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Globally, tomato is the second most cultivated vegetable crop next to potato, preferentially grown in temperate climates. Processing tomatoes are generally produced in field conditions, in which soilborne pathogens have serious impacts on tomato yield and quality by causing diseases of the tomato root system. Major processing tomato-producing countries have documented soilborne diseases caused by a variety of pathogens including bacteria, fungi, nematodes, and oomycetes, which are of economic importance and may threaten food security. Recent field surveys in the Australian processing tomato industry showed that plant growth and yield were significantly affected by soilborne pathogens, especially Fusarium oxysporum and Pythium species. Globally, different management methods have been used to control diseases such as the use of resistant tomato cultivars, the application of fungicides, and biological control. Among these methods, biocontrol has received increasing attention due to its high efficiency, target-specificity, sustainability and public acceptance. The application of biocontrol is a mix of different strategies, such as applying antagonistic microorganisms to the field, and using the beneficial metabolites synthesized by these microorganisms. This review provides a broad review of the major soilborne fungal/oomycete pathogens of the field processing tomato industry affecting major global producers, the traditional and biological management practices for the control of the pathogens, and the various strategies of the biological control for tomato soilborne diseases. The advantages and disadvantages of the management strategies are discussed, and highlighted is the importance of biological control in managing the diseases in field processing tomatoes under the pressure of global climate change.

Powdery mildew fungi (Erysiphaceae) are widespread obligate biotrophic plant pathogens. Thus, applying genetic and omics approaches to study these fungi remains a major challenge, particularly for species with hemiendophytic mycelium. These belong to a distinct phylogenetic lineage within the family Erysiphaceae. To date, only a single draft genome assembly is available for this clade, obtained for Leveillula taurica. Here, we generated the first draft genome assemblies of Pleochaeta shiraiana and Phyllactinia moricola, two tree-parasitic powdery mildew species with hemiendophytic mycelium, representing two genera that have not yet been investigated with genomics tools. The Pleochaeta shiraiana assembly was 96,769,103 bp in length and consisted of 14,447 scaffolds, and the Phyllactinia moricola assembly was 180,382,532 bp in length on 45,569 scaffolds. Together with the draft genome of L. taurica, these resources will be pivotal for understanding the molecular basis of the lifestyle of these fungi, which is unique within the family Erysiphaceae.

Charcoal rot is an important soilborne disease caused by a range of Macrophomina species, which affects a broad range of commercially important crops worldwide. Even though Macrophomina species are fungal pathogens of substantial economic importance, their mechanism of pathogenicity and host spectrum are poorly understood. There is an urgent need to better understand the biology, epidemiology, and evolution of Macrophomina species, which, in turn, will aid in improving charcoal rot management strategies. Here, we present the first high-quality genome assembly and annotation of Macrophomina tecta strain BRIP 70781 associated with charcoal rot symptoms on sorghum. Hybrid assembly integrating long reads generated by Oxford Nanopore Technology and short Illumina paired-end reads resulted in 43 contigs with a total assembly size of ∼54 Mb, and an N50 of 3.4 Mb. In total, 12,926 protein-coding genes and 7,036 repeats were predicted. Genome comparisons detected accumulation of DNA transposons in Macrophomina species associated with sorghum. The first reference genome of M. tecta generated in this study will contribute to more comparative and population genomics studies of Macrophomina species.

Powdery mildew fungi (Erysiphaceae), common obligate biotrophic pathogens of many plants, including important agricultural and horticultural crops, represent a monophyletic lineage within the Ascomycota. Within the Erysiphaceae, molecular phylogenetic relationships and DNA-based species and genera delimitations were up to now mostly based on nuclear ribosomal DNA (nrDNA) phylogenies. This is the first comprehensive genome-scale phylogenetic analysis of this group using 751 single-copy orthologous sequences extracted from 24 selected powdery mildew genomes and 14 additional genomes from Helotiales, the fungal order that includes the Erysiphaceae. Representative genomes of all powdery mildew species with publicly available whole-genome sequencing (WGS) data that were of sufficient quality were included in the analyses. The 24 powdery mildew genomes included in the analysis represented 17 species belonging to eight out of 19 genera recognized within the Erysiphaceae. The epiphytic genera, all but one represented by multiple genomes, belonged each to distinct, well-supported lineages. Three hemiendophytic genera, each represented by a single genome, together formed the hemiendophytic lineage. Out of the 14 other taxa from the Helotiales, Arachnopeziza araneosa, a saprobic species, was the only taxon that grouped together with the 24 genome-sequenced powdery mildew fungi in a monophyletic clade. The close phylogenetic relationship between the Erysiphaceae and Arachnopeziza was revealed earlier by a phylogenomic study of the Leotiomycetes. Further analyses of powdery mildew and Arachnopeziza genomes may discover signatures of the evolutionary processes that have led to obligate biotrophy from a saprobic way of life. A separate phylogeny was produced using the 18S, 5.8S, and 28S nrDNA sequences of the same set of powdery mildew specimens and compared to the genome-scale phylogeny. The nrDNA phylogeny was largely congruent to the phylogeny produced using 751 orthologs. This

Epigenomics has become a significant research interest at a time when rapid environmental changes are occurring. Epigenetic mechanisms mainly result from systems like DNA methylation, histone modification, and RNA interference. Epigenetic mechanisms are gaining importance in classical genetics, developmental biology, molecular biology, cancer biology, epidemiology, and evolution. Epigenetic mechanisms play important role in the action and interaction of plant genes during development, and also have an impact on classical plant breeding programs, inclusive of novel variation, single plant heritability, hybrid vigor, plant-environment interactions, stress tolerance, and performance stability. The epigenetics and epigenomics may be significant for crop adaptability and pliability to ambient alterations, directing to the creation of stout climate-resilient elegant crop cultivars. In this review, we have summarized recent progress made in understanding the epigenetic mechanisms in plant responses to biotic and abiotic stresses and have also tried to provide the ways for the efficient utilization of epigenomic mechanisms in developing climate-resilient crop cultivars, especially in chickpea, and other legume crops.

Net blotches caused by Pyrenophora teres are important foliar fungal diseases of barley and result in significant yield losses of up to 40%. The two types of net blotch, net-form net blotch and spot-form net blotch, are caused by P. teres f. teres (Ptt) and P. teres f. maculata (Ptm), respectively. This study is the first to use a cross between Ptt and Ptm to identify quantitative trait loci (QTL) associated with virulence and leaf symptoms. A genetic map consisting of 1,965 Diversity Arrays Technology (DArT) markers was constructed using 351 progenies of the Ptt/Ptm cross. Eight barley cultivars showing differential reactions to the parental isolates were used to phenotype the hybrid progeny isolates. Five QTL associated with virulence and four QTL associated with leaf symptoms were identified across five linkage groups. Phenotypic variation explained by these QTL ranged from 6 to 16%. Further phenotyping of selected progeny isolates on 12 more barley cultivars revealed that three progeny isolates are moderately to highly virulent across these cultivars. The results of this study suggest that accumulation of QTL in hybrid isolates can result in enhanced virulence.

Dickeya species cause soft rots on many commercial crops. Here, we present the draft genomes of Dickeya oryzae (BRIP 64262) and Dickeya zeae (BRIP 64263) isolates causing soft rot on banana (Musa spp.) and pineapple (Ananas comosus) plants, respectively. This expands the range of available genomes from plant-pathogenic Dickeya species.

The early detection of pathogen infections in plants has become an important aspect of integrated disease management. Although previous research demonstrated the idea of applying digital technologies to monitor and predict plant health status, there is no effective system for detecting pathogen infection before symptomatology appears. This paper presents the use of a low-cost and portable electronic nose coupled with machine learning (ML) models for early disease detection. Several artificial neural network models were developed to predict plant physiological data and classify processing tomato plants and soil samples according to different levels of pathogen inoculum by using e-nose outputs as inputs, plant physiological data, and the level of infection as targets. Results showed that the pattern recognition models based on different infection levels had an overall accuracy of 94.4-96.8% for tomato plants and between 94.81% and 96.22% for soil samples. For the prediction of plant physiological parameters (photosynthesis, stomatal conductance, and transpiration) using regression models or tomato plants, the overall correlation coefficient was 0.97-0.99, with very significant slope values in the range 0.97-1. The performance of all models shows no signs of under or overfitting. It is hence proven accurate and valid to use the electronic nose coupled with ML modeling for effective early disease detection of processing tomatoes and could also be further implemented to monitor other abiotic and biotic stressors.

Net blotch diseases result in significant yield losses to barley industries worldwide. They occur as net-form and spot-form net blotch caused by Pyrenophora teres f. teres and P. teres f. maculata, respectively. Hybridization between the forms was proposed to be rare, but recent identifications of field hybrids has renewed interest in the frequency and mechanisms underlying hybridization. This study investigates the mating preference of P. teres f. teres, P. teres f. maculata, and laboratory-produced hybrids in vitro, using 24 different isolates and four different experimental setups. Two crosses in our study produced ascospores during two intervals separated by a 32- to 35-day period of no ascospore production. For these crosses, P. teres f. teres isolates mated with isolates of the same form during the early ascospore production interval, and produced hybrids during the later interval. P. teres f. maculata isolates did not mate with isolates of the same form, but instead hybridized with P. teres f. teres isolates. Analyses based on DArTseq markers confirmed that laboratory-produced hybrids, when given the choice to mate with both P. teres f. teres and P. teres f. maculata, mated with P. teres f. teres isolates. These results unravel a novel concept that P. teres f. teres seems to have a greater reproduction vigor than P. teres f. maculata, which could lead to increased prevalence of hybrid incidences in vivo.

The rapid and widespread evolution of fungicide resistance remains a challenge for crop disease management. The demethylation inhibitor (DMI) class of fungicides is a widely used chemistry for managing disease, but there has been a gradual decline in efficacy in many crop pathosystems. Reliance on DMI fungicides has increased resistance in populations of the plant pathogenic fungus Cercospora beticola worldwide. To better understand the genetic and evolutionary basis for DMI resistance in C. beticola, a genome-wide association study (GWAS) and selective sweep analysis were conducted for the first time in this species. We performed whole-genome resequencing of 190 C. beticola isolates infecting sugar beet (Beta vulgaris ssp. vulgaris). All isolates were phenotyped for sensitivity to the DMI tetraconazole. Intragenic markers on chromosomes 1, 4, and 9 were significantly associated with DMI fungicide resistance, including a polyketide synthase gene and the gene encoding the DMI target CbCYP51. Haplotype analysis of CbCYP51 identified a synonymous mutation (E170) and nonsynonymous mutations (L144F, I387M, and Y464S) associated with DMI resistance. Genome-wide scans of selection showed that several of the GWAS mutations for fungicide resistance resided in regions that have recently undergone a selective sweep. Using radial plate growth on selected media as a fitness proxy, we did not find a trade-off associated with DMI fungicide resistance. Taken together, we show that population genomic data from a crop pathogen can allow the identification of mutations conferring fungicide resistance and inform about their origins in the pathogen population.

Worldwide, most isolates of Macrophomina (Botryosphaeriaceae) have been attributed to the generalist phytopathogen M. phaseolina. Since 2014, three cryptic species of Macrophomina have been recognised by molecular methods. This study elucidates the taxonomy of Macrophomina species associated with broadacre and horticultural crops in Australia. A five-locus phylogenetic analysis of 80 isolates of Macrophomina from 28 plant species in Australia, combined with genealogical concordance phylogenetic species recognition and coalescent-based species delimitation approaches, found M. phaseolina, M. pseudophaseolina and supported the introduction of M. tecta sp. nov. Macrophomina phaseolina was the most frequently isolated (88%). Macrophomina pseudophaseolina is reported for the first time in Australia. Macrophomina tecta was isolated from stems of Sorghum bicolor and Vigna radiata with charcoal rot symptoms in New South Wales and Queensland. The potential for two or more Macrophomina species to co-infect the same host has implications for disease epidemiology and pathogen evolution. Future investigations into the distribution, biology, host range and population diversity of the new Macrophomina records are needed.

Powdery mildews are among the most important plant pathogens worldwide, which are often attacked in the field by mycoparasitic fungi belonging to the genus Ampelomyces. The taxonomy of the genus Ampelomyces is unresolved, but well-supported molecular operational taxonomic units were repeatedly defined suggesting that the genus may include at least four to seven species. Some Ampelomyces strains were commercialized as biocontrol agents of crop pathogenic powdery mildews. However, the genomic mechanisms underlying their mycoparasitism are still poorly understood. To date, the draft genome of a single Ampelomyces strain, designated as HMLAC 05119, has been released. We report a high-quality, annotated hybrid draft genome assembly of A. quisqualis strain BRIP 72107, which, based on phylogenetic analyses, is not conspecific with HMLAC 05119. The constructed genome is 40.38 Mb in size, consisting of 24 scaffolds with an N50 of 2.99 Mb and 96.2% completeness. Our analyses revealed "bipartite" structure of Ampelomyces genomes, where GC-balanced genomic regions are interspersed by longer or shorter stretches of AT-rich regions. This is also a hallmark of many plant pathogenic fungi and provides further evidence for evolutionary affinity of Ampelomyces species to plant pathogenic fungi. The high-quality genome and annotation produced here provide an important resource for future genomic studies of mycoparasitisim to decipher molecular mechanisms underlying biocontrol processes and natural tritrophic interactions.

This article is the 13th contribution in the Fungal Diversity Notes series, wherein 125 taxa from four phyla, ten classes, 31 orders, 69 families, 92 genera and three genera incertae sedis are treated, demonstrating worldwide and geographic distribution. Fungal taxa described and illustrated in the present study include three new genera, 69 new species, one new combination, one reference specimen and 51 new records on new hosts and new geographical distributions. Three new genera, Cylindrotorula (Torulaceae), Scolecoleotia (Leotiales genus incertae sedis) and Xenovaginatispora (Lindomycetaceae) are introduced based on distinct phylogenetic lineages and unique morphologies. Newly described species are Aspergillus lannaensis, Cercophora dulciaquae, Cladophialophora aquatica, Coprinellus punjabensis, Cortinarius alutarius, C. mammillatus, C. quercoflocculosus, Coryneum fagi, Cruentomycena uttarakhandina, Cryptocoryneum rosae, Cyathus uniperidiolus, Cylindrotorula indica, Diaporthe chamaeropicola, Didymella azollae, Diplodia alanphillipsii, Dothiora coronicola, Efibula rodriguezarmasiae, Erysiphe salicicola, Fusarium queenslandicum, Geastrum gorgonicum, G. hansagiense, Helicosporium sexualis, Helminthosporium chiangraiensis, Hongkongmyces kokensis, Hydrophilomyces hydraenae, Hygrocybe boertmannii, Hyphoderma australosetigerum, Hyphodontia yunnanensis, Khaleijomyces umikazeana, Laboulbenia divisa, Laboulbenia triarthronis, Laccaria populina, Lactarius pallidozonarius, Lepidosphaeria strobelii, Longipedicellata megafusiformis, Lophiotrema lincangensis, Marasmius benghalensis, M. jinfoshanensis, M. subtropicus, Mariannaea camelliae, Melanographium smilaxii, Microbotryum polycnemoides, Mimeomyces digitatus, Minutisphaera thailandensis, Mortierella solitaria, Mucor harpali, Nigrograna jinghongensis, Odontia huanrenensis, O. parvispina, Paraconiothyrium ajrekarii, Parafuscosporella niloticus, Phaeocytostroma yomensis, Phaeoisaria synnematicus, Phanerochaete hainanensis, Pleop

Novel species of fungi described in this study include those from various countries as follows: Antarctica, Cladosporium arenosum from marine sediment sand. Argentina, Kosmimatamyces alatophylus (incl. Kosmimatamyces gen. nov.) from soil. Australia, Aspergillus banksianus, Aspergillus kumbius, Aspergillus luteorubrus, Aspergillus malvicolor and Aspergillus nanangensis from soil, Erysiphe medicaginis from leaves of Medicago polymorpha, Hymenotorrendiella communis on leaf litter of Eucalyptus bicostata, Lactifluus albopicri and Lactifluus austropiperatus on soil, Macalpinomyces collinsiae on Eriachne benthamii, Marasmius vagus on soil, Microdochium dawsoniorum from leaves of Sporobolus natalensis, Neopestalotiopsis nebuloides from leaves of Sporobolus elongatus, Pestalotiopsis etonensis from leaves of Sporobolus jacquemontii, Phytophthora personensis from soil associated with dying Grevillea mccutcheonii. Brazil, Aspergillus oxumiae from soil, Calvatia baixaverdensis on soil, Geastrum calycicoriaceum on leaf litter, Greeneria kielmeyerae on leaf spots of Kielmeyera coriacea. Chile, Phytophthora aysenensis on collar rot and stem of Aristotelia chilensis. Croatia, Mollisia gibbospora on fallen branch of Fagus sylvatica. Czech Republic, Neosetophoma hnaniceana from Buxus sempervirens. Ecuador, Exophiala frigidotolerans from soil. Estonia, Elaphomyces bucholtzii in soil. France, Venturia paralias from leaves of Euphorbia paralias. India, Cortinarius balteatoindicus and Cortinarius ulkhagarhiensis on leaf litter. Indonesia, Hymenotorrendiella indonesiana on Eucalyptus urophylla leaf litter. Italy, Penicillium taurinense from indoor chestnut mill. Malaysia, Hemileucoglossum kelabitense on soil, Satchmopsis pini on dead needles of Pinus tecunumanii. Poland, Lecanicillium praecognitum on insects' frass. Portugal, Neodevriesia aestuarina from saline water. Republic of Korea, Gongronella namwonensis from freshwater. Russia, Candida pellucida from Exomias pellucidus, Heterocepha

Novel species of fungi described in this study include those from various countries as follows: Antarctica, Cladosporium arenosum from marine sediment sand. Argentina, Kosmimatamyces alatophylus (incl. Kosmimatamyces gen. nov.) from soil. Australia, Aspergillus banksianus, Aspergillus kumbius, Aspergillus luteorubrus, Aspergillus malvicolor and Aspergillus nanangensis from soil, Erysiphe medicaginis from leaves of Medicago polymorpha, Hymenotorrendiella communis on leaf litter of Eucalyptus bicostata, Lactifluus albopicri and Lactifluus austropiperatus on soil, Macalpinomyces collinsiae on Eriachne benthamii, Marasmius vagus on soil, Microdochium dawsoniorum from leaves of Sporobolus natalensis, Neopestalotiopsis nebuloides from leaves of Sporobolus elongatus, Pestalotiopsis etonensis from leaves of Sporobolus jacquemontii, Phytophthora personensis from soil associated with dying Grevillea mccutcheonii. Brazil, Aspergillus oxumiae from soil, Calvatia baixaverdensis on soil, Geastrum calycicoriaceum on leaf litter, Greeneria kielmeyerae on leaf spots of Kielmeyera coriacea. Chile, Phytophthora aysenensis on collar rot and stem of Aristotelia chilensis. Croatia, Mollisia gibbospora on fallen branch of Fagus sylvatica. Czech Republic, Neosetophoma hnaniceana from Buxus sempervirens. Ecuador, Exophiala frigidotolerans from soil. Estonia, Elaphomyces bucholtzii in soil. France, Venturia paralias from leaves of Euphorbia paralias. India, Cortinarius balteatoindicus and Cortinarius ulkhagarhiensis on leaf litter. Indonesia, Hymenotorrendiella indonesiana on Eucalyptus urophylla leaf litter. Italy, Penicillium taurinense from indoor chestnut mill. Malaysia, Hemileucoglossum kelabitense on soil, Satchmopsis pini on dead needles of Pinus tecunumanii. Poland, Lecanicillium praecognitum on insects’ frass. Portugal, Neodevriesia aestuarina from saline water. Republic of Korea, Gongronella namwonensis from freshwater. Russia, Candida pellucida from Exomias pellucidus, Heterocepha

Elsinoë fawcettii, a necrotrophic fungal pathogen, causes citrus scab on numerous citrus varieties around the world. Known pathotypes of E. fawcettii are based on host range; additionally, cryptic pathotypes have been reported and more novel pathotypes are thought to exist. E. fawcettii produces elsinochrome, a non-host selective toxin which contributes to virulence. However, the mechanisms involved in potential pathogen-host interactions occurring prior to the production of elsinochrome are unknown, yet the host-specificity observed among pathotypes suggests a reliance upon such mechanisms. In this study we have generated a whole genome sequencing project for E. fawcettii, producing an annotated draft assembly 26.01 Mb in size, with 10,080 predicted gene models and low (0.37%) coverage of transposable elements. A small proportion of the assembly showed evidence of AT-rich regions, potentially indicating genomic regions with increased plasticity. Using a variety of computational tools, we mined the E. fawcettii genome for potential virulence genes as candidates for future investigation. A total of 1,280 secreted proteins and 276 candidate effectors were predicted and compared to those of other necrotrophic (Botrytis cinerea, Parastagonospora nodorum, Pyrenophora tritici-repentis, Sclerotinia sclerotiorum and Zymoseptoria tritici), hemibiotrophic (Leptosphaeria maculans, Magnaporthe oryzae, Rhynchosporium commune and Verticillium dahliae) and biotrophic (Ustilago maydis) plant pathogens. Genomic and proteomic features of known fungal effectors were analysed and used to guide the prioritisation of 120 candidate effectors of E. fawcettii. Additionally, 378 carbohydrate-active enzymes were predicted and analysed for likely secretion and sequence similarity with known virulence genes. Furthermore, secondary metabolite prediction indicated nine additional genes potentially involved in the elsinochrome biosynthesis gene cluster than previously described. A further 21 secon

In contrast to Eurasia and North America, powdery mildews (Ascomycota, Erysiphales) are understudied in Australia. There are over 900 species known globally, with fewer than currently 60 recorded from Australia. Some of the Australian records are doubtful as the identifications were presumptive, being based on host plant-pathogen lists from overseas. The goal of this study was to provide the first comprehensive catalog of all powdery mildew species present in Australia. The project resulted in (i) an up-to-date list of all the taxa that have been identified in Australia based on published DNA barcode sequences prior to this study; (ii) the precise identification of 117 specimens freshly collected from across the country; and (iii) the precise identification of 30 herbarium specimens collected between 1975 and 2013. This study confirmed 42 species representing 10 genera, including two genera and 13 species recorded for the first time in Australia. In Eurasia and North America, the number of powdery mildew species is much higher. Phylogenetic analyses of powdery mildews collected from Acalypha spp. resulted in the transfer of Erysiphe acalyphae to Salmonomyces, a resurrected genus. Salmonomyces acalyphae comb. nov. represents a newly discovered lineage of the Erysiphales. Another taxonomic change is the transfer of Oidium ixodiae to Golovinomyces. Powdery mildew infections have been confirmed on 13 native Australian plant species in the genera Acacia, Acalypha, Cephalotus, Convolvulus, Eucalyptus, Hardenbergia, Ixodia, Jagera, Senecio, and Trema. Most of the causal agents were polyphagous species that infect many other host plants both overseas and in Australia. All powdery mildews infecting native plants in Australia were phylogenetically closely related to species known overseas. The data indicate that Australia is a continent without native powdery mildews, and most, if not all, species have been introduced since the European colonization of the continent.

Novel species of fungi described in this study include those from various countries as follows: Antarctica, Cladosporium arenosum from marine sediment sand. Argentina, Kosmimatamyces alatophylus (incl. Kosmimatamyces gen. nov.) from soil. Australia, Aspergillus banksianus, Aspergillus kumbius, Aspergillus luteorubrus, Aspergillus malvicolor and Aspergillus nanangensis from soil, Erysiphe medicaginis from leaves of Medicago polymorpha, Hymenotorrendiella communis on leaf litter of Eucalyptus bicostata, Lactifluus albopicri and Lactifluus austropiperatus on soil, Macalpinomyces collinsiae on Eriachne benthamii, Marasmius vagus on soil, Microdochium dawsoniorum from leaves of Sporobolus natalensis, Neopestalotiopsis nebuloides from leaves of Sporobolus elongatus, Pestalotiopsis etonensis from leaves of Sporobolus jacquemontii, Phytophthora personensis from soil associated with dying Grevillea mccutcheonii. Brazil, Aspergillus oxumiae from soil, Calvatia baixaverdensis on soil, Geastrum calycicoriaceum on leaf litter, Greeneria kielmeyerae on leaf spots of Kielmeyera coriacea. Chile, Phytophthora aysenensis on collar rot and stem of Aristotelia chilensis. Croatia, Mollisia gibbospora on fallen branch of Fagus sylvatica. Czech Republic, Neosetophoma hnaniceana from Buxus sempervirens. Ecuador, Exophiala frigidotolerans from soil. Estonia, Elaphomyces bucholtzii in soil. France, Venturia paralias from leaves of Euphorbia paralias. India, Cortinarius balteatoindicus and Cortinarius ulkhagarhiensis on leaf litter. Indonesia, Hymenotorrendiella indonesiana on Eucalyptus urophylla leaf litter. Italy, Penicillium taurinense from indoor chestnut mill. Malaysia, Hemileucoglossum kelabitense on soil, Satchmopsis pini on dead needles of Pinus tecunumanii. Poland, Lecanicillium praecognitum on insects' frass. Portugal, Neodevriesia aestuarina from saline water. Republic of Korea, Gongronella namwonensis from freshwater. Russia, Candida pellucida from Exomias pellucidus, Heterocepha

Novel species of fungi described in this study include those from various countries as follows: Antarctica,Apenidiella antarctica from permafrost, Cladosporium fildesense from an unidentified marine sponge. Argentina,Geastrum wrightii on humus in mixed forest. Australia, Golovinomyces glandulariae on Glandularia aristigera,Neoanungitea eucalyptorum on leaves of Eucalyptus grandis, Teratosphaeria corymbiicola on leaves of Corymbiaficifolia, Xylaria eucalypti on leaves of Eucalyptus radiata. Brazil, Bovista psammophila on soil, Fusarium awaxy onrotten stalks of Zea mays, Geastrum lanuginosum on leaf litter covered soil, Hermetothecium mikaniae-micranthae(incl. Hermetothecium gen. nov.) on Mikania micrantha, Penicillium reconvexovelosoi in soil, Stagonosporopsis vannacciifrom pod of Glycine max. British Virgin Isles, Lactifluus guanensis on soil. Canada, Sorocybe oblongisporaon resin of Picea rubens. Chile, Colletotrichum roseum on leaves of Lapageria rosea. China, Setophoma cavernafrom carbonatite in Karst cave. Colombia, Lareunionomyces eucalypticola on leaves of Eucalyptus grandis. CostaRica, Psathyrella pivae on wood. Cyprus, Clavulina iris on calcareous substrate. France, Chromosera ambiguaand Clavulina iris var. occidentalis on soil. French West Indies, Helminthosphaeria hispidissima on dead wood.Guatemala, Talaromyces guatemalensis in soil. Malaysia, Neotracylla pini (incl. Tracyllales ord. nov. and Neotracyllagen. nov.) and Vermiculariopsiella pini on needles of Pinus tecunumanii. New Zealand, Neoconiothyriumviticola on stems of Vitis vinifera, Parafenestella pittospori on Pittosporum tenuifolium, Pilidium novae-zelandiaeon Phoenix sp. Pakistan, Russula quercus-floribundae on forest floor. Portugal, Trichoderma aestuarinum fromsaline water. Russia, Pluteus liliputianus on fallen branch of deciduous tree, Pluteus spurius on decaying deciduous wood or soil. South Africa, Alloconiothyrium encephalarti, Phyllosticta encephalarticola and Neothyrostromaencephalarti (

This paper represents the third contribution in the Genera of Phytopathogenic Fungi (GOPHY) series. The series provides morphological descriptions, information about the pathology, distribution, hosts and disease symptoms for the treated genera, as well as primary and secondary DNA barcodes for the currently accepted species included in these. This third paper in the GOPHY series treats 21 genera of phytopathogenic fungi and their relatives including: Allophoma, Alternaria, Brunneosphaerella, Elsinoe, Exserohilum, Neosetophoma, Neostagonospora, Nothophoma, Parastagonospora, Phaeosphaeriopsis, Pleiocarpon, Pyrenophora, Ramichloridium, Seifertia, Seiridium, Septoriella, Setophoma, Stagonosporopsis, Stemphylium, Tubakia and Zasmidium. This study includes three new genera, 42 new species, 23 new combinations, four new names, and three typifications of older names.

The bacterium Curtobacterium flaccumfaciens pv. flaccumfaciens (Cff) is the cause of tan spot (in some regions known as ‘wilt’) on mungbean (Vigna radiata) and other legumes worldwide. The pathogen was first reported in mungbean paddocks in Queensland in 1984, and subsequently in New South Wales in 1986, causing yield losses of up to 25% in hot and dry seasons. No chemical control is available, and disease management relies on pathogen exclusion, through the use of clean seed, and deployment of moderately susceptible varieties. Breeding programs are currently working to incorporate better resistance into new mungbean varieties. The success of breeding programs depends on a thorough understanding of the genetic diversity and evolution of the pathogen population(s). This project was designed to elucidate the genotypic diversity of Cff population(s) and investigate sources of inoculum that contribute to tan spot epidemics in the northern grains region (Queensland and northern New South Wales). Whole genome re-sequencing of 100 Cff isolates detected moderate genotypic diversity, with a narrower genetic background compared to the global Cff population. One highly adapted clonal lineage was found to dominate the population with a frequency of 45%. This study showcases how population genomics studies can be used to test hypotheses relating to disease epidemiology and provide useful information for resistance breeding programs. The results provide insights on Cff population structure and epidemiology, and have direct application for breeding programs by providing a set of Cff isolates that represent the genetic diversity of the pathogen population(s) in the northern grains region.

Novel species of fungi described in this study include those from various countries as follows: Antarctica, Apenidiella antarctica from permafrost, Cladosporium fildesense from an unidentified marine sponge. Argentina, Geastrum wrightii on humus in mixed forest. Australia, Golovinomyces glandulariae on Glandularia aristigera, Neoanungitea eucalyptorum on leaves of Eucalyptus grandis, Teratosphaeria corymbiicola on leaves of Corymbia ficifolia, Xylaria eucalypti on leaves of Eucalyptus radiata. Brazil, Bovista psammophila on soil, Fusarium awaxy on rotten stalks of Zea mays, Geastrum lanuginosum on leaf litter covered soil, Hermetothecium mikaniae-micranthae (incl. Hermetothecium gen. nov.) on Mikania micrantha, Penicillium reconvexovelosoi in soil, Stagonosporopsis vannaccii from pod of Glycine max. British Virgin Isles, Lactifluus guanensis on soil. Canada, Sorocybe oblongispora on resin of Picea rubens. Chile, Colletotrichum roseum on leaves of Lapageria rosea. China, Setophoma caverna from carbonatite in Karst cave. Colombia, Lareunionomyces eucalypticola on leaves of Eucalyptus grandis. Costa Rica, Psathyrella pivae on wood. Cyprus, Clavulina iris on calcareous substrate. France, Chromosera ambigua and Clavulina iris var. occidentalis on soil. French West Indies, Helminthosphaeria hispidissima on dead wood. Guatemala, Talaromyces guatemalensis in soil. Malaysia, Neotracylla pini (incl. Tracyllales ord. nov. and Neotracylla gen. nov.) and Vermiculariopsiella pini on needles of Pinus tecunumanii. New Zealand, Neoconiothyrium viticola on stems of Vitis vinifera

Net form of net blotch caused by Pyrenophora teres f. teres (Ptt) is a major foliar disease of barley (Hordeum vulgare) worldwide. Knowledge of the evolution of P. teres f. teres pathogen populations is important for development of durable host-plant resistance. This study was conducted to investigate changes in genetic structure of a Ptt population within a barley field during three cropping years. The susceptible barley cultivar Henley was inoculated with Ptt isolate NB050. Leaf samples were collected during the year 2013–2015 and 174 single spore Ptt isolates stored. Genotyping using Diversity Arrays Technology markers identified that 25% of isolates were clones of the inoculated isolate and 75% of isolates were multi-locus genotypes (MLGs) differing from the original inoculated genotype. The novel genotypes likely originated from a combination of wind-borne spores from neighbouring fields, infected seed and sexual recombination in the field. The rapid change in the genotypic composition of the Ptt population in this study suggests adaptive potential of novel genotypes and demonstrates the need for barley breeders to use multiple sources of host-plant resistance to safeguard against resistance being overcome. This article is protected by copyright. All rights reserved.

Novel species of fungi described in this study include those from various countries as follows: Antarctica, Apenidiella antarctica from permafrost, Cladosporium fildesense from an unidentified marine sponge. Argentina, Geastrum wrightii on humus in mixed forest. Australia, Golovinomyces glandulariae on Glandularia aristigera, Neoanungitea eucalyptorum on leaves of Eucalyptus grandis, Teratosphaeria corymbiicola on leaves of Corymbia ficifolia, Xylaria eucalypti on leaves of Eucalyptus radiata. Brazil, Bovista psammophila on soil, Fusarium awaxy on rotten stalks of Zea mays, Geastrum lanuginosum on leaf litter covered soil, Hermetothecium mikaniae-micranthae (incl. Hermetothecium gen. nov.) on Mikania micrantha, Penicillium reconvexovelosoi in soil, Stagonosporopsis vannaccii from pod of Glycine max. British Virgin Isles, Lactifluus guanensis on soil. Canada, Sorocybe oblongispora on resin of Picea rubens. Chile, Colletotrichum roseum on leaves of Lapageria rosea. China, Setophoma caverna from carbonatite in Karst cave. Colombia, Lareunionomyces eucalypticola on leaves of Eucalyptus grandis. Costa Rica, Psathyrella pivae on wood. Cyprus, Clavulina iris on calcareous substrate. France, Chromosera ambigua and Clavulina iris var. occidentalis on soil. French West Indies, Helminthosphaeria hispidissima on dead wood. Guatemala, Talaromyces guatemalensis in soil. Malaysia, Neotracylla pini (incl. Tracyllales ord. nov. and Neotracylla gen. nov.) and Vermiculariopsiella pini on needles of Pinus tecunumanii. New Zealand, Neoconiothyrium viticola on stems of Vitis vinifera, Parafenestella pittospori on Pittosporum tenuifolium, Pilidium novae-zelandiae on Phoenix sp. Pakistan, Russula quercus-floribundae on forest floor. Portugal, Trichoderma aestuarinum from saline water. Russia, Pluteus liliputianus on fallen branch of deciduous tree, Pluteus spurius on decaying deciduous wood or soil. South Africa, Alloconiothyrium encephalarti, Phyllosticta encephalarticola and Neothyrostro

This paper represents the third contribution in the Genera of Phytopathogenic Fungi (GOPHY) series. The series provides morphological descriptions, information about the pathology, distribution, hosts and disease symptoms for the treated genera, as well as primary and secondary DNA barcodes for the currently accepted species included in these. This third paper in the GOPHY series treats 21 genera of phytopathogenic fungi and their relatives including: Allophoma, Alternaria, Brunneosphaerella, Elsinoe, Exserohilum, Neosetophoma, Neostagonospora, Nothophoma, Parastagonospora, Phaeosphaeriopsis, Pleiocarpon, Pyrenophora, Ramichloridium, Seifertia, Seiridium, Septoriella, Setophoma, Stagonosporopsis, Stemphylium, Tubakia and Zasmidium. This study includes three new genera, 42 new species, 23 new combinations, four new names, and three typifications of older names.

© 2019 Westerdijk Fungal Biodiversity Institute This paper represents the third contribution in the Genera of Phytopathogenic Fungi (GOPHY) series. The series provides morphological descriptions, information about the pathology, distribution, hosts and disease symptoms for the treated genera, as well as primary and secondary DNA barcodes for the currently accepted species included in these. This third paper in the GOPHY series treats 21 genera of phytopathogenic fungi and their relatives including: Allophoma, Alternaria, Brunneosphaerella, Elsinoe, Exserohilum, Neosetophoma, Neostagonospora, Nothophoma, Parastagonospora, Phaeosphaeriopsis, Pleiocarpon, Pyrenophora, Ramichloridium, Seifertia, Seiridium, Septoriella, Setophoma, Stagonosporopsis, Stemphylium, Tubakia and Zasmidium. This study includes three new genera, 42 new species, 23 new combinations, four new names, and three typifications of older names.

Draft genomes of the species Annulohypoxylon stygium, Aspergillus mulundensis, Berkeleyomyces basicola (syn. Thielaviopsis basicola), Ceratocystis smalleyi, two Cercospora beticola strains, Coleophoma cylindrospora, Fusarium fracticaudum, Phialophora cf. hyalina and Morchella septimelata are presented. Both mating types (MAT1-1 and MAT1-2) of Cercospora beticola are included. Two strains of Coleophoma cylindrospora that produce sulfated homotyrosine echinocandin variants, FR209602, FR220897 and FR220899 are presented. The sequencing of Aspergillus mulundensis, Coleophoma cylindrospora and Phialophora cf. hyalina has enabled mapping of the gene clusters encoding the chemical diversity from the echinocandin pathways, providing data that reveals the complexity of secondary metabolism in these different species. Overall these genomes provide a valuable resource for understanding the molecular processes underlying pathogenicity (in some cases), biology and toxin production of these economically important fungi.

Cercospora leaf spot (CLS), caused by Cercospora beticola, is a major disease of Beta vulgaris worldwide. No sexual stage is known for C. beticola but in its asexual form it overwinters on infected plant debris as pseudostromata, and travels short distances by rain splash-dispersed conidiospores. Cercospora beticola infects a broad range of host species and may be seedborne. The relative contribution of these inoculum sources to CLS epidemics on table beet is not well understood. Pathogen isolates collected from table beet, Swiss chard and common lambsquarters in mixed-cropping farms and monoculture fields in New York and Hawaii, USA, were genotyped (n = 600) using 12 microsatellite markers. All isolates from CLS symptoms on lambsquarters were identified as C. chenopodii. Sympatric populations of C. beticola derived from Swiss chard and table beet were not genetically differentiated. Results suggested that local (within field) inoculum sources may be responsible for the initiation of CLS epidemics in mixed-cropping farms, whereas external sources of inoculum may be contributing to CLS epidemics in the monoculture fields in New York. New multiplex PCR assays were developed for mating-type determination for C. beticola. Implications of these findings for disease management are discussed.

Ray blight, a destructive disease of Asteraceae worldwide, is caused by three morphologically similar but phylogenetically distinct species; Stagonosporopsis chrysanthemi, S. inoxydabilis and S. tanaceti. Stagonosporopsis chrysanthemi has been reported as a specific pathogen of chrysanthemum while S. inoxydabilis has been found associated with various Asteraceae. Stagonosporopsis tanaceti has only been reported in Australia, causing substantial crop loss on pyrethrum. All three species were shown to infect and cause disease on in vitro grown pyrethrum plants, hence, S. chrysanthemi and S. inoxydabilis may pose a significant biosecurity threat to the Australian pyrethrum industry. All these Stagonosporopsis species are also Level 2 quarantine pathogens in Europe. Rapid and accurate detection and differentiation of these species is a priority for ray blight management in Australia and in Europe. Accordingly, three species-specific PCR-based assays, targeted to the intergenic spacer of the nuclear ribosomal DNA, were developed. The specificity of each assay was confirmed against 21 Stagonosporopsis spp. as well as 14 pathogenic and saprophytic fungal species commonly found in association with pyrethrum in Australia. The primers were highly sensitive and specific to the target species, detecting down to 4Â fg of genomic DNA. These primers were further used in a multiplex PCR to differentiate the presence of the three Stagonosporopsis spp. based on variable sized amplicons in a single reaction.

The genomes of Chrysoporthe austroafricana, Diplodia scrobiculata, Fusarium nygami, Leptographium lundbergii, Limonomyces culmigenus, Stagonosporopsis tanaceti, and Thielaviopsis punctulata are presented in this genome announcement. These seven genomes are from endophytes, plant pathogens and economically important fungal species. The genome sizes range from 26.6 Mb in the case of Leptographium lundbergii to 44 Mb for Chrysoporthe austroafricana. The availability of these genome data will provide opportunities to resolve longstanding questions regarding the taxonomy of species in these genera, and may contribute to our understanding of the lifestyles through comparative studies with closely related organisms.

Many fungi are pathogenic on plants and cause significant damage in agriculture and forestry. They are also part of the natural ecosystem and may play a role in regulating plant numbers/density. Morphological identification and analysis of plant pathogenic fungi, while important, is often hampered by the scarcity of discriminatory taxonomic characters and the endophytic or inconspicuous nature of these fungi. Molecular (DNA sequence) data for plant pathogenic fungi have emerged as key information for diagnostic and classification studies, although hampered in part by non-standard laboratory practices and analytical methods. To facilitate current and future research, this study provides phylogenetic synopses for 25 groups of plant pathogenic fungi in the Ascomycota, Basidiomycota, Mucormycotina (Fungi), and Oomycota, using recent molecular data, up-to-date names, and the latest taxonomic insights. Lineage-specific laboratory protocols together with advice on their application, as well as general observations, are also provided. We hope to maintain updated backbone trees of these fungal lineages over time and to publish them jointly as new data emerge. Researchers of plant pathogenic fungi not covered by the present study are invited to join this future effort. Bipolaris, Botryosphaeriaceae, Botryosphaeria, Botrytis, Choanephora, Colletotrichum, Curvularia, Diaporthe, Diplodia, Dothiorella, Fusarium, Gilbertella, Lasiodiplodia, Mucor, Neofusicoccum, Pestalotiopsis, Phyllosticta, Phytophthora, Puccinia, Pyrenophora, Pythium, Rhizopus, Stagonosporopsis, Ustilago and Verticillium are dealt with in this paper.

This study attempts to estimate the potential impacts of climate change on the rice production in Malaysia. The crop model ORYZA2000 was used to simulate rice yield of MR 219 variety in eight granary areas of Malaysia from 1999-2007. The model predicted a reduction in rice yield of 0.36 t ha -1 under the scenario of an increase in temperature by 2°C and at the current CO 2 level of 383 ppm. With the reduction in rice yield, the economic loss to the Malaysian rice industry was estimated at RM162.531 million per year. Under the scenario of increase of CO 2 concentration from 383 to 574 ppm and with 2°C rise in temperature, it can be predicted that there will also be a decline in rice yield by 0.69 t ha -1 and consequently the economic loss will be at RM299.145 million per year for the rice industry. With the above potential impacts, some adaptation and mitigation strategies to overcome the adverse effects of climate change on rice production were recommended.