Vegetative incompatibility is a fungal allorecognition system characterised by the inability of genetically distinct conspecific fungal strains to form a viable heterokaryon and is controlled by multiple polymorphic loci termed vic (vegetative incompatibility) or het (heterokaryon incompatibility). We have genetically identified and characterised the first vic locus in the economically important, plant-pathogenic, necrotrophic fungus Botrytis cinerea. A bulked segregant approach coupled with whole genome Illumina sequencing of near-isogenic lines of B. cinerea was used to map a vic locus to a 60-kb region of the genome. Within that locus, we identified two adjacent, highly polymorphic open reading frames, Bcvic1 and Bcvic2, which encode predicted proteins that contain domain architectures implicated in vegetative incompatibility in other filamentous fungi. Bcvic1 encodes a predicted protein containing a putative serine esterase domain, a NACHT family of NTPases domain, and several Ankyrin repeats. Bcvic2 encodes a putative syntaxin protein containing a SNARE domain; such proteins typically function in vesicular transport. Deletion of Bcvic1 and Bcvic2 individually had no effect on vegetative incompatibility. However, deletion of the region containing both Bcvic1 and Bcvic2 resulted in mutant lines that were severely restricted in growth and showed loss of vegetative incompatibility. Complementation of these mutants by ectopic expression restored the growth and vegetative incompatibility phenotype, indicating that Bcvic1 and Bcvic2 are controlling vegetative incompatibility at this vic locus.

Phytophthora Clade 5 is a very poorly studied group of species of oomycete chromists, consisting of only two known species P. castaneae (≡ P. katsurae, nom. illegit.) and P. heveae with most isolates from East Asia and the Pacific Islands. However, isolates of two important disease-causing chromists in Clade 5, one of kauri (Agathis australis) in New Zealand, the other of coconut (Cocos nucifera) in Hawaii, poorly match the current species descriptions. To verify whether these isolates belong to separate species a detailed morphological study and phylogenetic analysis consisting of eight genetic loci was conducted. On the basis of genetic and morphological differences and host specificity, we present the formal description of two new species in Clade 5, Phytophthora agathidicida sp. nov. and Phytophthora cocois sp. nov. To clarify the typification of the other Clade 5 species, an authentic ex-holotype culture of Phytophthora castaneae is designated and P. heveae is lectotypified and epitypified.

Historically a single name, Stephanospora flava, was applied to all collections of Stephanospora in Australasia. We used morphological characters with molecular support to differentiate and describe nine novel cryptic species, and refine the circumscription of S. flava. Stephanospora flava is herein restricted to bispored collections from Tasmania, and the quadrisporic Stephanospora tetraspora is raised to species level. Six species (four new) are endemic to Australia, S. flava s.s, S. tetraspora comb. nov., Stephanospora sheoak, Stephanospora cribbae, Stephanospora hystrispora, and Stephanospora occidentiaustralis. Three species Stephanospora poropingao, Stephanospora pounamu, and Stephanospora kanuka are endemic to New Zealand; and one species, Stephanospora aorangi occurs in both Australia and New Zealand. Two other new species, Stephanospora novae-caledoniae and Stephanospora papua, are endemic to New Caledonia or Papua New Guinea, respectively. Analyses of three nuclear gene regions (ITS, ef-1, and LSU) are consistent with current classifications of the family Stephanosporaceae. Athelidium aurantiacum is an outlier, with a strongly supported core of Cristinia (Clade I), Lindtneria (Clade II), Stephanospora, Mayamontana, and Lindtneria trachyspora (Clade III), and a novel lineage of environmental and sporocarp sequences (Clade IV). Taxonomic and nomenclatural issues raised by the presence of both type species of Stephanospora (Stephanospora caroticolor) and Lindtneria (L. trachyspora) in the same clade are discussed.

Background: 'Candidatus Phytoplasma australiense' is associated with at least nine diseases in Australia and New Zealand. The impact of this phytoplasma is considerable, both economically and environmentally. The genome of a NZ isolate was sequenced in an effort to understand its pathogenicity and ecology. Comparison with a closely related Australian isolate enabled us to examine mechanisms of genomic rearrangement.Results: The complete genome sequence of a strawberry lethal yellows (SLY) isolate of 'Candidatus Phytoplasma australiense' was determined. It is a circular genome of 959,779 base pairs with 1126 predicted open reading frames. Despite being 80 kbp larger than another 'Ca. Phytoplasma australiense' isolate PAa, the variation between housekeeping genes was generally less than 1% at a nucleotide level. The difference in size between the two isolates was largely due to the number and size of potential mobile units (PMUs), which contributed to some changes in gene order. Comparison of the genomes of the two isolates revealed that the highly conserved 5' UTR of a putative DNA-directed RNA polymerase seems to be associated with insertion and rearrangement events. Two types of PMUs have been identified on the basis of the order of three to four conserved genes, with both PMUs appearing to have been present in the last common ancestor of 'Ca. Phytoplasma asteris' and 'Ca. Phytoplasma australiense'. Comparison with other phytoplasma genomes showed that modification methylases were, in general, species-specific. A putative methylase (xorIIM) found in 'Ca. Phytoplasma australiense' appeared to have no analogue in any other firmicute, and we believe has been introduced by way of lateral gene transfer. A putative retrostransposon (ltrA) analogous to that found in OY-M was present in both isolates, although all examples in PAa appear to be fragments. Comparative analysis identified highly conserved 5' and 3' UTR regions of ltrA, which may indicate how the gene is excised and inserted.Conclusions: Comparison of two assembled 'Ca. Phytoplasma australiense' genomes has shown they possess a high level of plasticity. This comparative analysis has yielded clues as to how rearrangements occur, and the identification of sets of genes that appear to be associated with these events.

Species‐ and population‐specific differences in fungicide resistance and aggressiveness within Botrytis makes basic data on genetic diversity important for understanding disease caused by this fungus. Genetic diversity of Botrytis was surveyed between 2008 and 2012 from grapes from five New Zealand wine‐growing regions. A total of 1226 isolates were gathered from symptomless flower buds at the start of the growing season and 1331 isolates from diseased fruit at harvest. Two species were found, B. cinerea and B. pseudocinerea. Botrytis pseudocinerea was common in both Auckland vineyards sampled, and infrequent elsewhere. However, even in Auckland, it was rarely isolated from diseased fruit. The presence of the Boty and Flipper transposons was assessed. Isolates with all four transposon states (Boty only, Flipper only, both Boty and Flipper, no transposons) were found for both species. Both vineyards in the Auckland region had high numbers of Flipper‐only isolates at flowering; both vineyards from the Waipara region had high numbers of Boty‐only isolates at flowering. Most isolates from diseased fruit at harvest contained both transposons. These observations suggest that B. pseudocinerea, and isolates with one or both of the transposons missing, may be less aggressive than B. cinerea, or than isolates with both transposons present. Two clades were resolved within B. pseudocinerea, only one of which has been reported from European vineyards. Phylogenetic diversity within B. cinerea in New Zealand was similar to that known from Europe, including isolates that appear to match Botrytis ‘Group S’. The taxonomic implications of this genetic diversity are discussed.

‘Candidatus Phytoplasma australiense’ is associated with a number of plant diseases in New Zealand. The only known vector of this pathogen was Zeoliarus atkinsoni, a planthopper considered to be monophagous on New Zealand flax (Phormium spp.). The work carried out shows that Z. oppositus, which is polyphagous, is able to vector ‘Ca. P. australiense’ to both Coprosma robusta (karamu) and Cordyline australis (New Zealand cabbage tree). Although transmission was achieved to both these species, the disease symptomatology was more evident in C. australis. Two approaches were taken to achieve transmission. First, insects were collected from areas around symptomatic Coprosma plants and caged directly on test plants. Second, insects were collected from grasses and sedges in areas where disease was less evident and were fed on known infected Coprosma plants prior to being caged on test plants. Transmission was achieved using both approaches, although transmission was far greater (30% compared with 4%) from insects that were directly applied. Phytoplasma DNA was detected in 12% of Z. oppositus individuals tested during all the trials. This work identifies a new vector for ‘Ca. P. australiense’ and contributes to our understanding of the ecology of Cordyline sudden decline and Coprosma lethal decline.

Four species of the sequestrate fungal genus Elaphomyces are reported from New Zealand: Elaphomyces bollardii sp. nov. associated with Leptospermum spp. and Kunzea ericoides, E. luteicrustus sp. nov. associated with Nothofagus menziesii, E. putridus sp. nov. associated with Nothofagus spp., and an unnamed species associated with Nothofagus spp.

Sclerotinia sclerotiorum and Botrytis cinerea are closely related necrotrophic plant pathogenic fungi notable for their wide host ranges and environmental persistence. These attributes have made these species models for understanding the complexity of necrotrophic, broad host-range pathogenicity. Despite their similarities, the two species differ in mating behaviour and the ability to produce asexual spores. We have sequenced the genomes of one strain of S. sclerotiorum and two strains of B. cinerea. The comparative analysis of these genomes relative to one another and to other sequenced fungal genomes is provided here. Their 38-39 Mb genomes include 11,860-14,270 predicted genes, which share 83% amino acid identity on average between the two species. We have mapped the S. sclerotiorum assembly to 16 chromosomes and found large-scale co-linearity with the B. cinerea genomes. Seven percent of the S. sclerotiorum genome comprises transposable elements compared to <1% of B. cinerea. The arsenal of genes associated with necrotrophic processes is similar between the species, including genes involved in plant cell wall degradation and oxalic acid production. Analysis of secondary metabolism gene clusters revealed an expansion in number and diversity of B. cinerea-specific secondary metabolites relative to S. sclerotiorum. The potential diversity in secondary metabolism might be involved in adaptation to specific ecological niches. Comparative genome analysis revealed the basis of differing sexual mating compatibility systems between S. sclerotiorum and B. cinerea. The organization of the mating-type loci differs, and their structures provide evidence for the evolution of heterothallism from homothallism. These data shed light on the evolutionary and mechanistic bases of the genetically complex traits of necrotrophic pathogenicity and sexual mating. This resource should facilitate the functional studies designed to better understand what makes these fungi such successful and persistent pathogens of agronomic crops.

This study focussed on two components of the forest ecosystem at a small spatial scale: coarse woody debris (CWD), defined as fallen dead wood ≥ 10 cm diameter and ≥ 1 m length, and the macrofungal assemblages found on wood, soil and litter in native forest at different times of regeneration since the natural disturbance of wildfire. The CWD on the forest floor and standing dead wood (stags) in four 50  50m plots (= 1 ha total area) with differing wildfire histories in a Eucalyptus obliqua dominated native wet sclerophyll forest in southern Tasmania, Australia, were quantified and mapped. The CWD volumes obtained were amongst the highest in the world. Analyses showed that although a plot size of 0.25 ha was too small to give an accurate measurement of volume, it was large enough to contain dead wood having attributes that reflected the stand structure resulting from wildfire disturbance. Therefore, a plot’s wildfire history can be deduced from the CWD and stags of a 0.25 ha plot. The substrates wood (dead wood and standing trees), soil and litter in each plot were surveyed for macrofungal fruit bodies at approximately fortnightly intervals for 14 months. A total of 849 macrofungal species was recorded from 1ha of native forest. Wood supported 410 species of which 295 were on CWD but not exclusively, i.e., a few species were found on CWD and soil or on CWD and litter. The majority of the remaining species on wood was supported by ‘other dead wood’ (a category containing dead wood that did not fit into CWD), which contained many species not in common with those on CWD. It was concluded that macrofungal species richness on CWD is not affected by decay class; however, length or surface area explained between 45–48% of the variation in species richness. Of the 495 species found fruiting on soil, 330 were known to be ectomycorrhizal and 165 were considered decomposers. In addition, 146 species of macrofungi were associated with litter. It was found, using temperature and rainfall data, that the appearance of fruit bodies is seasonal but not directly attributable to rainfall events. There was a better correlation using the indigenous peoples’ concept of three seasons than when using the four European-based seasons. In essence, each plot contained a distinctive mycota, reflecting its chronosequence history, site characteristics (e.g., soil type, soil pH) or microclimate. To maintain the macrofungal diversity associated with the differing plots, a mosaic of multi-aged stands in the managed forest landscape is needed to provide inoculum for the reestablishment of macrofungal communities in forests at different times of regeneration. In addition, reserves should be as large as possible (at least 1ha) to encompass the variability (due to site characteristics, vegetation type, etc.) in the forest landscape and

Understanding the nature of the relationship between viruses and their fungal hosts is critical in determining the ecological significance of mycoviruses and their potential usage as biological control agents. Two flexuous viruses belonging to the family Flexiviridae, Botrytis virus F (BVF) and Botrytis virus X (BVX), from Botrytis cinerea have previously been completely sequenced, providing the opportunity to examine their interaction with B. cinerea at molecular level. In addition, studying their impact on the virulence of Botrytis is also of great interest. In order to study the fungus/virus interaction four basic tools were developed: i) an efficient transfection protocol to introduce viruses into uninfected fungal isolates (ii) a transformation protocol to incorporate plasmid DNA into Botrytis, iii) a consistent and reliable real-time PCR detection method for BVF and BVX to study the effect of virus transfections, and iv) an immunoassay for BVX to visualize the virus distribution and movement within the mycelia and also between compatible fungal strains. These tools will enable the study of the relationship between the fungus and the mycoviruses at the cellular level.

Mycoviruses (fungal viruses) are reviewed with emphasis on plant pathogenic fungi. Based on the presence of virus-like particles and unencapsidated dsRNAs, mycoviruses are common in all major fungal groups. Over 80 mycovirus species have been officially recognized from ten virus families, but a paucity of nucleic acid sequence data makes assignment of many reported mycoviruses difficult. Although most of the particle types recognized to date are isometric, a variety of morphologies have been found and, additionally, many apparently unencapsidated dsRNAs have been reported. Until recently, most characterized mycoviruses have dsRNA genomes, but ssRNA mycoviruses now constitute about one-third of the total. Two hypotheses for the origin of mycoviruses of plant pathogens are discussed: the first that they are of unknown but ancient origin and have coevolved along with their hosts, the second that they have relatively recently moved from a fungal plant host into the fungus. Although mycoviruses are typically readily transmitted through asexual spores, transmission through sexual spores varies with the host fungus. Evidence for natural horizontal transmission has been found. Typically, mycoviruses are apparently symptomless (cryptic) but beneficial effects on the host fungus have been reported. Of more practical interest to plant pathologists are those viruses that confer a hypovirulent phenotype, and the scope for using such viruses as biocontrol agents is reviewed. New tools are being developed based on host genome studies that will help to address the intellectual challenge of understanding the fungal-virus interactions and the practical challenge of manipulating this relationship to develop novel biocontrol agents for important plant pathogens.

Hydrophobins are a remarkable class of small cysteine-rich proteins found exclusively in fungi. They self-assemble to form robust polymeric monolayers that are highly amphipathic and play numerous roles in fungal biology, such as in the formation and dispersal of aerial spores and in pathogenic and mutualistic interactions. The polymeric form can be reversibly disassembled and is able to reverse the wettability of a surface, leading to many proposals for nanotechnological applications over recent years. The surprising properties of hydrophobins and their potential for commercialization have led to substantial efforts to delineate their morphology and molecular structure. In this review, we summarize the progress that has been made using a variety of spectroscopic and microscopic approaches towards understanding the molecular mechanisms underlying hydrophobin structure.

The taxonomy and nomenclature of the fungus commonly referred to as Stropharia aurantiaca was investigated. Molecular analysis of the ribosomal RNA large subunit gene confirmed the exclusion of the species from Stropharia. The results from further molecular and morphological comparison with type species indicated that 'S. aurantiaca' is congeneric with a number of other taxa currently placed in Leratiomyces, Stropharia and Weraroa. These taxa are transferred to Leratiomyces and an emended diagnosis and brief discussion of this genus are provided.

Homologs of the gene encoding the hydrophobin EAS from Neurospora crassa have been identified both in the other conidial species of Neurospora (N. discreta, N. intermedia, N. sitophila, and N. tetrasperma) and selected aconidial species (N. africana, N. dodgei, N. lineolata, N. pannonica, and N. terricola). Southern blot analysis indicated the presence of a single gene in all species examined. EAS-like proteins were purified from the conidial species and each was shown to be the proteolytically processed gene-product of the corresponding eas homolog. While EAS-like proteins were not detected in the aconidial species, putative eas transcripts were detected in some isolates following RT-PCR and the aerial hyphae of these species were hydrophobic. DNA sequences of the coding region of the eas homologs were amplified by PCR and cloned and sequenced from all species except N. pannonica. Phylogenetic analysis of these sequences produced two clusters, the first comprising the conidiating species N. crassa, N. intermedia, N. sitophila, and N. tetrasperma forming a closely related group with N. discreta more distant, and the second comprising the aconidial species N. africana, N. dodgei, N. lineolata forming another closely related group with N. terricola more distant.