Staff Publications

Staff Publications

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    'Staff publications' is the digital repository of Wageningen University & Research

    'Staff publications' contains references to publications authored by Wageningen University staff from 1976 onward.

    Publications authored by the staff of the Research Institutes are available from 1995 onwards.

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    Experimental demonstration of the benefits of somatic fusion and the consequences for allorecognition
    Bastiaans, E. ; Debets, A.J.M. ; Aanen, D.K. - \ 2015
    Evolution 69 (2015)4. - ISSN 0014-3820 - p. 1091 - 1099.
    vegetative incompatibility - neurospora-crassa - heterokaryon incompatibility - natural-populations - filamentous fungi - recognition - evolution - selection - genetics - cooperation
    Allorecognition, the ability to distinguish “self” from “nonself” based on allelic differences at allorecognition loci, is common in all domains of life. Allorecognition restricts the opportunities for social parasitism, and is therefore crucial for the evolution of cooperation. However, the maintenance of allorecognition diversity provides a paradox. If allorecognition is costly relative to cooperation, common alleles will be favored. Thus, the cost of allorecognition may reduce the genetic variation upon which allorecognition crucially relies, a prediction now known as “Crozier's paradox.” We establish the relative costs of allorecognition, and their consequences for the short-term evolution of recognition labels theoretically predicted by Crozier. We use fusion among colonies of the fungus Neurospora crassa, regulated by highly variable allorecognition genes, as an experimental model system. We demonstrate that fusion among colonies is mutually beneficial, relative to absence of fusion upon allorecognition. This benefit is due not only to absence of mutual antagonism, which occurs upon allorecognition, but also to an increase in colony size per se. We then experimentally demonstrate that the benefit of fusion selects against allorecognition diversity, as predicted by Crozier. We discuss what maintains allorecognition diversity
    Natural Variation of Heterokaryon Incompatibility Gene het-c in Podospora anserina Reveals Diversifying Selection
    Bastiaans, E. ; Debets, A.J.M. ; Aanen, D.K. ; Diepeningen, A.D. van; Saupe, S.J. ; Paoletti, M. - \ 2014
    Molecular Biology and Evolution 31 (2014)4. - ISSN 0737-4038 - p. 962 - 974.
    plant immune-system - glycolipid transfer protein - chestnut blight fungus - amino-acid sites - vegetative incompatibility - neurospora-crassa - cell-death - cryphonectria-parasitica - membrane interaction - filamentous fungi
    In filamentous fungi, allorecognition takes the form of heterokaryon incompatibility, a cell death reaction triggered when genetically distinct hyphae fuse. Heterokaryon incompatibility is controlled by specific loci termed het-loci. In this article, we analyzed the natural variation in one such fungal allorecognition determinant, the het-c heterokaryon incompatibility locus of the filamentous ascomycete Podospora anserina. The het-c locus determines an allogenic incompatibility reaction together with two unlinked loci termed het-d and het-e. Each het-c allele is incompatible with a specific subset of the het-d and het-e alleles. We analyzed variability at the het-c locus in a population of 110 individuals, and in additional isolates from various localities. We identified a total of 11 het-c alleles, which define 7 distinct incompatibility specificity classes in combination with the known het-d and het-e alleles. We found that the het-c allorecognition gene of P. anserina is under diversifying selection. We find a highly unequal allele distribution of het-c in the population, which contrasts with the more balanced distribution of functional groups of het-c based on their allorecognition function. One explanation for the observed het-c diversity in the population is its function in allorecognition. However, alleles that are most efficient in allorecognition are rare. An alternative and not exclusive explanation for the observed diversity is that het-c is involved in pathogen recognition. In Arabidopsis thaliana, a homolog of het-c is a pathogen effector target, supporting this hypothesis. We hypothesize that the het-c diversity in P. anserina results from both its functions in pathogen-defense, and allorecognition
    Selection against somatic parasitism can maintain allorecognition in fungi
    Czaran, T. ; Hoekstra, R.F. ; Aanen, D.K. - \ 2014
    Fungal Genetics and Biology 73 (2014). - ISSN 1087-1845 - p. 128 - 137.
    vegetative incompatibility - neurospora-crassa - kin discrimination - filamentous fungi - self-recognition - botryllus-schlosseri - marine-invertebrates - ascomycete fungi - cell parasitism - genetic-control
    Fusion between multicellular individuals is possible in many organisms with modular, indeterminate growth, such as marine invertebrates and fungi. Although fusion may provide various benefits, fusion usually is restricted to close relatives by allorecognition, also called heterokaryon or somatic incompatibility in fungi. A possible selective explanation for allorecognition is protection against somatic parasites. Such mutants contribute less to colony functions but more to reproduction. However, previous models testing this idea have failed to explain the high diversity of allorecognition alleles in nature. These models did not, however, consider the possible role of spatial structure. We model the joint evolution of allorecognition and somatic parasitism in a multicellular organism resembling an asexual ascomycete fungus in a spatially explicit simulation. In a 1000-by-1000 grid, neighbouring individuals can fuse, but only if they have the same allotype. Fusion with a parasitic individual decreases the total reproductive output of the fused individuals, but the parasite compensates for this individual-level fitness reduction by a disproportional share of the offspring. Allorecognition prevents the invasion of somatic parasites, and vice versa, mutation towards somatic parasitism provides the selective conditions for extensive allorecognition diversity. On the one hand, if allorecognition diversity did not build up fast enough, somatic parasites went to fixation; conversely, once parasites had gone to fixation no allorecognition diversity built up. On the other hand, the mere threat of parasitism could select for high allorecognition diversity, preventing invasion of somatic parasites. Moderate population viscosity combined with weak global dispersal was optimal for the joint evolution of allorecognition and protection against parasitism. Our results are consistent with the widespread occurrence of allorecognition in fungi and the low degree of somatic parasitism. We discuss the implications of our results for allorecognition in other organism groups.
    Transcriptome sequencing uncovers the Avr5 avirulence gene of the tomato leaf mould pathogen Cladosporium fulvum
    Mesarich, C.H. ; Griffiths, S.A. ; Burgt, A. van der; Okmen, B. ; Beenen, H. ; Etalo, D.W. ; Joosten, M.H.A.J. ; Wit, P.J.G.M. de - \ 2014
    Molecular Plant-Microbe Interactions 27 (2014)8. - ISSN 0894-0282 - p. 846 - 857.
    fungal effector proteins - cf-2-dependent disease resistance - aspergillus-nidulans - secreted proteins - candidate effectors - neurospora-crassa - allelic variation - virulence factor - signal peptides - plant-pathogens
    The Cf-5 gene of tomato confers resistance to strains of the fungal pathogen Cladosporium fulvum carrying the avirulence gene Avr5. Although Cf-5 has been cloned, Avr5 has remained elusive. We report the cloning of Avr5 using a combined bioinformatic and transcriptome sequencing approach. RNA-Seq was performed on the sequenced race 0 strain (0WU; carrying Avr5), as well as a race 5 strain (IPO 1979; lacking a functional Avr5 gene) during infection of susceptible tomato. Forty-four in planta–induced C. fulvum candidate effector (CfCE) genes of 0WU were identified that putatively encode a secreted, small cysteine-rich protein. An expressed transcript sequence comparison between strains revealed two polymorphic CfCE genes in IPO 1979. One of these conferred avirulence to IPO 1979 on Cf-5 tomato following complementation with the corresponding 0WU allele, confirming identification of Avr5. Complementation also led to increased fungal biomass during infection of susceptible tomato, signifying a role for Avr5 in virulence. Seven of eight race 5 strains investigated escape Cf-5-mediated resistance through deletion of the Avr5 gene. Avr5 is heavily flanked by repetitive elements, suggesting that repeat instability, in combination with Cf-5-mediated selection pressure, has led to the emergence of race 5 strains deleted for the Avr5 gene.
    Actin dynamics in Phytophthora infestans; rapidly reorganizing cables and immobile, long-lived plaques
    Meijer, H.J.G. ; Hua, C. ; Kots, K. ; Ketelaar, T. ; Govers, F. - \ 2014
    Cellular Microbiology 16 (2014)6. - ISSN 1462-5814 - p. 948 - 961.
    oomycete achlya-bisexualis - f-actin - hyphal growth - tip growth - quantitative-analysis - aspergillus-nidulans - arabidopsis-thaliana - neurospora-crassa - saprolegnia-ferax - patch movement
    The actin cytoskeleton is a dynamic but well organized intracellular framework that is essential for proper functioning of eukaryotic cells. Here, we use the actin binding peptide Lifeact to investigate the in vivo actin cytoskeleton dynamics in the oomycete plant pathogen Phytophthora infestans. Lifeact-eGFP labelled thick and thin actin bundles and actin filament plaques allowing visualization of actin dynamics. All actin structures in the hyphae were cortically localized. In growing hyphae actin filament cables were axially oriented in the sub-apical region whereas in the extreme apex in growing hyphae, waves of fine F-actin polymerization were observed. Upon growth termination, actin filament plaques appeared in the hyphal tip. The distance between a hyphal tip and the first actin filament plaque correlated strongly with hyphal growth velocity. The actin filament plaques were nearly immobile with average lifetimes exceeding one hour, relatively long when compared to the lifetime of actin patches known in other eukaryotes. Plaque assembly required ~30 seconds while disassembly was accomplished in ~10 sec. Remarkably, plaque disassembly was not accompanied with internalization and the formation of endocytic vesicles. These findings suggest that the functions of actin plaques in oomycetes differ from those of actin patches present in other organisms.
    MITEs in the promoters of effector genes allow prediction of novel virulence genes in Fusarium oxysporum
    Schmidt, S.M. ; Houterman, P.M. ; Schreiver, I. ; Ma, L. ; Amyotte, S. ; Chellappan, B. ; Boeren, S. ; Takken, F.L.W. ; Rep, M. - \ 2013
    BMC Genomics 14 (2013). - ISSN 1471-2164 - 21 p.
    f-sp lycopersici - eukaryotic transposable elements - pathogenic fungi - xylem sap - ltr-retrotransposon - genome organization - neurospora-crassa - formae-speciales - dna transposons - infected tomato
    Background The plant-pathogenic fungus Fusarium oxysporum f.sp.lycopersici (Fol) has accessory, lineage-specific (LS) chromosomes that can be transferred horizontally between strains. A single LS chromosome in the Fol4287 reference strain harbors all known Fol effector genes. Transfer of this pathogenicity chromosome confers virulence to a previously non-pathogenic recipient strain. We hypothesize that expression and evolution of effector genes is influenced by their genomic context. Results To gain a better understanding of the genomic context of the effector genes, we manually curated the annotated genes on the pathogenicity chromosome and identified and classified transposable elements. Both retro- and DNA transposons are present with no particular overrepresented class. Retrotransposons appear evenly distributed over the chromosome, while DNA transposons tend to concentrate in large chromosomal subregions. In general, genes on the pathogenicity chromosome are dispersed within the repeat landscape. Effector genes are present within subregions enriched for DNA transposons. A miniature Impala (mimp) is always present in their promoters. Although promoter deletion studies of two effector gene loci did not reveal a direct function of the mimp for gene expression, we were able to use proximity to a mimp as a criterion to identify new effector gene candidates. Through xylem sap proteomics we confirmed that several of these candidates encode proteins secreted during plant infection. Conclusions Effector genes in Fol reside in characteristic subregions on a pathogenicity chromosome. Their genomic context allowed us to develop a method for the successful identification of novel effector genes. Since our approach is not based on effector gene similarity, but on unique genomic features, it can easily be extended to identify effector genes in Fo strains with different host specificities.
    Genome-wide survey of repetitive DNA elements in the button mushroom Agaricus bisporus
    Foulongne-Oriol, M. ; Murat, C. ; Castanera, R. ; Ramírez, L. ; Sonnenberg, A.S.M. - \ 2013
    Fungal Genetics and Biology 55 (2013). - ISSN 1087-1845 - p. 6 - 21.
    simple sequence repeats - rice blast fungus - magnaporthe-oryzae - neurospora-crassa - chromosome ends - transposable elements - molecular markers - variable-number - evolution - microsatellites
    Repetitive DNA elements are ubiquitous constituents of eukaryotic genomes. The biological roles of these repetitive elements, supposed to impact genome organization and evolution, are not completely elucidated yet. The availability of whole genome sequence offers the opportunity to draw a picture of the genome- wide distribution of these elements and provide insights into potential mechanisms of genome plasticity. The present study uses in silico approaches to describe tandem repeats and transposable elements distribution in the genome of the button mushroom, Agaricus bisporus. Transposable elements comprised 12.43% of the assembled genome, and 66% of them were found clustered in the centromeric or telomeric regions. Methylation of retrotransposon has been demonstrated. A total of 1996 mini-, 4062 micro-, and 37 satellites motifs were identified. The microsatellites appeared widely and evenly spread over the whole genome sequence, whereas the minisatellites were not randomly distributed. Indeed, minisatellites were found to be associated with transposable elements clusters. Telomeres exhibited a specific sequence with a TnAGn signature. A comparison between the two available genome sequences of A. bisporus was also performed and sheds light on the genetic divergence between the two varieties. Beyond their role in genome structure, repeats provide a virtually endless source of molecular markers useful for genetic studies in this cultivated species.
    Sexual selection in fungi
    Nieuwenhuis, B.P.S. ; Aanen, D.K. - \ 2012
    Journal of Evolutionary Biology 25 (2012)12. - ISSN 1010-061X - p. 2397 - 2411.
    mating-type genes - schizophyllum-commune - neurospora-crassa - mate choice - saccharomyces-cerevisiae - filamentous ascomycete - cryphonectria-parasitica - cryptococcus-neoformans - microbotryum-violaceum - aspergillus-nidulans
    The significance of sexual selection, the component of natural selection associated with variation in mating success, is well established for the evolution of animals and plants, but not for the evolution of fungi. Even though fungi do not have separate sexes, most filamentous fungi mate in a hermaphroditic fashion, with distinct sex roles, that is, investment in large gametes (female role) and fertilization by other small gametes (male role). Fungi compete to fertilize, analogous to male-male competition, whereas they can be selective when being fertilized, analogous to female choice. Mating types, which determine genetic compatibility among fungal gametes, are important for sexual selection in two respects. First, genes at the mating-type loci regulate different aspects of mating and thus can be subject to sexual selection. Second, for sexual selection, not only the two sexes (or sex roles) but also the mating types can form the classes, the members of which compete for access to members of the other class. This is significant if mating-type gene products are costly, thus signalling genetic quality according to Zahavi's handicap principle. We propose that sexual selection explains various fungal characteristics such as the observed high redundancy of pheromones at the B mating-type locus of Agaricomycotina, the occurrence of multiple types of spores in Ascomycotina or the strong pheromone signalling in yeasts. Furthermore, we argue that fungi are good model systems to experimentally study fundamental aspects of sexual selection, due to their fast generation times and high diversity of life cycles and mating systems.
    Diverse Lifestyles and Strategies of Plant Pathogenesis Encoded in the Genomes of Eighteen Dothideomycetes Fungi
    Ohm, R.A. ; Feau, N. ; Henrissat, B. ; Schoch, C.L. ; Horwitz, B.A. ; Barry, K.W. ; Condon, B.J. ; Copeland, A.C. ; Dhillon, B. ; Glaser, F. ; Hesse, C.N. ; Kosti, I. ; LaButti, K. ; Lindquist, E.A. ; Lucas, S. ; Salamov, A.A. ; Bradshaw, R.E. ; Ciuffetti, L. ; Hamelin, R.C. ; Kema, G.H.J. ; Lawrence, C. ; Scott, J.A. ; Spatafora, J.W. ; Turgeon, B.G. ; Wit, P.J.G.M. de; Zhong, S. ; Goodwin, S.B. ; Grigoriev, I.V. - \ 2012
    PLoS Pathogens 8 (2012)12. - ISSN 1553-7366
    ascomycete leptosphaeria-maculans - nonribosomal peptide synthetases - induced point mutations - polyketide synthase - cochliobolus-heterostrophus - colletotrichum-graminicola - fusarium-graminearum - stagonospora-nodorum - phylogenetic trees - neurospora-crassa
    The class Dothideomycetes is one of the largest groups of fungi with a high level of ecological diversity including many plant pathogens infecting a broad range of hosts. Here, we compare genome features of 18 members of this class, including 6 necrotrophs, 9 (hemi)biotrophs and 3 saprotrophs, to analyze genome structure, evolution, and the diverse strategies of pathogenesis. The Dothideomycetes most likely evolved from a common ancestor more than 280 million years ago. The 18 genome sequences differ dramatically in size due to variation in repetitive content, but show much less variation in number of (core) genes. Gene order appears to have been rearranged mostly within chromosomal boundaries by multiple inversions, in extant genomes frequently demarcated by adjacent simple repeats. Several Dothideomycetes contain one or more gene-poor, transposable element (TE)-rich putatively dispensable chromosomes of unknown function. The 18 Dothideomycetes offer an extensive catalogue of genes involved in cellulose degradation, proteolysis, secondary metabolism, and cysteine-rich small secreted proteins. Ancestors of the two major orders of plant pathogens in the Dothideomycetes, the Capnodiales and Pleosporales, may have had different modes of pathogenesis, with the former having fewer of these genes than the latter. Many of these genes are enriched in proximity to transposable elements, suggesting faster evolution because of the effects of repeat induced point (RIP) mutations. A syntenic block of genes, including oxidoreductases, is conserved in most Dothideomycetes and upregulated during infection in L. maculans, suggesting a possible function in response to oxidative stress.
    High prevalence of a fungal prion
    Debets, A.J.M. ; Dalstra, H.J.P. ; Slakhorst, S.M. ; Koopmanschap-Memelink, A.B. ; Hoekstra, R.F. ; Saupe, S.J. - \ 2012
    Proceedings of the National Academy of Sciences of the United States of America 109 (2012)26. - ISSN 0027-8424 - p. 10432 - 10437.
    podospora-anserina - vegetative incompatibility - het-s - heterokaryon incompatibility - neurospora-crassa - meiotic drive - yeast prion - mechanism - diseases - genes
    Prions are infectious proteins that cause fatal diseases in mammals. Prions have also been found in fungi, but studies on their role in nature are scarce. The proposed biological function of fungal prions is debated and varies from detrimental to benign or even beneficial. [Het-s] is a prion of the fungus Podospora anserina. The het-s locus exists as two antagonistic alleles that constitute an allorecognition system: the het-s allele encoding the protein variant capable of prion formation and the het-S allele encoding a protein variant that cannot form a prion. We document here that het-s alleles, capable of prion formation, are nearly twice as frequent as het-S alleles in a natural population of 112 individuals. Then, we report a 92% prevalence of [Het-s] prion infection among the het-s isolates and find evidence of the role of the [Het-s]/het-S allorecognition system on the incidence of infection by a deleterious senescence plasmid. We explain the het-s/het-S allele ratios by the existence of two selective forces operating at different levels. We propose that during the somatic stage, the role of [Het-s]/HET-S in allorecognition leads to frequency-dependent selection for which an equilibrated frequency would be optimal. However, in the sexual cycle, the [Het-s] prion causes meiotic drive favoring the het-s allele. Our findings indicate that [Het-s] is a selected and, therefore, widespread prion whose activity as selfish genetic element is counteracted by balancing selection for allorecognition polymorphism
    Comparative Genomics Yields Insights into Niche Adaptation of Plant Vascular Wilt Pathogens
    Klosterman, S.J. ; Subbarao, K.V. ; Kang, S. ; Veronese, P. ; Gold, S.E. ; Thomma, B.P.H.J. ; Chen, Z.J. ; Henrissat, B. ; Lee, Y.H. ; Park, J. ; Garcia-Pedrajas, M.D. ; Barbara, D.J. ; Anchieta, A. ; Jonge, R. de; Santhanam, P. ; Maruthachalam, K. ; Atallah, Z. ; Amyotte, S.G. ; Paz, Z. ; Inderbitzin, P. ; Hayes, R.J. ; Heiman, D.I. ; Young, S. ; Zeng, Q. ; Engels, R. ; Galagan, J. ; Cuomo, C. ; Dobinson, K.F. ; Ma, L.J. - \ 2011
    PLoS Pathogens 7 (2011)7. - ISSN 1553-7366 - 19 p.
    induced point mutation - cladosporium-fulvum - verticillium wilt - fusarium-oxysporum - nep1-like proteins - maximum-likelihood - transcription factor - neurospora-crassa - virulence factor - effector ecp6
    The vascular wilt fungi Verticillium dahliae and V. albo-atrum infect over 200 plant species, causing billions of dollars in annual crop losses. The characteristic wilt symptoms are a result of colonization and proliferation of the pathogens in the xylem vessels, which undergo fluctuations in osmolarity. To gain insights into the mechanisms that confer the organisms' pathogenicity and enable them to proliferate in the unique ecological niche of the plant vascular system, we sequenced the genomes of V. dahliae and V. albo-atrum and compared them to each other, and to the genome of Fusarium oxysporum, another fungal wilt pathogen. Our analyses identified a set of proteins that are shared among all three wilt pathogens, and present in few other fungal species. One of these is a homolog of a bacterial glucosyltransferase that synthesizes virulence-related osmoregulated periplasmic glucans in bacteria. Pathogenicity tests of the corresponding V. dahliae glucosyltransferase gene deletion mutants indicate that the gene is required for full virulence in the Australian tobacco species Nicotiana benthamiana. Compared to other fungi, the two sequenced Verticillium genomes encode more pectin-degrading enzymes and other carbohydrate-active enzymes, suggesting an extraordinary capacity to degrade plant pectin barricades. The high level of synteny between the two Verticillium assemblies highlighted four flexible genomic islands in V. dahliae that are enriched for transposable elements, and contain duplicated genes and genes that are important in signaling/transcriptional regulation and iron/lipid metabolism. Coupled with an enhanced capacity to degrade plant materials, these genomic islands may contribute to the expanded genetic diversity and virulence of V. dahliae, the primary causal agent of Verticillium wilts. Significantly, our study reveals insights into the genetic mechanisms of niche adaptation of fungal wilt pathogens, advances our understanding of the evolution and development of their pathogenesis, and sheds light on potential avenues for the development of novel disease management strategies to combat destructive wilt diseases.
    Genome analysis of the necrotrophic fungal pathogens Sclerotinia sclerotiorum and Botrytis cinerea
    Amselem, J. ; Cuomo, C.A. ; Kan, J.A.L. van; Viaud, M. ; Benito, E.P. ; Couloux, A. ; Coutinho, P.M. ; Vries, R.P. de; Dyer, P.S. ; Fillinger, S. ; Fournier, E. ; Gout, L. ; Hahn, M. ; Kohn, L. ; Lapalu, N. ; Plummer, K.M. ; Pradier, J.M. ; Quévillon, E. ; Sharon, A. ; Simon, A. ; Have, A. ten; Tudzynski, B. ; Tudzynski, P. ; Wincker, P. ; Andrew, M. ; Anthouard, V. ; Beever, R.E. ; Beffa, R. ; Benoit, I. ; Bouzid, O. ; Brault, B. ; Chen, Z. ; Choquer, M. ; Collemare, J. ; Cotton, P. ; Danchin, E.G. ; Silva, C. Da; Gautier, A. ; Giraud, C. ; Giraud, T. ; Gonzalez, C. ; Grossetete, S. ; Güldener, U. ; Henrissat, B. ; Howlett, B.J. ; Kodira, C. ; Kretschmer, M. ; Lappartient, A. ; Leroch, M. ; Levis, C. ; Mauceli, E. ; Neuvéglise, C. ; Oeser, B. ; Pearson, M. ; Poulain, J. ; Poussereau, N. ; Quesneville, H. ; Rascle, C. ; Schumacher, J. ; Ségurens, B. ; Sexton, A. ; Silva, E. ; Sirven, C. ; Soanes, D.M. ; Talbot, N.J. ; Templeton, M. ; Yandava, C. ; Yarden, O. ; Zeng, Q. ; Rollins, J.A. ; Lebrun, M.H. ; Dickman, M. - \ 2011
    Plos Genetics 7 (2011)8. - ISSN 1553-7404 - 27 p.
    rice blast fungus - development-specific protein - expressed sequence tags - programmed cell-death - mating-type loci - oxalic-acid - neurospora-crassa - arabidopsis-thaliana - secondary metabolism - molecular phylogeny
    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
    EBR1, a novel Zn2Cys6 transcription factor, affects virulence and apical dominance of hyphal tip in Fusarium graminearum
    Zhao, C. ; Waalwijk, C. ; Wit, P.J.G.M. de; Lee, T.A.J. van der; Tang, D. - \ 2011
    Molecular Plant-Microbe Interactions 24 (2011)12. - ISSN 0894-0282 - p. 1407 - 1418.
    multiple sequence alignment - aspergillus-nidulans - gibberella-zeae - saccharomyces-cerevisiae - aflatoxin biosynthesis - binuclear cluster - neurospora-crassa - reduced virulence - female fertility - plant infection
    Zn2Cys6 transcription factors are unique to fungi and have been reported to be involved in different regulatory functions. Here, we characterized EBR1 (enhanced branching 1), a novel Zn2Cys6 transcription factor of Fusarium graminearum. Knocking out EBR1 in F. graminearum PH-1 caused reduction of both radial growth and virulence. The conidia of knock-out strain PH-1¿ebr1 germinated faster than those of wild-type PH-1, but the conidiation of the mutant was significantly reduced. Detailed analysis showed that the reduced radial growth might be due to reduced apical dominance of the hyphal tip, leading to increased hyphal branching. Inoculation assays on wheat heads with a green fluorescent protein (GFP)-labeled PH-1¿ebr1 mutant showed that it was unable to penetrate the rachis of the spikelets. Protein fusion with GFP showed that EBR1 is localized in the nucleus of both conidia and hyphae. Knocking out the orthologous gene FOXG_05408 in F. oxysporum f. sp. lycopersici caused a much weaker phenotype than the PH-1¿ebr1 mutant, which may be due to the presence of multiple orthologous genes in this fungus. Transformation of FOXG_05408 into PH-1¿ebr1 restored the mutant phenotype. Similar to EBR1, FOXG_05408 is localized in the nucleus of F. oxysporum f. sp. lycopersici. Possible functions of EBR1 and its relation with other fungal transcription factors are discussed
    A novel mode of chromosomal evolution peculiar to filamentous Ascomycete fungi
    Hane, J.K. ; Rouxel, T. ; Howlett, B.J. ; Kema, G.H.J. ; Goodwin, S.B. ; Oliver, R.P. - \ 2011
    Genome Biology 12 (2011). - ISSN 1474-7596 - 16 p.
    pathogen stagonospora-nodorum - genome sequence - medicago-truncatula - neurospora-crassa - gene-transfer - wheat - phylogeny - synteny - conservation - organization
    Background - Gene loss, inversions, translocations, and other chromosomal rearrangements vary among species, resulting in different rates of structural genome evolution. Major chromosomal rearrangements are rare in most eukaryotes, giving large regions with the same genes in the same order and orientation across species. These regions of macrosynteny have been very useful for locating homologous genes in different species and to guide the assembly of genome sequences. Previous analyses in the fungi have indicated that macrosynteny is rare; instead, comparisons across species show no synteny or only microsyntenic regions encompassing usually five or fewer genes. To test the hypothesis that chromosomal evolution is different in the fungi compared to other eukaryotes, synteny was compared between species of the major fungal taxa. Results - These analyses identified a novel form of evolution in which genes are conserved within homologous chromosomes, but with randomized orders and orientations. This mode of evolution is designated mesosynteny, to differentiate it from micro- and macrosynteny seen in other organisms. Mesosynteny is an alternative evolutionary pathway very different from macrosyntenic conservation. Surprisingly, mesosynteny was not found in all fungal groups. Instead, mesosynteny appears to be restricted to filamentous Ascomycetes and was most striking between species in the Dothideomycetes. Conclusions - The existence of mesosynteny between relatively distantly related Ascomycetes could be explained by a high frequency of chromosomal inversions, but translocations must be extremely rare. The mechanism for this phenomenon is not known, but presumably involves generation of frequent inversions during meiosis
    Dual transcriptional profiling of a bacterial/fungal confrontation: Collimonas fungivorans versus Aspergillus niger
    Mela, F. ; Fritsche, K. de; Boer, W. de; Veen, J.A. van; Graaff, L.H. de; Berg, M. van den; Leveau, J.H.J. - \ 2011
    ISME Journal 5 (2011)9. - ISSN 1751-7362 - p. 1494 - 1504.
    probe level data - gene-expression - corynebacterium-glutamicum - bacillus-subtilis - ribosomal-proteins - neurospora-crassa - fungal hyphae - fusaric acid - citric-acid - growth
    Interactions between bacteria and fungi cover a wide range of incentives, mechanisms and outcomes. The genus Collimonas consists of soil bacteria that are known for their antifungal activity and ability to grow at the expense of living fungi. In non-contact confrontation assays with the fungus Aspergillus niger, Collimonas fungivorans showed accumulation of biomass concomitant with inhibition of hyphal spread. Through microarray analysis of bacterial and fungal mRNA from the confrontation arena, we gained new insights into the mechanisms underlying the fungistatic effect and mycophagous phenotype of collimonads. Collimonas responded to the fungus by activating genes for the utilization of fungal-derived compounds and for production of a putative antifungal compound. In A. niger, differentially expressed genes included those involved in lipid and cell wall metabolism and cell defense, which correlated well with the hyphal deformations that were observed microscopically. Transcriptional profiles revealed distress in both partners: downregulation of ribosomal proteins and upregulation of mobile genetic elements in the bacteria and expression of endoplasmic reticulum stress and conidia-related genes in the fungus. Both partners experienced nitrogen shortage in each other's presence. Overall, our results indicate that the Collimonas/Aspergillus interaction is a complex interplay between trophism, antibiosis and competition for nutrients
    Comparative genome sequence analysis underscores mycoparasitism as the ancestral life style of Trichoderma
    Kubichek, C.P. ; Tamayo Ramos, J.A. - \ 2011
    Genome Biology 12 (2011)4. - ISSN 1474-7596 - 15 p.
    induced systemic resistance - plant-root colonization - cell-wall - aspergillus-nidulans - eukaryotic genomes - hypocrea-jecorina - neurospora-crassa - hydrophobin gene - pathogenic fungi - dna-sequences
    Background: Mycoparasitism, a lifestyle where one fungus is parasitic on another fungus, has special relevance when the prey is a plant pathogen, providing a strategy for biological control of pests for plant protection. Probably, the most studied biocontrol agents are species of the genus Hypocrea/Trichoderma. Results: Here we report an analysis of the genome sequences of the two biocontrol species Trichoderma atroviride (teleomorph Hypocrea atroviridis) and Trichoderma virens (formerly Gliocladium virens, teleomorph Hypocrea virens), and a comparison with Trichoderma reesei (teleomorph Hypocrea jecorina). These three Trichoderma species display a remarkable conservation of gene order (78 to 96%), and a lack of active mobile elements probably due to repeat-induced point mutation. Several gene families are expanded in the two mycoparasitic species relative to T. reesei or other ascomycetes, and are overrepresented in non-syntenic genome regions. A phylogenetic analysis shows that T. reesei and T. virens are derived relative to T. atroviride. The mycoparasitism-specific genes thus arose in a common Trichoderma ancestor but were subsequently lost in T. reesei. Conclusions: The data offer a better understanding of mycoparasitism, and thus enforce the development of improved biocontrol strains for efficient and environmentally friendly protection of plants
    Horizontal gene and chromosome transfer in plantpathogenic fungi affecting host range
    Mehrabi, R. ; Bahkali, A.H. ; Abd-Elsalam, K.A. ; M'Barek, S. Ben; Mirzadi Gohari, A. ; Karimi Jashini, M. ; Stergiopoulos, I. ; Kema, G.H.J. ; Wit, P.J.G.M. de - \ 2011
    FEMS Microbiology Reviews 35 (2011)3. - ISSN 0168-6445 - p. 542 - 554.
    conidial anastomosis tubes - japanese pear pathotype - polyketide t-toxin - alternaria-alternata - nectria-haematococca - cochliobolus-heterostrophus - fusarium-oxysporum - neurospora-crassa - hyphal fusion - colletotrichum-gloeosporioides
    Plant pathogenic fungi adapt quickly to changing environments including overcoming plant disease resistance genes. This is usually achieved by mutations in single effector genes of the pathogens, enabling them to avoid recognition by the host plant. In addition, horizontal gene transfer (HGT) and horizontal chromosome transfer (HCT) provide a means for pathogens to broaden their host range. Recently, several reports have appeared in the literature on HGT, HCT and hybridization between plant pathogenic fungi that affect their host range, including species of Stagonospora/Pyrenophora, Fusarium and Alternaria. Evidence is given that HGT of the ToxA gene from Stagonospora nodorum to Pyrenophora tritici-repentis enabled the latter fungus to cause a serious disease in wheat. A nonpathogenic Fusarium species can become pathogenic on tomato by HCT of a pathogenicity chromosome from Fusarium oxysporum f.sp lycopersici, a wellknown pathogen of tomato. Similarly, Alternaria species can broaden their host range by HCT of a single chromosome carrying a cluster of genes encoding hostspecific toxins that enabled them to become pathogenic on new hosts such as apple, Japanese pear, strawberry and tomato, respectively. The mechanisms HGT and HCT and their impact on potential emergence of fungal plant pathogens adapted to new host plants will be discussed
    Calorie restriction in the filamentous fungus Podospora anserina
    Diepeningen, A.D. van; Slakhorst-Wandel, S.M. ; Koopmanschap-Memelink, A.B. ; Ikink, G.J. ; Debets, A.J.M. ; Hoekstra, R.F. - \ 2010
    Experimental Gerontology 45 (2010)7-8. - ISSN 0531-5565 - p. 516 - 524.
    life-span extension - mitochondrial-dna rearrangements - fluorescent pigment lipofuscin - dietary restriction - linear plasmids - excision-amplification - neurospora-crassa - cancer incidence - senescence - pal2-1
    Calorie restriction (CR) is a regimen of reduced food intake that, although the underlying mechanism is unknown, in many organisms leads to life span extension. Podospora anserina is one of the few known ageing filamentous fungi and the ageing process and concomitant degeneration of mitochondria have been well-studied. CR in P. anserina increases not only life span but also forestalls the ageing-related decline in fertility. Here we review what is known about CR in P. anserina and about possibly involved mechanisms like enhanced mitochondrial stability, reduced production of reactive oxygen species and changes in the OXPHOS machinery. Additionally, we present new microscopic data on mitochondrial dynamics under rich nutritional and CR conditions at different points in life. Lines that have grown under severe CR for more than 50× the normal life span, show no accumulation of age-related damage, though fecundity is reduced in some of these lines. Finally, we discuss the possible role of CR in P. anserina in nature and the effect of CR at different points in life
    The het-c heterokaryon incompatibility gene in Aspergillus niger
    Diepeningen, A.D. van; Pal, K. ; Lee, T. ; Hoekstra, R.F. ; Debets, A.J.M. - \ 2009
    Mycological Research 113 (2009)2. - ISSN 0953-7562 - p. 222 - 229.
    programmed cell-death - neurospora-crassa - vegetative incompatibility - filamentous fungi - podospora-anserina - mating-type - locus - nidulans - sequence - protein
    Heterokaryon incompatibility among Aspergillus niger strains is a widespread phenomenon that is observed as the inability to form stable heterokaryons. The genetic basis of heterokaryon incompatibility reactions is well established in some sexual filamentous fungi but largely unknown in presumed asexual species, such as A. niger. To test whether the genes that determine heterokaryon incompatibility in Neurospora crassa, such as het-c, vib-1 and pin-c, have a similar function in A. niger, we performed a short in silico search for homologues of these genes in the A. niger and several related genomes. For het-c, pin-c and vib-1 we did indeed identify putative orthologues. We then screened a genetically diverse worldwide collection of incompatible black Aspergilli for polymorphisms in the het-c orthologue. No size variation was observed in the variable het-c indel region that determines the specificity in N. crassa. Sequence comparison showed only minor variation in the number of glutamine coding triplets. However, introduction of one of the three N. crassa alleles (het-c2) in A. niger by transformation resulted in an abortive phenotype, reminiscent of the heterokaryon incompatibility in N. crassa. We conclude that although the genes required are present and the het-c homologue could potentially function as a heterokaryon incompatibility gene, het-c has no direct function in heterokaryon incompatibility in A. niger because the necessary allelic variation is absent
    Ga and Gß Proteins Regulate the Cyclic AMP Pathway That Is Required for Development and Pathogenicity of the Phytopathogen Mycosphaerella graminicola
    Mehrabi, A. ; M'Barek, S. Ben; Lee, T.A.J. van der; Waalwijk, C. ; Wit, P.J.G.M. de; Kema, G.H.J. - \ 2009
    Eukaryotic Cell 8 (2009)7. - ISSN 1535-9778 - p. 1001 - 1013.
    map kinase gene - neurospora-crassa - adenylyl-cyclase - magnaporthe-grisea - fusarium-oxysporum - gamma-subunits - hyphal fusion - colletotrichum-lagenarium - cryphonectria-parasitica - saccharomyces-cerevisiae
    We identified and functionally characterized genes encoding three G alpha proteins and one G beta protein in the dimorphic fungal wheat pathogen Mycosphaerella graminicola, which we designated MgGpa1, MgGpa2, MgGpa3, and MgGpb1, respectively. Sequence comparisons and phylogenetic analyses showed that MgGPA1 and MgGPA3 are most related to the mammalian G alpha(i) and G alpha(s) families, respectively, whereas MgGPA2 is not related to either of these families. On potato dextrose agar (PDA) and in yeast glucose broth (YGB), MgGpa1 mutants produced significantly longer spores than those of the wild type (WT), and these developed into unique fluffy mycelia in the latter medium, indicating that this gene negatively controls filamentation. MgGpa3 mutants showed more pronounced yeast-like growth accompanied with hampered filamentation and secreted a dark-brown pigment into YGB. Germ tubes emerging from spores of MgGpb1 mutants were wavy on water agar and showed a nested type of growth on PDA that was due to hampered filamentation, numerous cell fusions, and increased anastomosis. Intracellular cyclic AMP (cAMP) levels of MgGpb1 and MgGpa3 mutants were decreased, indicating that both genes positively regulate the cAMP pathway, which was confirmed because the WT phenotype was restored by adding cAMP to these mutant cultures. The cAMP levels in MgGpa1 mutants and the WT were not significantly different, suggesting that this gene might be dispensable for cAMP regulation. In planta assays showed that mutants of MgGpa1, MgGpa3, and MgGpb1 are strongly reduced in pathogenicity. We concluded that the heterotrimeric G proteins encoded by MgGpa3 and MgGpb1 regulate the cAMP pathway that is required for development and pathogenicity in M. graminicola.
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