A phylogenetic hypothesis of Ustilaginomycotina based on multiple gene analyses and morphological data

The identity of Cintractia carpophila var. kenaica: reclassification of a North American smut on Carex micropoda as a distinct species of Anthracoidea

Cintractia carpophila var. kenaica, a neglected taxon described from Alaska more than half a century ago, is re-described and illustrated. Its nomenclature and taxonomic status are discussed. This smut species is characterised by small spores with a very finely verruculose surface rarely enclosed by a thin, hyaline, mucilaginous sheath, a wall with 2-5 distinct internal swellings, and parasitism on Carex micropoda (Carex sect. Dornera). It is reallocated to the genus Anthracoidea as a distinct species, Anthracoidea kenaica comb. nov., and assigned to Anthracoidea section Leiosporae which includes species having smooth or very finely verruculose spores. Morphological and biological characteristics of the five most similar Anthracoidea species are contrasted and discussed.

Evolution of uni- and bifactorial sexual compatibility systems in fungi

Mating systems, that is, whether organisms give rise to progeny by selfing, inbreeding or outcrossing, strongly affect important ecological and evolutionary processes. Large variations in mating systems exist in fungi, allowing the study of their origin and consequences. In fungi, sexual incompatibility is determined by molecular recognition mechanisms, controlled by a single mating-type locus in most unifactorial fungi. In Basidiomycete fungi, however, which include rusts, smuts and mushrooms, a system has evolved in which incompatibility is controlled by two unlinked loci. This bifactorial system probably evolved from a unifactorial system. Multiple independent transitions back to a unifactorial system occurred. It is still unclear what force drove evolution and maintenance of these contrasting inheritance patterns that determine mating compatibility. Here, we give an overview of the evolutionary factors that might have driven the evolution of bifactoriality from a unifactorial system and the transitions back to unifactoriality. Bifactoriality most likely evolved for selfing avoidance. Subsequently, multiallelism at mating-type loci evolved through negative frequency-dependent selection by increasing the chance to find a compatible mate. Unifactoriality then evolved back in some species, possibly because either selfing was favoured or for increasing the chance to find a compatible mate in species with few alleles. Owing to the existence of closely related unifactorial and bifactorial species and the increasing knowledge of the genetic systems of the different mechanisms, Basidiomycetes provide an excellent model for studying the different forces that shape breeding systems.

Ustilago maydis natural antisense transcript expression alters mRNA stability and pathogenesis

Ustilago maydis infection of Zea mays leads to the production of thick-walled diploid teliospores that are the dispersal agent for this pathogen. Transcriptome analyses of this model biotrophic basidiomycete fungus identified natural antisense transcripts (NATs) complementary to 247 open reading frames. The U. maydis NAT cDNAs were fully sequenced and annotated. Strand-specific RT-PCR screens confirmed expression and identified NATs preferentially expressed in the teliospore. Targeted screens revealed four U. maydis NATs that are conserved in a related fungus. Expression of NATs in haploid cells, where they are not naturally occurring, resulted in increased steady-state levels of some complementary mRNAs. The expression of one NAT, as-um02151, in haploid cells resulted in a twofold increase in complementary mRNA levels, the formation of sense-antisense double-stranded RNAs, and unchanged Um02151 protein levels. This led to a model for NAT function in the maintenance and expression of stored teliospore mRNAs. In testing this model by deletion of the regulatory region, it was determined that alteration in NAT expression resulted in decreased pathogenesis in both cob and seedling infections. This annotation and functional analysis supports multiple roles for U. maydis NATs in controlling gene expression and influencing pathogenesis.

Shivasia gen. nov. for the Australasian smut Ustilago solida that historically shifted through five different genera

The generic position of the enigmatic smut fungus Ustilago solida is evaluated applying molecular phylogenetic analyses using ITS and LSU rDNA sequences as well as light and scanning electron microscopical investigations of several collections of this species. Ustilago solida has previously been included in five different genera (Ustilago, Urocystis, Sorosporium, Cintractia, and Tolyposporium), however, molecular analyses revealed that this smut does not belong to any of these genera and represents a distinct ustilaginalean lineage. The closest known phylogenetic relative of Ustilago solida is Heterotolyposporium lepidospermatis, the type species of the monotypic genus Heterotolyposporium. Both smuts differ considerably in both LSU sequences and in several morphological traits, such as the structure of sori and the characteristics of spore balls. Accordingly, the new genus Shivasia is described to accommodate Ustilago solida. This smut infects different Schoenus species (Cyperaceae) in Australia and New Zealand. The description of Shivasia increases the number of endemic smut genera in Australasia to ten. Compared to all other continents the number of endemic smut genera is exceptionally high, which may point at fast evolving characters and/or may be caused by the regional history, including the long-term geographic isolation of Australasia.

A new species of Antherospora supports the systematic placement of its host plant

The morphology and phylogeny of anther smut specimens on Tractema verna collected in the United Kingdom were investigated using light microscopy, scanning electron microscopy and partial rDNA sequence analyses. The anther smut of Tractema verna shows similarity to Antherospora eucomis, A. scillae, A. tourneuxii, A. urgineae, A. vaillantii, and A. vindobonensis but differs in spore size range, spore wall thickness, host plant genera and considerable divergences of ITS and LSU sequences. Consequently, the smut is described here as a new species, Antherospora tractemae. The host plant was formerly included in the genus Scilla (S. verna), but recently moved to a distinct genus Tractema. Molecular phylogenetic analyses reveal that Antherospora tractemae is sister to the lineage of Muscari-parasitizing Antherospora and only distantly related to the Scilla-parasitizing Antherospora species. Thus, the phylogenetic placement of the smut fungus supports the systematic placement of its host plant.

Sympodiomycopsis kandeliae sp. nov., a basidiomycetous anamorphic fungus from mangroves, and reclassification of Sympodiomycopsis lanaiensis as Jaminaea lanaiensis comb. nov

Three ustilaginomycetous anamorphic strains were isolated from flowers of Kandelia candel in mangrove forests of Taiwan. Phylogenetic analyses based on the combined sequences of internal transcribed spacer 1 (ITS1)-5.8S-ITS2 and the D1/D2 domain of the large-subunit (LSU) rDNA indicated that the closest recognized species was Sympodiomycopsis paphiopedili. The results of a DNA–DNA hybridization experiment and the physiological characteristics showed that the three strains represent a novel species within the genus Sympodiomycopsis. The name Sympodiomycopsis kandeliae sp. nov. is proposed, with FIRDI 007T (=BCRC 23165T =CBS 11676T) as the type strain. In addition, based on phenotypic characteristics and the phylogenetic analyses of the combined sequences of the ITS region and D1/D2 domain of the LSU rDNA, Sympodiomycopsis lanaiensis was clustered with the genus Jaminaea. A new combination, Jaminaea lanaiensis comb. nov. (type strain LM418T =DSM 18755T =ATCC MYA-4092T =NRRL Y-48466T =CBS 10858T =BCRC 23177T), is proposed.

Current state and perspectives of fungal DNA barcoding and rapid identification procedures

Fungal research is experiencing a new wave of methodological improvements that most probably will boost mycology as profoundly as molecular phylogeny has done during the last 15 years. Especially the next generation sequencing technologies can be expected to have a tremendous effect on fungal biodiversity and ecology research. In order to realise the full potential of these exciting techniques by accelerating biodiversity assessments, identification procedures of fungi need to be adapted to the emerging demands of modern large-scale ecological studies. But how should fungal species be identified in the near future? While the answer might seem trivial to most microbiologists, taxonomists working with fungi may have other views. In the present review, we will analyse the state of the art of the so-called barcoding initiatives in the light of fungi, and we will seek to evaluate emerging trends in the field. We will furthermore demonstrate that the usability of DNA barcoding as a major tool for identification of fungi largely depends on the development of high-quality sequence databases that are thoroughly curated by taxonomists and systematists.

Ustilago maydis infection strongly alters organic nitrogen allocation in maize and stimulates productivity of systemic source leaves

The basidiomycete Ustilago maydis is the causal agent of corn smut disease and induces tumor formation during biotrophic growth in its host maize (Zea mays). We have conducted a combined metabolome and transcriptome survey of infected leaves between 1 d post infection (dpi) and 8 dpi, representing infected leaf primordia and fully developed tumors, respectively. At 4 and 8 dpi, we observed a substantial increase in contents of the nitrogen-rich amino acids glutamine and asparagine, while the activities of enzymes involved in primary nitrogen assimilation and the content of ammonia and nitrate were reduced by 50% in tumors compared with mock controls. Employing stable isotope labeling, we could demonstrate that U. maydis-induced tumors show a reduced assimilation of soil-derived (15)NO(3)(-) and represent strong sinks for nitrogen. Specific labeling of the free amino acid pool of systemic source leaves with [(15)N]urea revealed an increased import of organic nitrogen from systemic leaves to tumor tissue, indicating that organic nitrogen provision supports the formation of U. maydis-induced tumors. In turn, amino acid export from systemic source leaves was doubled in infected plants. The analysis of the phloem amino acid pool revealed that glutamine and asparagine are not transported to the tumor tissue, although these two amino acids were found to accumulate within the tumor. Photosynthesis was increased and senescence was delayed in systemic source leaves upon tumor development on infected plants, indicating that the elevated sink demand for nitrogen could determine photosynthetic rates in source leaves.

The range of molecular methods for typing Malassezia

PURPOSE OF REVIEW

The recent sequencing of the whole genome of Malassezia globosa and M. restricta forms the basis for molecular epidemiology studies and instigates investigations into their respective virulence factors. Thus, reviewing current knowledge on Malassezia molecular typing methods would reveal the pros and cons of each method and would highlight potential scarcity of epidemiological data regarding this ubiquitous fungal commensal and pathogen.

RECENT FINDINGS

Methods employed for Malassezia molecular typing can be categorized into those detecting sequence variations of strains and those that selectively amplify polymorphic DNA markers for discriminating Malassezia species subtypes. The former exploit rRNA gene sequence variations in order to trace M. globosa, M. restricta and M.pachydermatis subtypes associated with specific skin diseases, or detect M. furfur geographical variations. Polymorphic DNA amplification methods, such as amplified fragment length polymorphism analysis, demonstrated association of M. furfur subtypes with the origin of the strain (skin or systemic isolate), whereas PCR-fingerprinting of the mini-satellite DNA clustered M. furfur strains according to their geographic origin and disease origin. Moreover, much typing work has already been performed regarding the zoophilic species M. pachydermatis and the relevant methods can be adapted for studying the anthropophilic Malassezia species.

SUMMARY

In the near future, molecular typing will be a powerful tool in epidemiological studies that could be employed for the elucidation of the pathobiology of Malassezia species in associated skin diseases

Malassezia furfur fingerprints as possible markers for human phylogeography

Malassezia furfur was the first species described within the cosmopolitan yeast genus Malassezia, which now comprises 13 species. Reported isolation rates of these species from healthy and diseased human skin show geographic variations. PCR-fingerprinting with the wild-type phage M13 primer (5'-GAGGGTGGCGGTTCT-3') was applied to investigate phylogeographic associations of M. furfur strains isolated from Scandinavians residing permanently in Greece, in comparison to clinical isolates from Greek, Bulgarian and Chinese native residents. Seven M. furfur strains from Scandinavians were compared with the Neotype strain (CBS1878), CBS global collection strains (n=10) and clinical isolates from Greece (n=4), Bulgaria (n=15) and China (n=6). Scandinavian, Greek and Bulgarian M. furfur strains mostly formed distinct group clusters, providing initial evidence for an association with the host's geographical origin and with the underlying skin condition. These initial data address the hypothesis that M. furfur could be a eukaryotic candidate eligible for phylogeographic studies.

The evolution of 5S ribosomal RNA genes linked to the rDNA units of fungal species

5S ribosomal RNA (rRNA) genes are known to move in and out of various tandemly repeated eukaryotic gene families during evolution. Here, we investigated the organization of 5S rRNA genes linked to the ribosomal DNA (rDNA) units in 147 fungal species using available sequence and genome databanks. Whereas some fungal species have no 5S rRNA genes in their rDNA units, others have one or two 5S rRNA copies linked on the same or the opposite strand. There were at least 13 independent changes during the evolution of fungal species. These include two 5S rRNA genes loss, five 5S rRNA genes inversions and six 5S rRNA genes insertions (including duplications). The lower frequency of 5S rRNA genes loss might be due to the fact that these events are more likely to affect fitness. The maximum time required for 5S rRNA gene organization to change between related species was estimated to be 7.5 millions years based on the sequences of the elongation factor alpha genes of Candida glabrata and Saccharomyces mikatae. This time is much longer than the homogenization time predicted from theoretical and experimental studies and likely reflects the lack of closely related species or strains in our data set.

Farysizyma gen. nov., an anamorphic genus in the Ustilaginales to accommodate three novel epiphytic basidiomycetous yeast species from America, Europe and Asia

Among many isolates that resulted from four independent surveys of yeasts associated with plants in Brazil, the USA, Portugal and Taiwan, we have characterized eighteen basidiomycetous strains, two of which were conspecific with the type strain of Rhodotorula acheniorum, whereas the remaining sixteen isolates appeared not to correspond to any previously described species. Microsatellite-PCR fingerprinting with primers M13 and (GTG)5 confirmed that the latter strains formed three genetically distinct groups. Each group was considered to represent a distinct species based on nucleotide sequences of the D1/D2 domains of the 26S rRNA gene and the internal transcribed spacer (ITS) region. Phylogenetic analyses of sequence data placed the putative novel species in a clade with R. acheniorum and the dimorphic smut fungus Farysia chardoniana. A novel anamorphic genus, Farysizyma, is created to accommodate the three undescribed species, which were named Farysizyma itapuensis, Farysizyma setubalensis and Farysizyma taiwaniana. A new combination, Farysizyma acheniorum, is proposed for R. acheniorum, which may represent the yeast-phase anamorph of Farysia thuemenii.

Dandruff-associated Malassezia genomes reveal convergent and divergent virulence traits shared with plant and human fungal pathogens

Fungi in the genus Malassezia are ubiquitous skin residents of humans and other warm-blooded animals. Malassezia are involved in disorders including dandruff and seborrheic dermatitis, which together affect >50% of humans. Despite the importance of Malassezia in common skin diseases, remarkably little is known at the molecular level. We describe the genome, secretory proteome, and expression of selected genes of Malassezia globosa. Further, we report a comparative survey of the genome and secretory proteome of Malassezia restricta, a close relative implicated in similar skin disorders. Adaptation to the skin environment and associated pathogenicity may be due to unique metabolic limitations and capabilities. For example, the lipid dependence of M. globosa can be explained by the apparent absence of a fatty acid synthase gene. The inability to synthesize fatty acids may be complemented by the presence of multiple secreted lipases to aid in harvesting host lipids. In addition, an abundance of genes encoding secreted hydrolases (e.g., lipases, phospholipases, aspartyl proteases, and acid sphingomyelinases) was found in the M. globosa genome. In contrast, the phylogenetically closely related plant pathogen Ustilago maydis encodes a different arsenal of extracellular hydrolases with more copies of glycosyl hydrolase genes. M. globosa shares a similar arsenal of extracellular hydrolases with the phylogenetically distant human pathogen, Candida albicans, which occupies a similar niche, indicating the importance of host-specific adaptation. The M. globosa genome sequence also revealed the presence of mating-type genes, providing an indication that Malassezia may be capable of sex.