The nuclear ribosomal internal transcribed spacer (ITS) region is the formal fungal barcode and in most cases the marker of choice for the exploration of fungal diversity in environmental samples. Two problems are particularly acute in the pursuit of satisfactory taxonomic assignment of newly generated ITS sequences: (i) the lack of an inclusive, reliable public reference data set and (ii) the lack of means to refer to fungal species, for which no Latin name is available in a standardized stable way. Here, we report on progress in these regards through further development of the UNITE database (http://unite.ut.ee) for molecular identification of fungi. All fungal species represented by at least two ITS sequences in the international nucleotide sequence databases are now given a unique, stable name of the accession number type (e.g. Hymenoscyphus pseudoalbidus|GU586904|SH133781.05FU), and their taxonomic and ecological annotations were corrected as far as possible through a distributed, third-party annotation effort. We introduce the term ‘species hypothesis’ (SH) for the taxa discovered in clustering on different similarity thresholds (97–99%). An automatically or manually designated sequence is chosen to represent each such SH. These reference sequences are released (http://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and in the QIIME pipeline. The system and the data will be updated automatically as the number of public fungal ITS sequences grows. We invite everybody in the position to improve the annotation or metadata associated with their particular fungal lineages of expertise to do so through the new Web-based sequence management system in UNITE.

http://web.stanford.edu/~kpeay/papers/Koljalg_2013_MEC.pdf

Towards a unified paradigm for sequence-based identification of fungi

The endophytic continuum.

The question of how many species of Fungi there are has occasioned much speculation, with figures mostly posited from around half a million to 10 million, and in one extreme case even a sizable portion of the spectacular number of 1 trillion. Here we examine new evidence from various sources to derive an updated estimate of global fungal diversity. The rates and patterns in the description of new species from the 1750s show no sign of approaching an asymptote and even accelerated in the 2010s after the advent of molecular approaches to species delimitation. Species recognition studies of (semi-)cryptic species hidden in morpho-species complexes suggest a weighted average ratio of about an order of magnitude for the number of species recognized after and before such studies. New evidence also comes from extrapolations of plant:fungus ratios, with information now being generated from environmental sequence studies, including comparisons of molecular and fieldwork data from the same sites. We further draw attention to undescribed species awaiting discovery in biodiversity hot spots in the tropics, little-explored habitats (such as lichen-inhabiting fungi), and material in collections awaiting study. We conclude that the commonly cited estimate of 1.5 million species is conservative and that the actual range is properly estimated at 2.2 to 3.8 million. With 120,000 currently accepted species, it appears that at best just 8%, and in the worst case scenario just 3%, are named so far. Improved estimates hinge particularly on reliable statistical and phylogenetic approaches to analyze the rapidly increasing amount of environmental sequence data.

Fungal Diversity Revisited: 2.2 to 3.8 Million Species

http://orton.catie.ac.cr/repdoc/A4828i/A4828i.pdf

Understanding the diversity of foliar endophytic fungi: progress, challenges, and frontiers

Endophytic fungi in forest trees: are they mutualists?

Summary
A new species of the hyphomycete genus Chalara is described It has been frequently isolated from stems and branches and sometimes also from roots of wilting and dying Fraxinus excelsior in Poland It differs from previously described species of Chalara by its small, short cylindrical phialoconidia extruded in chains or in slimy droplets, morphological features of the phialophores and by colony characteristics It is non-tolerant to cycloheximide

Chalara fraxinea sp. nov. associated with dieback of ash (Fraxinus excelsior) in Poland

Summary Ash dieback caused by the mitosporic ascomycete Chalara fraxinea is a novel disease of major concern affecting Fraxinus excelsior and Fraxinus angustifolia in large parts of Europe. Recently, its teleomorph was detected and assigned to Hymenoscyphus albidus, which has been known from Europe since 1851. In this study, we present molecular evidence for the existence of two morphologically very similar taxa, H. albidus, which is lectotypified and Hymenoscyphus pseudoalbidus sp. nov. Differences were found between the species in the loci calmodulin, translation elongation factor 1-a and the internal transcribed spacers of the rDNA genes, and strong differentiation was obtained with ISSR markers. It is likely that H. albidus is a non-pathogenic species, whereas H. pseudoalbidus is a virulent species causing ash dieback. Genotyping herbarium specimens showed that H. pseudoalbidus has been present in Switzerland for at least 30 years prior to the outbreak of the epidemic.

/pdf/cryptic-speciation-in-hymenoscyphus-albidus-ntmu2tlxch.pdf

Cryptic speciation in Hymenoscyphus albidus

Summary

Ash dieback, caused by the pathogen Chalara fraxinea, is an emerging lethal disease of Fraxinus excelsior, threatening the host species in large parts of Europe. The ascomycete Hymenoscyphus albidus (Helotiaceae, Helotiales) was identified as the teleomorph of C. fraxinea by culturing from ascospores, morphological comparison and nuclear ribosomal internal transcribed spacer (ITS) sequencing.

The teleomorph of Chalara fraxinea, the causal agent of ash dieback

Summary

The mitosporic fungus Chalara fraxinea (Ascomycota) is associated with dieback of common ash, an emerging disease of Fraxinus excelsior (Oleaceae) in Europe. The pathogenicity of C. fraxinea was demonstrated by field inoculations on young trees.

Pathogenicity of Chalara fraxinea.

Chalara fraxinea is a fungus currently threatening ash trees (Fraxinus excelsior) in several European countries. This emerging pathogen was assigned to the EPPO’s alert list and therefore accurate detection and identification tools are needed. Because of its slow growth rate on agar media and the frequent presence of fast-growing saprotrophic fungi within the host tissue, classical isolation techniques are time-consuming and sometimes inefficient. In this study, we used species-specific polymorphisms observed within the internal transcribed spacer region to design a primer pair and a dual-labelled probe to be used in a real-time PCR assay for the detection of C. fraxinea. The test proved to be specific, based on in silico and in vitro assessments, and could detect as little as 20 fg of C. fraxinea DNA. A protocol was developed in order to detect the pathogen directly in plant tissue and proved to be more efficient and rapid than isolation on agar plates. This new tool should be useful both for monitoring and to conduct epidemiology research on this emerging pathogen.

Tadeusz Kowalski

Papers

Chalara fraxinea sp. nov. associated with dieback of ash (Fraxinus excelsior) in Poland

Cryptic speciation in Hymenoscyphus albidus

The teleomorph of Chalara fraxinea, the causal agent of ash dieback

Pathogenicity of Chalara fraxinea.

Rapid in planta detection of Chalara fraxinea by a real-time PCR assay using a dual-labelled probe