Neurospora crassa is a central organism in the history of twentieth-century genetics, biochemistry and molecular biology. Here, we report a high-quality draft sequence of the N. crassa genome. The approximately 40-megabase genome encodes about 10,000 protein-coding genes--more than twice as many as in the fission yeast Schizosaccharomyces pombe and only about 25% fewer than in the fruitfly Drosophila melanogaster. Analysis of the gene set yields insights into unexpected aspects of Neurospora biology including the identification of genes potentially associated with red light photobiology, genes implicated in secondary metabolism, and important differences in Ca2+ signalling as compared with plants and animals. Neurospora possesses the widest array of genome defence mechanisms known for any eukaryotic organism, including a process unique to fungi called repeat-induced point mutation (RIP). Genome analysis suggests that RIP has had a profound impact on genome evolution, greatly slowing the creation of new genes through genomic duplication and resulting in a genome with an unusually low proportion of closely related genes.

SUMMARY: We present an analysis of over 1,100 of the ∼10,000 predicted proteins encoded by the genome sequence of the filamentous fungusNeurospora crassa. Seven major areas ofNeurosporagenomics and biology are covered. First, the basic features of the genome, including the automated assembly, gene calls, and global gene analyses are summarized. The second section covers components of the centromere and kinetochore complexes, chromatin assembly and modification, and transcription and translation initiation factors. The third area discusses genome defense mechanisms, including repeat induced point mutation, quelling and meiotic silencing, and DNA repair and recombination. In the fourth section, topics relevant to metabolism and transport include extracellular digestion; membrane transporters; aspects of carbon, sulfur, nitrogen, and lipid metabolism; the mitochondrion and energy metabolism; the proteasome; and protein glycosylation, secretion, and endocytosis. Environmental sensing is the focus of the fifth section with a treatment of two-component systems; GTP-binding proteins; mitogen-activated protein, p21-activated, and germinal center kinases; calcium signaling; protein phosphatases; photobiology; circadian rhythms; and heat shock and stress responses. The sixth area of analysis is growth and development; it encompasses cell wall synthesis, proteins important for hyphal polarity, cytoskeletal components, the cyclin/cyclin-dependent kinase machinery, macroconidiation, meiosis, and the sexual cycle. The seventh section covers topics relevant to animal and plant pathogenesis and human disease. The results demonstrate that a large proportion ofNeurosporagenes do not have homologues in the yeastsSaccharomyces cerevisiaeandSchizosaccharomyces pombe. The group of unshared genes includes potential new targets for antifungals as well as loci implicated in human and plant physiology and disease.

Single molecule, real-time (SMRT) sequencing from Pacific Biosciences is increasingly used in many areas of biological research including de novo genome assembly, structural-variant identification, haplotype phasing, mRNA isoform discovery, and base-modification analyses. High-quality, public datasets of SMRT sequences can spur development of analytic tools that can accommodate unique characteristics of SMRT data (long read lengths, lack of GC or amplification bias, and a random error profile leading to high consensus accuracy). In this paper, we describe eight high-coverage SMRT sequence datasets from five organisms (Escherichia coli, Saccharomyces cerevisiae, Neurospora crassa, Arabidopsis thaliana, and Drosophila melanogaster) that have been publicly released to the general scientific community (NCBI Sequence Read Archive ID SRP040522). Data were generated using two sequencing chemistries (P4C2 and P5C3) on the PacBio RS II instrument. The datasets reported here can be used without restriction by the research community to generate whole-genome assemblies, test new algorithms, investigate genome structure and evolution, and identify base modifications in some of the most widely-studied model systems in biological research.

Pyrenophora teres, the causal agent of net blotch of barley (Hordeum vulgare L.), induces a combination of necrosis and extensive chlorosis in susceptible barley cultivars. Cell-free filtrates from both net and spot forms of P. teres; P. teres f. sp. teres, and P. teres f. sp. maculata were found to contain phytotoxic low molecular weight compounds (LMWCs) and proteinaceous metabolites which appear to be responsible for different components of the symptoms induced by the two forms of the pathogen in a susceptible cultivar of barley (cv. Sloop). Proteins induced only brown necrotic spots or lesions similar to those induced by the pathogens 72 h after inoculation. In contrast, LMWCs induced general chlorosis seen 240 h after inoculation but not the localized necrosis. Neither hydrolyzed or heat- or protease-treated proteinaceous metabolites induced the symptoms. This is the first report of the involvement of proteins produced by P. teres in symptom development during net blotch disease of barley.

Novel species of fungi described in this study include those from various countries as follows: Argentina, Septoria reinamora on leaf spots of Mutisia spinosa. Australia, Cortinarius albofolliculus on mossy soil, Cortinarius descensoriformis among leaf litter, Cortinarius kaki among leaf litter, Cortinarius lissosporus in leaf litter, Cortinarius malogranatus in leaf litter, Cortinarius meletlac on soil in mixed forest, Cortinarius sebosioides in long decayed wood litter, Helicogermslita australiensis as an endophyte from healthy leaves of Archontophoenix cunninghamiana, Puccinia clemensiorum on culms of Eleocharis ochrostachys, Puccinia geethae on leaves of Cyperus brevifolius, Puccinia marjaniae on leaves of Nymphoides indica, Puccinia scleriae-rugosae on leaves of Scleria rugosa. Brazil, Dactylaria calliandrae on living leaf of Calliandra tweediei, Mucor cerradoensis from soil, Musicillium palmae on living leaves of unidentified palm species, Neodendryphiella agapanthi from stalks of Agapanthus praecox, Parafusicladium riodejaneiroanum on living leaves of native bamboo, Parapenidiella melastomatis on living leaves of unidentified Melastomataceae, Pararamichloridium ouropretoense on living leaves of unidentified Poaceae, Pentagonomyces endophyticus (incl. Pentagonomyces gen. nov.) as endophytic from roots of Musa acuminata, Polyschema endophytica from healthy roots of coffee plant, Purimyces endophyticus as root endophyte of Cattleya locatellii, Ramularia rhododendri on living leaves of Rhododendron sp., Staphylotrichum soli from soil, Trichoderma sexdentis from leaves inside a nest of the leaf-cutting ant Atta sexdens rubropilosa, Wiesneriomyces soli from soil. France, Cosmospora nemaniae on dead or effete stromata of Nemania cf. colliculosa, Inocybe alnobetulae in subalpine green alder stands, Stylonectria hygrophila on dead twigs of Betula pubescens. Germany, Coniochaeta corticalis from bark humus, Coniochaeta fermentaria from fermentation residues from biogas plants, Coniochaeta fibricola from softwood fibres, Coniochaeta weberae from bark humus, Inocybe canicularis on calcareous to more acidic soil with conifers. Iceland, Inocybe islandica associated with Dryas octopetala. India, Vishniacozyma indica on dead twigs. Iran, Botryotrichum lycii on rotten leaf of Lycium depressum. Italy, Cuphophyllus dolomiticus among Salix retusa, Salix reticulata and Dryas octopetala, Inocybe subentolomospora on moss with the presence of Alnus incana, Populus nigra and Salix spp. Malaysia, Catenulostroma pellitae on leaf spots of Eucalyptus pellita. Mexico, Colletotrichum mexicanus from fruit of Persea americana cv. Hass. New Caledonia (France), Cortinarius caeloculus, Cortinarius luteigemellus and Cortinarius perpensus on soil under Nothofagus aequilateralis. New Zealand, Cytospora braithwaitei on branch of Malus domestica. Pakistan, Callistosporium khalidii on humus soil, Entoloma lilacinum on litter in conifer forest, Laccaria decolorans on litter in broad-leaved subtropical forest. Poland, Pseudoneoconiothyrium modrzynanum from resin of Larix decidua ssp. polonica, Tuberculiforma enigmatica isolated from sooty mould community on Quercus robur leaves. Portugal, Clavulus hemisphaericus (incl. Clavulus gen. nov.) on mossy slopes and under Laurus leaf litter, Entoloma daegae on sandy, granitic soil, Hygrocybe aurantiocitrina under laurel forest, Hygrocybe sanguineolutea gregarious in laurel forest, Hygrocybe vulcanica on mossy areas of laurel forest areas, Pachyphlodes algarvensis on sandy soil under Cistus salvifolius, Quercus suber and Pinus pinea. South Africa, Amycosphaerella podalyriae on leaf of Podalyria calyptrata, Erythrobasidium eucalypti from the gut of Gonipterus sp., Letendraea goniomae on leaves of Gonioma kamassi, Pezicula brabeji and Sphaerulina brabeji on twigs of Brabejum stellatifolium, Stachybotrys conicosiae on dead flower head of Conicosia elongata, Talaromyces ignescens from soil. Spain, Cortinarius phaeobrunneus on soil under Quercus ilex and Q. faginea, Inocybe pini-halepensis among grass and fallen leaves of Pinus halepensis, Inocybe subporcorum in sandy soils under Quercus ilex subsp. ballota and Pinus pinaster, Mycena morenoi on dead leaves of Betula pubescens and Salix atrocinerea, Pachyphlodes iberica on clayey and loamy soil under Quercus ilex and Quercus rotundifolia, Ramariopsis coronata in laurel forest. Switzerland, Inocybe minata in a bog on very wet acidic soil with Salix spp. and Betula spp. Thailand, Hypocrella khonsanitii on scale insects (Coccidae), Petchiella hymenopterorum on hymenopteran pupae in the nest (Hymenoptera). Trinidad and Tobago, Neodevriesia maravalensis from office swab. Türkiye, Russula anatolica under Quercus vulcanica. UK, Paracylindrosporium dactylorhizae (incl. Paracylindrosporium gen. nov.) on leaf spots of Dactylorhiza sp., Niesslia hepworthiae and Niesslia libertiae on living leaves of Libertia grandiflora. Ukraine, Lichenohendersonia cetrariae on thallus of terricolous Cetraria aculeata. USA, Atromagnispora indianensis (incl. Atromagnispora gen. nov.) on submerged wood in a freshwater stream, Cytospora michiganensis from utility room (settle plate), Exophiala aeris from air (settle plate), Hongoboletus americanus from mixed pine-hardwood forest, Lorrainsmithia pennsylvanica from bedroom, air, Superstratomyces massachusettsanus from lyse buffer. Vietnam, Aspergillus halopiscium on dry marine anchovy Stolephorus commersonnii. Morphological and culture characteristics are supported by DNA barcodes.