An unexpected diversity of powdery mildew species infecting the Fabaceae in Australia

The Fabaceae family has been reported to host more than fifty species of powdery mildew worldwide. Despite being commonly found on fabaceous hosts throughout Australia, the accurate identification of many powdery mildew species remains uncertain. The objective of this study was to identify powdery mildew species that naturally occur on fabaceous hosts in Australia and provide insight into those native and weedy species that may host crop pathogens and contribute to disease in cropping systems. The ribosomal DNA internal transcribed spacer (ITS) sequences and morphology of 34 fresh and 40 herbarium powdery mildew specimens infecting diverse Fabaceae species in Australia were characterised in this study. Altogether, a total of eleven powdery mildew species were identified from 51 Fabaceae species. Podosphaera xanthii was the most common powdery mildew in this study and was detected on 18 host species across ten genera. Ten species of Erysiphe were confirmed on 37 host species covering 17 host genera, with E. diffusa and E. cf. trifoliorum the most prevalent. This work provides the most comprehensive catalogue of powdery mildew species infecting legume hosts throughout Australia.

Phylogeny and taxonomy of the genera of Erysiphaceae, part 7: Phyllactinieae

The seventh part of this series devoted to the phylogeny and taxonomy of powdery mildews presents the phylogeny and taxonomy of species assigned to the genera Leveillula, Phyllactinia, Pleochaeta, and Queirozia (Erysiphaceae tribe Phyllactinieae). Phylogenetic trees based on multiple loci (ITS+28S, CAM, GADPH, GS, IGS, RPB2, and TUB) are presented. All species with available sequence data are included. The present analyses aim at providing a reference for analyses of powdery mildews of tribe Phyllactinieae. A special focus is on the generic distinction at the base of tribe Phyllactinieae and between Leveillula and Phyllactinia. The inclusion of a larger number of phylogenetically basal Phyllactinia spp. and multiple loci allowed a better insight into the phylogeny of tribe Phyllactinieae and confirmed that Leveillula spp. are nested within the Phyllactinia clade. As a consequence, Leveillula is reduced to synonymy with Phyllactinia. Additionally, Queirozia was found to be nested within the Pleochaeta clade, and as such we have reduced Queirozia to synonymy with Pleochaeta. Multiple species have been sequenced for the first time, in particular multiple North American species. Erysiphe betulae, E. orbicularis, E. polychaeta, E. saxaouli, Phyllactinia antarctica, Ph. broussonetiae-kaempferi, Ph. hamamelidis, Ph. kakicola, Ph. pyri-serotinae, Ph. salmonii, Ph. zanthoxylicola, Uncinula lynchii, and U. shiraiana are epitypified. The new species Ph. amelanchieris, sp. nov. Ph. fraxini-pennsylvanicae, sp. nov. and Ph. oemleriae, sp. nov. are described, and the new combinations Phyllactinia buddlejae, Ph. cleomes, Ph. cylindrospora, Ph. farinosa, Ph. golovinii, Ph. guilanensis, Ph. jaczewskii, Ph. lactucae-seriolae, Ph. lactucarum, Ph. lanugiosa, Ph. lappae, Ph. mindii, Ph. oxalidicola, Ph. picridis, Ph. rubiae, Ph. saxaoulii, Ph. taurica, Ph. thevenotiae, Ph. ulmi (comb. et stat. nov.), Ph. verbasci, Ph. wissadulae, and Pleochaeta erysiphoides are introduced. Furthermore, Phyllactinia sect. Basiphyllactinia, sect. nov. Phyllactinia sect. Leveillula, comb. et stat. nov. and Pleochaeta sect. Ovulariopsis, comb. et stat. nov. are presented.

An emerging fungal disease is spreading across the globe and affecting the blueberry industry

Powdery mildew is an economically important disease caused by c. 1000 different fungal species. Erysiphe vaccinii is an emerging powdery mildew species that is impacting the blueberry industry. Once confined to North America, E. vaccinii is now spreading rapidly across major blueberry-growing regions, including China, Morocco, Mexico, and the USA, threatening millions in losses. This study documents its recent global spread by analyzing both herbarium specimens, some over 150-yr-old, and fresh samples collected world-wide. Our findings were integrated into a 'living phylogeny' via T-BAS to simplify pathogen identification and enable rapid responses to new outbreaks. We identified 50 haplotypes, two primary introductions world-wide, and revealed a shift from a generalist to a specialist pathogen. This research provides insights into the complexities of host specialization and highlights the need to address this emerging global threat to blueberry production.

Phylogeny and taxonomy of the genera of Erysiphaceae, part 6: Erysiphe (the "Microsphaera lineage" part 2)

This is the sixth contribution in a series devoted to the phylogeny and taxonomy of powdery mildews. This part includes our third treatment of the species of the genus Erysiphe. It continues the previous contribution on the phylogenetic-taxonomic assessment of the species belonging to the "Microsphaera lineage." Since this is a large lineage, we have split the treatment of the "Microsphaera lineage" into two parts. Phylogenetic trees based on rDNA are supplemented by sequences of additional markers (CAM, GAPDH, GS, RPB2, and TUB). The "Erysiphe trifoliorum complex" is a challenging group that belongs to the "Microsphaera lineage." Adequate clarification of this complex will be possible when additional worldwide multilocus sequence analyses are performed. The new species Erysiphe acetosae, E. acmisponis, E. lathyrina, E. salmoniana, and E. santalicola are described, and the new combinations E. biuncinata and E. pavoniae are introduced. Specimens of several species have been sequenced for the first time, particularly North American species, such as Erysiphe caryae, E. ceanothi, E. juglandis-nigrae, and E. ravenelii. Erysiphe syringae is lectotypified and 15 species names are epitypified in order to provide ex-epitype reference sequences. For other species, non-ex-type reference sequences are proposed for phylogenetic-taxonomic purposes. Ex-type sequences for Erysiphe baptisiicola, E. sesbaniae, Microsphaera sydowiana, M. umbilici, and Oidium pavoniae have been retrieved.

Peziza nivalis and relatives-spring fungi of wide distribution

Several members of the genus Peziza sensu stricto occur at the edge of melting snow. These nivicolous species have been widely reported in the Northern Hemisphere and are also known from Australia and New Zealand. We have used 16 specimens from North America and Australia to study morphology and to perform DNA sequencing. In sequence analyses, we have used ITS1 and ITS2 (internal transcribed spacers), 28S, RPB2 (RNA polymerase II gene), and two genes new to these studies, GAPDH (glyceraldehyde-3-phosphate dehydrogenase) and HSP90 (heat shock protein 90). Although not all regions are available for all samples, we have recognized the following species: Peziza heimii, P. nivalis, and P. nivis. Phylogenetic analyses were done using ITS alone; combined ITS1-5.8S-ITS2, 28S, and RPB2; ITS, and 28S, RPB2, GAPDH, and HSP90. Even with this augmented set of genes and despite their widespread occurrence in North America, Europe, Australia, and New Zealand, we have not definitively distinguished species within this group. To assess these results, pairwise homoplasy index (PHI) analysis was employed. This showed evidence of recombination among the samples of P. nivalis and further supports the view of P. nivalis as a monophyletic cosmopolitan species. As part of this study, we also examined the variation in ITS copies in P. echinospora, for which a genome is available.

Designing A Novel Primer Set for GAPDH Gene to Enhance Taxonomic and Phylogenetic Studies of Golovinomyces Species

Golovinomyces (Erysiphaceae, Ascomycota) is an obligate plant pathogenic group causing powdery mildew on diverse angiosperm plants, including economically significant crops. Despite advancements in the taxonomy and phylogeny of Golovinomyces species using ribosomal DNA markers (ITS and LSU), several taxonomic issues remain unresolved. Previously, the glyceraldehyde-3-phosphate dehydrogenase (GAPDH) gene, which exhibits higher nucleotide variation, has been proposed as an additional marker for powdery mildew species. In this study, we designed a new primer set (GoGPD-F and GoGPD-R) to improve the PCR success and efficiency of the GAPDH gene across various Golovinomyces species and dried herbarium specimens. The primers were successful in amplifying and sequencing the GAPDH gene in sixteen Golovinomyces species, including six species not previously registered in GenBank and two undescribed species. This development is a significant contribution to future research on the identification, taxonomy, and phylogeny of Golovinomyces species, offering a more robust tool for resolving existing taxonomic issues.

Powdery mildew caused by Erysiphe corylacearum: An emerging problem on hazelnut in Italy

Erysiphe corylacearum has recently been reported in northern Italy (Piedmont) and other European countries as the causal agent of a new emerging powdery mildew on hazelnut. This disease is much more dangerous than the common hazelnut powdery mildew caused by Phyllactinia guttata as it significantly reduces yield and quality of hazelnuts. This study aimed to perform morphological and molecular characterization of the fungal isolates from powdery mildew-infected plants in the Piedmont Italian region. Additionally, genetic diversity studies and pathogenicity tests were conducted. Thirty-six fungal isolates originating from symptomatic hazelnut plants exhibiting specific powdery mildew symptoms on the superior leaf side were identified morphologically as E. corylacearum. Single- and multilocus sequence typing of five loci (ITS, rpb2, CaM, GAPDH and GS) assigned all isolates as E. corylacearum. Multilocus and GAPDH phylogenetic studies resulted in the most efficient characterization of E. corylacearum. Studied fungal isolates were able to cause new emerging powdery mildew disease by fulfilling Koch's postulates. The emergence of powdery mildew disease in Italy revealed the E. corylacearum subgrouping, population expansion, and high nucleotide similarity with other recently identified E. corylacearum hazelnut isolates. To contain this harmful disease and inhibit the fungus spread into new geographical zones, it will be necessary to implement more rigorous monitoring in neighboring hazelnut plantations near infected hazelnuts, use sustainable fungicides and search for new biocontrol agents.

Phylogenomics reveals extensive misidentification of fungal strains from the genus Aspergillus

Modern taxonomic classification is often based on phylogenetic analyses of a few molecular markers, although single-gene studies are still common. Here, we leverage genome-scale molecular phylogenetics (phylogenomics) of species and populations to reconstruct evolutionary relationships in a dense data set of 710 fungal genomes from the biomedically and technologically important genus Aspergillus. To do so, we generated a novel set of 1,362 high-quality molecular markers specific for Aspergillus and provided profile Hidden Markov Models for each, facilitating their use by others. Examining the resulting phylogeny helped resolve ongoing taxonomic controversies, identified new ones, and revealed extensive strain misidentification (7.59% of strains were previously misidentified), underscoring the importance of population-level sampling in species classification. These findings were corroborated using the current standard, taxonomically informative loci. These findings suggest that phylogenomics of species and populations can facilitate accurate taxonomic classifications and reconstructions of the Tree of Life.IMPORTANCEIdentification of fungal species relies on the use of molecular markers. Advances in genomic technologies have made it possible to sequence the genome of any fungal strain, making it possible to use genomic data for the accurate assignment of strains to fungal species (and for the discovery of new ones). We examined the usefulness and current limitations of genomic data using a large data set of 710 publicly available genomes from multiple strains and species of the biomedically, agriculturally, and industrially important genus Aspergillus. Our evolutionary genomic analyses revealed that nearly 8% of publicly available Aspergillus genomes are misidentified. Our work highlights the usefulness of genomic data for fungal systematic biology and suggests that systematic genome sequencing of multiple strains, including reference strains (e.g., type strains), of fungal species will be required to reduce misidentification errors in public databases.

Phylogeny and taxonomy of the genera of Erysiphaceae, part 5: Erysiphe (the "Microsphaera lineage" part 1)

In this contribution, we offer the fifth installment of a series focusing on the phylogeny and taxonomy of powdery mildews. This paper is the second segment evaluating the genus Erysiphe. The first treatment of Erysiphe focused on phylogenetically basal species in the "Uncinula lineage." This research presents a phylogenetic-taxonomic assessment of species that form the group previously referred to as the "Microsphaera lineage." Given the size of the group, we split the treatment of this lineage of Erysiphe species into two parts based on their phylogenetic placement. Phylogenetic trees based on ITS+28S data are supplemented by sequences of additional markers (CAM, GADPH, GS, RPB2, and TUB). Included in the analysis of the Microsphaera lineage is the "Erysiphe aquilegiae complex" (group, clade, cluster), which encompasses sequences obtained from an assemblage of Erysiphe species with insufficient resolution in rDNA analyses. Attempts have been made to resolve this group at the species level by applying a multilocus approach. A detailed discussion of the "Erysiphe aquilegiae complex" is provided. Sequences are provided for the first time for several species, particularly North American species, such as Erysiphe aggregata, E. erineophila, E. parnassiae, and E. semitosta. Ex-type sequences for Microsphaera benzoin and M. magnusii have been retrieved. Alphitomorpha penicillata, Microsphaera vanbruntiana, and M. symphoricarpi are epitypified with ex-epitype sequences. The new species Erysiphe alnicola, E. deutziana, E. cornigena, E. lentaginis, and E. sambucina are described, the new combinations E. lauracearum, E. passiflorae, and E. sambucicola are introduced, and the new name E. santali is proposed.

Phylogeny and taxonomy of the genera of Erysiphaceae, part 4: Erysiphe (the "Uncinula lineage")

This is the fourth contribution within an ongoing series dedicated to the phylogeny and taxonomy of powdery mildews. This particular installment undertakes a comprehensive evaluation of a group previously referred to as the "Uncinula lineage" within Erysiphe. The genus Erysiphe is too large to be assessed in a single paper; thus, the treatment of Erysiphe is split into three parts, according to phylogenetic lineages. The first paper, presented here, discusses the most basal lineage of Erysiphe and its relationship to allied basal genera within tribe Erysipheae (i.e., Brasiliomyces and Salmonomyces). ITS+28S analyses are insufficient to resolve the basal assemblage of taxa within the Erysipheae. Therefore, phylogenetic multilocus examinations have been carried out to better understand the evolution of these taxa. The results of our analyses favor maintaining Brasiliomyces, Bulbomicroidium, and Salmonomyces as separate genera, at least for the interim, until further phylogenetic multilocus data are available for additional basal taxa within the Erysipheae. The current analyses also confirmed previous results that showed that the "Uncinula lineage" is not exclusively composed of Erysiphe species of sect. Uncinula but also includes some species that morphologically align with sect. Erysiphe, as well as species that had previously been assigned to Californiomyces and Typhulochaeta. Numerous sequences of Erysiphe species from the "Uncinula lineage" have been included in the present phylogenetic analyses and were confirmed by their position in well-supported species clades. Several species have been sequenced for the first time, including Erysiphe clintonii, E. couchii, E. geniculata, E. macrospora, and E. parvula. Ex-type sequences are provided for 16 taxa including E. nothofagi, E. trinae, and E. variabilis. Epitypes are designated and ex-epitype sequences are added for 18 taxa including Erysiphe carpophila, E. densa, and U. geniculata var. carpinicola. The new species Erysiphe canariensis is described, and the new names E. hosagoudarii and E. pseudoprunastri and the new combination E. ampelopsidis are introduced.

Potential Proallergenic Activity of Phytopathogenic Erysiphe palczewskii and Erysiphe convolvuli in in vitro Studies

Purpose

Allergic diseases have reached epidemic proportions globally, affecting nearly 30% of the world's population. One of the most prominent sources of allergens is fungi, causing up to 6% of respiratory diseases in the general population. However, the cause of respiratory allergies is not always identifiable. Therefore, we studied the ability of two representatives of common powdery mildew (Erysiphales), Erysiphe palczewskii and Erysiphe convolvuli, to induce a proinflammatory response in in vitro models of the upper and lower respiratory tract.

Materials and Methods

Two cell lines, BEAS-2B and A549, were used to mimic upper and lower respiratory epithelial cells. The toxicity of fungal extracts was assessed with MTT and flow cytometry assay. The production of reactive oxygen species in the cells was measured with flow cytometry. ELISA tests were used to determine the production of proinflammatory cytokines. The presence of the cell integrity marker was assessed with the immunofluorescence method.

Results

In both cell lines, the extract of E. palczewskii and E. convolvuli microfungi induced marked production of proinflammatory IL-1β, TNF-α, and GM-CSF cytokines involved in developing allergic reactions. The higher levels of these cytokines with higher reactive oxygen species synthesis positively correlated with the disruption of epithelial cell junctions.

Conclusion

We conclude that E. palczewskii and E. convolvuli microfungi have strong proinflammatory and proallergenic potential, but this finding needs in vivo confirmation.

Fungal taxonomy: A puzzle with many missing pieces

Fungi are multifaceted organisms found in almost all ecosystems on Earth, where they establish various types of symbiosis with other living beings. Despite being recognized by humans since ancient times, and the high number of works delving into their biology and ecology, much is still unknown about these organisms. Some criteria classically used for their study are nowadays limited, generating confusion in categorizing them, and even more, when trying to understand their genealogical relationships. To identify species within Fungi, phenotypic characters to date are not sufficient, and to construct a broad phylogeny or a phylogeny of a particular group, there are still gaps affecting the generated trees, making them unstable and easily debated. For health professionals, fungal identification at lower levels such as genus and species, is enough to select the most appropriate therapy for their control, understand the epidemiology of clinical pictures associated, and recognize outbreaks and antimicrobial resistance. However, the taxonomic location within the kingdom, information with apparently little relevance, can allow phylogenetic relationships to be established between fungal taxa, facilitating the understanding of their biology, distribution in nature, and pathogenic potential evolution. Advances in molecular biology and computer science techniques from the last 30 years have led to crucial changes aiming to establish the criteria to define a fungal species, allowing us to reach a kind of stable phylogenetic construction. However, there is still a long way to go, and it requires the joint work of the scientific community at a global level and support for basic research.

Extensive intragenomic variation in the internal transcribed spacer region of fungi

Fungi are among the most biodiverse organisms in the world. Accurate species identification is imperative for studies on fungal ecology and evolution. The internal transcribed spacer (ITS) rDNA region has been widely accepted as the universal barcode for fungi. However, several recent studies have uncovered intragenomic sequence variation within the ITS in multiple fungal species. Here, we mined the genome of 2414 fungal species to determine the prevalence of intragenomic variation and found that the genomes of 641 species, about one-quarter of the 2414 species examined, contained multiple ITS copies. Of those 641 species, 419 (∼65%) contained variation among copies revealing that intragenomic variation is common in fungi. We proceeded to show how these copies could result in the erroneous description of hundreds of fungal species and skew studies evaluating environmental DNA (eDNA) especially when making diversity estimates. Additionally, many genomes were found to be contaminated, especially those of unculturable fungi.

Phylogeny and taxonomy of the genera of Erysiphaceae, part 1: Golovinomyces

Powdery mildews are a monophyletic group of obligate plant pathogenic fungi in the family Erysiphaceae. Powdery mildews are economically important in that they cause damage to many agriculturally significant crops and plants in ecologically important habitats. In this contribution, we introduce a new series of publications focusing on the phylogeny and taxonomy of this group, with an emphasis on specimens collected from North America. The first part of the series focuses on the genus Golovinomyces and includes a section detailing the powdery mildew species concept. We conducted analyses of Golovinomyces spp. with available rDNA sequence data from GenBank and supplemented the data set with rDNA (ITS, 28S, IGS) as well as protein-coding (GAPDH) data from 94 North American collections. Many of the species evaluated are included in phylogenetic and morphological analyses for the first time, including the American species G. americanus, G. brunneopunctatus, G. californicus, G. greeneanus, G. hydrophyllacearum, and G. sparsus. A special emphasis was placed on acquiring ex-type or ex-epitype sequences or presenting reference sequences for phylogenetic-taxonomic purposes. Three new species, G. eurybiarum, G. galiorum, and G. malvacearum, are described, and the new combinations G. fuegianus, G. mutisiae, and G. reginae are introduced. Ex-holotype sequences of Erysiphe sparsa (≡ G. sparsus) reveal that it should be reduced to synonymy with G. ambrosiae, and ex-epitype sequences of G. valerianae reveal that it should be reduced to synonymy with G. orontii. Multiple epitypes are designated with ex-epitype sequences.