detection Systems ◽  
Conventional Microscope ◽  
Present Information

If the resolving power of a scanning electron microscope can be improved until it is comparable to that of a conventional microscope, it would serve as a valuable additional tool in many investigations.The salient feature of scanning microscopes is that the image-forming process takes place before the electrons strike the specimen. This means that several different detection systems can be employed in order to present information about the specimen. In our own particular work we have concentrated on the use of energy loss information in the beam which is transmitted through the specimen, but there are also numerous other possibilities (such as secondary emission, generation of X-rays, and cathode luminescence).Another difference between the pictures one would obtain from the scanning microscope and those obtained from a conventional microscope is that the diffraction phenomena are totally different. The only diffraction phenomena which would be seen in the scanning microscope are those which exist in the beam itself, and not those produced by the specimen.

Pragmatic versus Morphological/Syntactic Criteria for Language Referrals

1980 ◽  
Vol 11 (2) ◽  
pp. 85-94 ◽  
Author(s):  
Jack Damico ◽  
John W. Oller
Keyword(s):  
Grade Level ◽  
The State ◽  
Verb Agreement ◽  
Remedial Programs ◽  
Service Training ◽  
Traditional Approaches ◽  
Communicative Effectiveness

Two methods of identifying language disordered children are examined. Traditional approaches require attention to relatively superficial morphological and surface syntactic criteria, such as, noun-verb agreement, tense marking, pluralization. More recently, however, language testers and others have turned to pragmatic criteria focussing on deeper aspects of meaning and communicative effectiveness, such as, general fluency, topic maintenance, specificity of referring terms. In this study, 54 regular K-5 teachers in two Albuquerque schools serving 1212 children were assigned on a roughly matched basis to one of two groups. Group S received in-service training using traditional surface criteria for referrals, while Group P received similar in-service training with pragmatic criteria. All referrals from both groups were reevaluated by a panel of judges following the state determined procedures for assignment to remedial programs. Teachers who were taught to use pragmatic criteria in identifying language disordered children identified significantly more children and were more often correct in their identification than teachers taught to use syntactic criteria. Both groups identified significantly fewer children as the grade level increased.

Parasocial Interaction as More Than Friendship

2011 ◽  
Vol 23 (3) ◽  
pp. 122-132 ◽  
Author(s):  
Jayson L. Dibble ◽  
Sarah F. Rosaen
Keyword(s):  
Parasocial Interaction ◽  
Future Research ◽  
Two Measures ◽  
Traditional Approaches

This study supports the refinement of the concept of parasocial interaction (PSI) to apply to mediated personae that viewers might dislike. By contrast, traditional approaches have treated PSI as a sort of friendship with the mediated persona. Participants (N = 249) were randomly assigned to self-select a liked or disliked television persona. Various viewer reactions to that character were measured using two different measures of PSI. The data revealed that participants did experience PSI with disliked characters as well as liked characters, and that the two measures of PSI did not appear to assess the same construct. Implications for future research are discussed.

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