Taxonomy Of Fungi Research Articles

A phylogenetic framework for the kingdom Fungi based on 18S rRNA gene sequences

The usage of molecular phylogenetic approaches is critical to advance the understanding of systematics and community processes in the kingdom Fungi. Among the possible phylogenetic markers (or combinations of them), the 18S rRNA gene appears currently as the most prominent candidate due to its large availability in public databases and informative content. The purpose of this work was the creation of a reference phylogenetic framework that can serve as ready-to-use package for its application on fungal classification and community analysis. The current database contains 9329 representative 18S rRNA gene sequences covering the whole fungal kingdom, a manually curated alignment, an annotated and revised phylogenetic tree with all the sequence entries, updated information on current taxonomy, and recommendations of use. Out of 201 total fungal taxa with more than two sequences in the dataset, 179 were monophyletic. From another perspective, 66% of the entries had a tree-derived classification identical to that obtained from the NCBI taxonomy, whereas 34% differed in one or the other rank. Most of the differences were associated to missing taxonomic assignments in NCBI taxonomy, or the unexpected position of sequences that positioned out of their theoretically corresponding clades. The strong correlation observed with current fungal taxonomy evidences that 18S rRNA gene sequence-based phylogenies are adequate to reflect genealogy of Fungi at the levels of order and above, and justify their further usage and exploration.

Report of the Nomenclature Committee for Fungi: 21 – Lists from working groups

SummarySix lists of names from working groups set up under Art. 14.13 are approved, consisting of 3 names of families, 43 names of genera and 5 names of species, to be treated as conserved against the listed synonymous or homonymous names. Lists were compiled by working groups approved by the International Commission on the Taxonomy of Fungi and the Nomenclature Committee for Fungi: on Cordyceps, Diaporthales, Dothideomycetes, Hypocreales, Leotiomycetes, and Trichoderma and Hypocrea. Issues around interpretation of Art. 14.13 and 56.3 and implementation of Art. 57.2 are discussed.

なまものと標本がつなぎ広げる菌類分類学 : 菌類資料の特徴とその活用(これからの標本室〜ハーバリウムの管理・運営や情報発信,利用に関する新しい流れ〜,日本植物分類学会第14回大会(福島)公開シンポジウム講演記録)

なまものと標本がつなぎ広げる菌類分類学 : 菌類資料の特徴とその活用(これからの標本室〜ハーバリウムの管理・運営や情報発信,利用に関する新しい流れ〜,日本植物分類学会第14回大会(福島)公開シンポジウム講演記録)

Clustering of fungal hexosaminidase enzymes based on free alignment method using MLP neural network

Studies of biological evolution have generally focused on nucleotide or amino acid sequences of certain genes related to specific enzymes. Most phylogenetic tree constructions have been carried out using amino acid sequences and are used as a predictor to show evolutionary relationships. Phylogenetic analysis is usually performed based on multiple sequence alignment of a gene from different organisms including fungi. A number of programs have been introduced for gene clustering and phylogenetic analysis. For example, the most popular web-based program is Clustal Omega which is commonly used by biologists. When the number of uploaded sequences increases, this program not only works slowly but also the final constructed cladogram is confusing and incorrect from evolutionary point of view. In the present study, we used fungal hexosaminidases which are extracellular enzymes with a lot of applications in biotechnology but extremely varied and confusing in evolutionary terms. A standard taxonomy-based phylogenetic tree was constructed for 835 FH amino acid sequences retrieved from National Center for Biotechnology Information (NCBI) on March 16, 2015. Then a supervised multilayer perceptron (MLP) neural network was used to discriminate FH sequences. Based on relative frequency of amino acid in FH sequences, 41 neural networks were designed for seven levels from the phylum to family. Minimum accuracy of the neural network was equal to 99% at all seven discrimination levels. As a final step, an additional evaluation was performed on the designed model with 143 new released FH sequences extracted on July 1, 2015. The clustering results have shown a proper match with fungal taxonomy to show evolutionary relationships.

ToxGen: an improved reference database for the identification of type B-trichothecene genotypes in Fusarium.

Type B trichothecenes, which pose a serious hazard to consumer health, occur worldwide in grains. These mycotoxins are produced mainly by three different trichothecene genotypes/chemotypes: 3ADON (3-acetyldeoxynivalenol), 15ADON (15-acetyldeoxynivalenol) and NIV (nivalenol), named after these three major mycotoxin compounds. Correct identification of these genotypes is elementary for all studies relating to population surveys, fungal ecology and mycotoxicology. Trichothecene producers exhibit enormous strain-dependent chemical diversity, which may result in variation in levels of the genotype’s determining toxin and in the production of low to high amounts of atypical compounds. New high-throughput DNA-sequencing technologies promise to boost the diagnostics of mycotoxin genotypes. However, this requires a reference database containing a satisfactory taxonomic sampling of sequences showing high correlation to actually produced chemotypes. We believe that one of the most pressing current challenges of such a database is the linking of molecular identification with chemical diversity of the strains, as well as other metadata. In this study, we use the Tri12 gene involved in mycotoxin biosynthesis for identification of Tri genotypes through sequence comparison. Tri12 sequences from a range of geographically diverse fungal strains comprising 22 Fusarium species were stored in the ToxGen database, which covers descriptive and up-to-date annotations such as indication on Tri genotype and chemotype of the strains, chemical diversity, information on trichothecene-inducing host, substrate or media, geographical locality, and most recent taxonomic affiliations. The present initiative bridges the gap between the demands of comprehensive studies on trichothecene producers and the existing nucleotide sequence databases, which lack toxicological and other auxiliary data. We invite researchers working in the fields of fungal taxonomy, epidemiology and mycotoxicology to join the freely available annotation effort.

Extracellular peptidases as possible markers of fungal ecology

Fungi produce extracellular peptidases to break down proteins and polypeptides into smaller soluble molecules. These molecules are subsequently transported into the fungal cell, supplying osmotrophic nutrition. Although a variety of extracellular peptidases have been isolated from numerous fungal species, it remains largely unknown how the spectrum of secreted peptidases correlates with fungal ecology and taxonomy. In this study, we cultivated 17 fungal species on protein-enriched medium to compare the spectra of secreted peptidases produced by the fungi belonging to different ecological groups (pathogens, saprotrophs, symbionts) and taxonomic phyla (Ascomycota and Basidiomycota). Basidiomycetes predominantly produced metallopeptidases with neutral pH optima, while the species of ascomycetes secreted serine peptidases with alkaline pH optimum, mostly of the subtilisin-type. Fungal species with dominant activity of serine peptidases had, in general, much higher peptidase activity and were better adapted to growth on protein medium compared to the species with dominant metallopeptidase activity. Pathogenic fungi effectively cleaved the synthetic substrate specific for trypsin-like peptidases, while saprotrophic species were characterized by a relatively high aminopeptidase activity. Nevertheless, fungi have numerous genes encoding various types of peptidases, the spectra of fungal enzymes secreted on cultivation medium were to a major extent represented by the production of one class of peptidases that correlated with fungal taxonomic phylum. We suppose fungal strategies for cleaving polypeptides in experimental conditions are largely predetermined both by trophic status and phylogeny.

Current Status of Taxonomy of Pathogenic Yeasts.

Fungal taxonomy has been reconstructed on the basis of genome information, and new nomenclatural rules have been enacted from 2013. It has been proposed that Cryptococcus neoformans and Cryptococcus gattii be reclassified into two species (C. neoformans and Cryptococcus deneoformans) and five species (C. gattii, Cryptococcus bacillisporus, Cryptococcus deuterogattii, Cryptococcus tetragattii, and Cryptococcus decagattii), respectively. The genus Trichosporon has been reclassified into five genera. Trichosporon asahii, which is the causative agent of trichosporonosis, has been retained in the genus Trichosporon, while Trichosporon cutaneum has been transferred into a new genus, Cutaneotrichosporon.

Internal transcribed spacer sequence database of plant fungal pathogens: PFP-ITSS database

The nurseries and plantations of medicinally and economically important plants are facing challenge on health front as they are being rapidly exposed to fungal pathogens thereby affecting their health and productivity adversely. The plant pathogenic fungi significantly damage and reduce the flora of subcontinent. Lack of knowledge and trouble in identification of fungal pathogens, are imposing a peril to both the flora and human health all over the world. Albeit routine pathological techniques can be used for the identification of plant fungal pathogens but these methods are time consuming and often need sound knowledge in mycotaxonomy. Recently, molecular (DNA sequence) data has emerged with the nuclear ribosomal internal transcribed spacer (ITS) region (DNA barcoding) as crucial biomarker to disclose the necessary information for the taxonomic identification of plant pathogenic fungi. However, development of nucleotide sequence database of plant pathogenic fungi will enable authentic pathogen identification easy and quickly even by a person not trained in fungal taxonomy. This study presents the development of a new plant fungal pathogen -Internal Transcribed Spacer Sequence database (PFP- ITSS Database) holding 1215 ITS sequences collected from various sources. It represents 1215 plant fungal pathogens (PFP) in relation to their respective economical and medicinal plants; and is available at http://shaktisahislab.com/include/ITSdb. PFP-ITSS Database will provide useful information for better understanding of plant pathogenic fungi, which cause disease in both economical and medicinal plants.

Advances in Fungal Phylogenomics and Their Impact on Fungal Systematics.

In the past decade, advances in next-generation sequencing technologies and bioinformatic pipelines for phylogenomic analysis have led to remarkable progress in fungal systematics and taxonomy. A number of long-standing questions have been addressed using comparative analysis of genome sequence data, resulting in robust multigene phylogenies. These have added to, and often surpassed traditional morphology or single-gene phylogenetic methods. In this chapter, we provide a brief history of fungal systematics and highlight some examples to demonstrate the impact of phylogenomics on this field. We conclude by discussing some of the challenges and promises in fungal biology posed by the ongoing genomics revolution.

Improving taxonomic accuracy for fungi in public sequence databases: applying 'one name one species' in well-defined genera with Trichoderma/Hypocrea as a test case.

The ITS (nuclear ribosomal internal transcribed spacer) RefSeq database at the National Center for Biotechnology Information (NCBI) is dedicated to the clear association between name, specimen and sequence data. This database is focused on sequences obtained from type material stored in public collections. While the initial ITS sequence curation effort together with numerous fungal taxonomy experts attempted to cover as many orders as possible, we extended our latest focus to the family and genus ranks. We focused on Trichoderma for several reasons, mainly because the asexual and sexual synonyms were well documented, and a list of proposed names and type material were recently proposed and published. In this case study the recent taxonomic information was applied to do a complete taxonomic audit for the genus Trichoderma in the NCBI Taxonomy database. A name status report is available here: https://www.ncbi.nlm.nih.gov/Taxonomy/TaxIdentifier/tax_identifier.cgi. As a result, the ITS RefSeq Targeted Loci database at NCBI has been augmented with more sequences from type and verified material from Trichoderma species. Additionally, to aid in the cross referencing of data from single loci and genomes we have collected a list of quality records of the RPB2 gene obtained from type material in GenBank that could help validate future submissions. During the process of curation misidentified genomes were discovered, and sequence records from type material were found hidden under previous classifications. Source metadata curation, although more cumbersome, proved to be useful as confirmation of the type material designation. Database URL: http://www.ncbi.nlm.nih.gov/bioproject/PRJNA177353

Targeting Aflatoxin Biosynthetic Genes.

Chemical detoxification and physical destruction of aflatoxins in foods and feed commodities are mostly unattainable in a way that preserves the edibility of the food. Therefore, preventing mycotoxins in general and aflatoxins in particular from entering the food chain is a better approach. This requires early detection of the aflatoxin-causing organisms. Detection and quantification of aflatoxin-producing fungi has always been a challenge, especially within species of Aspergillus and Penicillium. Culture-based methods require a high level of expertise and a list of sophisticated equipment. Furthermore, even for a trained taxonomist, species that are identical in morphology, physiology, and nutritional aspects can be challenging to classify. Fungal taxonomy has changed over the past few decades; more species are being reclassified, and new species are being described due to advances in sequencing and genome assembly. These developments make the use of PCR-based approaches practical, rapid, and more reliable for the identification of fungi to the species level. This chapter presents a variety of protocols to detect and quantify aflatoxin-producing fungi using mycotoxin biosynthesis pathway genes.

Sequence-based classification and identification of Fungi

Fungal taxonomy and ecology have been revolutionized by the application of molecular methods and both have increasing connections to genomics and functional biology. However, data streams from traditional specimen- and culture-based systematics are not yet fully integrated with those from metagenomic and metatranscriptomic studies, which limits understanding of the taxonomic diversity and metabolic properties of fungal communities. This article reviews current resources, needs, and opportunities for sequence-based classification and identification (SBCI) in fungi as well as related efforts in prokaryotes. To realize the full potential of fungal SBCI it will be necessary to make advances in multiple areas. Improvements in sequencing methods, including long-read and single-cell technologies, will empower fungal molecular ecologists to look beyond ITS and current shotgun metagenomics approaches. Data quality and accessibility will be enhanced by attention to data and metadata standards and rigorous enforcement of policies for deposition of data and workflows. Taxonomic communities will need to develop best practices for molecular characterization in their focal clades, while also contributing to globally useful datasets including ITS. Changes to nomenclatural rules are needed to enable validPUBLICation of sequence-based taxon descriptions. Finally, cultural shifts are necessary to promote adoption of SBCI and to accord professional credit to individuals who contribute to community resources.

Fungal Community Structure of Different Degeneration Deyeuxia angustifolia Wetlands in Sanjiang Plain

To understand the wetland soil fungal community structure and diversity in different degeneration Deyeuxia angustifolia wetlands, the topsoil (0-20) of three different degeneration D. angustifolia wetlands were collected in the Sanjiang Plain field experiment station of the Institute of Nature and Ecology, Heilongjiang Academy of Sciences. The distribution and variation of soil fungal diversity were assessed by high-throughput sequencing method. The results showed that Shannon-Wiener index increased from marsh Deyeuxia angustifolia wetland marsh meadow Deyeuxia angustifolia wetland meadow Deyeuxia angustifolia wetland. Sequence blast showed that the fungal taxonomy belonged to Ascomycota, Basidiomycota, Chytridiomycota, Fungi_unclassified, Zygomycota, which dominant fungi were Fungi_unclassified (75.12%),Ascomycetes (56. 56%), Basidiomycetes (72.65%) in the three degeneration wetlands, respectively. The fungal structure compositions and diversities of marsh meadow Deyeuxia angustifolia wetland and meadow Deyeuxia angustifolia wetland were similar according to Heatmap analysis. The fungal community structure was influenced by soil nutrients (explained 88.62%) and plant composition (explained 9.85%) through the Variation partition analysis (VPA). In conclusion, the fungal community structure was significantly different, which was influenced by soil water content, in different degeneration Deyeuxia angustifolia wetlands in Sanjiang plain. The results may supply scientific basis for studying fungal diversity and spatial heterogeneity in degeneration wetlands.

Polymorphism and phylogenetic species delimitation in filamentous fungi from predominant mycobiota in withered grapes

Filamentous fungi are the main pathogens of withered grapes destined for passito wine production. Knowledge of which species inhabit these post-harvest fruits and their pathogenicity is essential in order to develop strategies to control infection, but is still scarce. This study investigated the predominant mycobiota of withered grapes through a cultivation-dependent approach. Strain and species heterogeneity was evidenced on examining isolates collected over three consecutive years. Colony morphology and PCR-restriction fragment length polymorphism (PCR-RFLP) analysis revealed the occurrence of several phenotypes and haplotypes, respectively. Strains were phylogenetically analyzed based on sequence typing of different genes or regions (e.g. calmodulin, β-tubulin and internal transcribed spacer region). Beside the most common necrotrophic-saprophytic species of Penicillium, Aspergillus, Alternaria and Botrytis species responsible for fruit rot, other saprobic species were identified (e.g. Trichoderma atroviride, Sarocladium terricola, Arthrinium arundinis and Diaporthe eres) generally not associated with post-harvest fruit diseases. Species such as Penicillium ubiquetum, Cladosporium pseudocladosporioides, Lichtheimia ramosa, Sarocladium terricola, Diaporthe nobilis, Bipolaris secalis, Paraconiothyrium fuckelii and Galactomyces reessii that had never previously been isolated from grapevine or grape were also identified. Moreover, it was not possible to assign a species to some isolates, while some members of Didymosphaeriaceae and Didymellaceae remained unclassified even at genus level. This study provides insights into the diversity of the epiphytic fungi inhabiting withered grapes and evidences the importance of their identification to understand the causes of fruit diseases. Finally, phylogenetic species delimitation furnished data of interest to fungal taxonomy.

Internal Transcribed Spacer (ITS) as Dna Barcoding to Identify Fungal Species: a Review

Despite the fact that fungi are important sources of both bioactive compounds and mycotoxins, and that they are very ubiquitous in our environment, their species identification is hampered by incomplete and often unclear literature. Fungi identification is primarily based on their phenotypic and physiological characteristics. Nowadays, many molecular methods to identify fungal species have been developed. One of the methods considered as a new concept to rapidly and accurately identify unknown fungal sample is DNA Barcoding. This literature review will outline the use of DNA barcoding approach to rapidly identify fungal species and the use of ITS region that recently has been designated as primary DNA barcode for fungal kingdom. “DNA barcode” is a short, highly variable and standardized DNA region with approximately 700 nucleotides in length, which is used as a unique pattern to identify living things. Internal Transcribed Spacer (ITS) region of nuclear DNA (rDNA) has become the most sequenced region to identify fungal taxonomy at species level, and even within species. ITS region is a highly polymorphic non-coding region with enough taxonomic units. Therefore, it is able to separate sequences into species level. Even though ribosomal ITS as a universal barcode marker for fungi is still hampered by few limitations, the ITS will remain as the key choice for fungal identification. The search for alternative regions as DNA marker to improve fungal identification, especially in specific heredities, has already started.

Generic names in Magnaporthales

The order Magnaporthales comprises about 200 species and includes the economically and scientifically important rice blast fungus andthe take-all pathogen of cereals, as well as saprotrophs and endophytes. Recent advances in phylogenetic analyses of these fungi resulted in taxonomic revisions. In this paper we list the 28 currently accepted genera in Magnaporthales with their type species and available gene and genome resources. The polyphyletic Magnaporthe 1972 is proposed for suppression, and Pyricularia 1880 and Nakataea 1939 are recommended for protection as the generic names for the rice blast fungus and the rice stem rot fungus, respectively. The rationale for the recommended names is also provided. These recommendations are made by the Pyricularia/Magnaporthe Working Group established under the auspices of the International Commission on the Taxonomy of Fungi (ICTF).

Genetic Analyses of the Internal Transcribed Spacer Sequences Suggest Introgression and Duplication in the Medicinal Mushroom Agaricus subrufescens.

The internal transcribed spacer (ITS) region of the nuclear ribosomal RNA gene cluster is widely used in fungal taxonomy and phylogeographic studies. The medicinal and edible mushroom Agaricus subrufescens has a worldwide distribution with a high level of polymorphism in the ITS region. A previous analysis suggested notable ITS sequence heterogeneity within the wild French isolate CA487. The objective of this study was to investigate the pattern and potential mechanism of ITS sequence heterogeneity within this strain. Using PCR, cloning, and sequencing, we identified three types of ITS sequences, A, B, and C with a balanced distribution, which differed from each other at 13 polymorphic positions. The phylogenetic comparisons with samples from different continents revealed that the type C sequence was similar to those found in Oceanian and Asian specimens of A. subrufescens while types A and B sequences were close to those found in the Americas or in Europe. We further investigated the inheritance of these three ITS sequence types by analyzing their distribution among single-spore isolates from CA487. In this analysis, three co-dominant markers were used firstly to distinguish the homokaryotic offspring from the heterokaryotic offspring. The homokaryotic offspring were then analyzed for their ITS types. Our genetic analyses revealed that types A and B were two alleles segregating at one locus ITSI, while type C was not allelic with types A and B but was located at another unlinked locus ITSII. Furthermore, type C was present in only one of the two constitutive haploid nuclei (n) of the heterokaryotic (n+n) parent CA487. These data suggest that there was a relatively recent introduction of the type C sequence and a duplication of the ITS locus in this strain. Whether other genes were also transferred and duplicated and their impacts on genome structure and stability remain to be investigated.

Taxonomic utility of old names in current fungal classification and nomenclature: Conflicts, confusion & clarifications

Fungal taxonomy has a long history and nomenclatural type specimens constitute an integral part of fungal classification and nomenclature. To date, type specimens/old names have served as excellent exemplars and references and have been the pillar for a stable classification and appropriate nomenclature. However, with an increase in the number of species being discovered and the practical problems associated with re-examination and over reliance of old names as exemplars, there is a need to reconsider our traditional taxonomic thinking towards such an approach. It is becoming increasingly clear that loaning specimens, especially of rare and old species, is becoming too tedious, difficult and in some cases, practically impossible. This paper addresses in detail some of the major practical difficulties in referring to old names from a stable nomenclatural system viewpoint, in particular, reluctance of herbaria to loan specimens and poor conditions of specimens. Specific case studies where problems are encountered that hinder references to old names are discussed. Last but not least, mycologists express their opinions and concerns and provide deductive conclusions based on facts and their long experience in mycology. With regards to fungal nomenclature, taxonomists, devoted to bring about rational changes to fungal taxonomy, should be encouraged to use more friendly and practical approaches, with minimum hassle to examine old specimens. We contemplate that this paper will provide potential solutions to facilitate future naming/classification of fungal species.

Species concepts commonly used in fungal taxonomy

Species concepts commonly used in fungal taxonomy

Evaluation of streptomyces and non-streptomyces actinomycetes isolates for growth promotion in Vigna radiata and their use as biocontrol agent against Sclerotium rolfsii

Two streptomyces (ARHS/PO26 and ARHS/PO27) and two non streptomyces (ARHS/Mn3 and ARHS/Mn7) actinomycetes isolates obtained from the rhizosphere soil of Solanum tuberosum and Mangifera indica were found to be phosphate solubilizers and showed antagonistic activity against Sclerotium rolfsii. Isolates ARHS/PO26 and ARHS/PO27 were identified morphologically and confirmed by the National Centre for Fungal Taxonomy, as Streptomyces griseus (NCFT 2578.08; NAIMCC-B-00916) and Streptomyces griseolus (NCFT 2579.08). ARHS/Mn 3 and Streptomyces griseolus (ARHS/PO27) could inhibit 68% and 59.7% growth of Sclerotium rolfsii in vitro. In vivo evaluation of the isolates ARHS/Mn 3, Streptomyces griseolus (ARHS/PO27) and Streptomyces griseus (ARHS/PO26) showed maximum growth promotion on Vigna radiata by enhancing key defense enzymes like chitinase, β-1,3-glucanase, phenylalanine ammonia lyase and peroxidase. The results emphasize the fact that soil actinomycetes could be used as potential biocontrol agents.