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.

    Full text documents are added when available. The database is updated daily and currently holds about 240,000 items, of which 72,000 in open access.

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    Data from: Combinations of Spok genes create multiple meiotic drivers in Podospora
    Vogan, Aaron A. ; Ament-Velásquez, S.L. ; Granger-Farbos, Alexandra ; Svedberg, Jesper ; Bastiaans, Eric ; Debets, Fons ; Coustou, Virginie ; Yvanne, Hélène ; Clavé, Corinne ; Saupe, Sven J. ; Johannesson, Hanna - \ 2019
    podospora anserina - meiotic drive - genomics - gene drive - Podospora pauciseta - Spore-killing - Spok - genomic conflict
    Meiotic drive is the preferential transmission of a particular allele during sexual reproduction. The phenomenon is observed as spore killing in multiple fungi. In natural populations of Podospora anserina, seven spore killer types (Psks) have been identified through classical genetic analyses. Here we show that the Spok gene-family underlies the Psks. The combination of Spok genes at different chromosomal locations defines the spore killer types and creates a killing hierarchy within the same population. We identify two novel Spok homologs located within a large (74-167 kbp) region (the Spok block) that resides in different chromosomal locations in given strains. We confirm that the SPOK protein performs both killing and resistance functions and show that these activities are dependent on distinct domains, a predicted nuclease and kinase domain. Genomic and phylogenetic analyses across ascomycetes suggest that the Spok genes disperse via cross-species transfer, and evolve by duplication and diversification within lineages.
    Meiotic drive of female-inherited supernumerary chromosomes in a pathogenic fungus
    Habig, Michael ; Kema, Gert Hj ; Holtgrewe Stukenbrock, Eva - \ 2018
    eLife 7 (2018). - ISSN 2050-084X - 20 p.
    accessory chromosome - B chromosome - chromosomes - gene expression - genetics - genomics - meiotic drive - selfish genetic elements - tetrad analysis - Zymoseptoria tritici

    Meiosis is a key cellular process of sexual reproduction that includes pairing of homologous sequences. In many species however, meiosis can also involve the segregation of supernumerary chromosomes, which can lack a homolog. How these unpaired chromosomes undergo meiosis is largely unknown. In this study we investigated chromosome segregation during meiosis in the haploid fungus Zymoseptoria tritici that possesses a large complement of supernumerary chromosomes. We used isogenic whole chromosome deletion strains to compare meiotic transmission of chromosomes when paired and unpaired. Unpaired chromosomes inherited from the male parent as well as paired supernumerary chromosomes in general showed Mendelian inheritance. In contrast, unpaired chromosomes inherited from the female parent showed non-Mendelian inheritance but were amplified and transmitted to all meiotic products. We concluded that the supernumerary chromosomes of Z. tritici show a meiotic drive and propose an additional feedback mechanism during meiosis, which initiates amplification of unpaired female-inherited chromosomes.

    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
    Rainfall-driven sex-ratio genes in African buffalo suggested by correlations between Y-chromosomal haplotype frequencies and foetal sex ratio
    Hooft, W.F. van; Prins, H.H.T. ; Getz, W.M. ; Jolles, A.E. ; Wieren, S.E. van; Greyling, B.J. ; Helden, P.D. ; Bastos, A.D.S. - \ 2010
    BMC Evolutionary Biology 10 (2010). - ISSN 1471-2148 - 11 p.
    cattle bos-taurus - syncerus-caffer - male-fertility - meiotic drive - bovine tuberculosis - drosophila-melanogaster - microsatellite analysis - natural-populations - sperm - selection
    Background - The Y-chromosomal diversity in the African buffalo (Syncerus caffer) population of Kruger National Park (KNP) is characterized by rainfall-driven haplotype frequency shifts between year cohorts. Stable Y-chromosomal polymorphism is difficult to reconcile with haplotype frequency variations without assuming frequency-dependent selection or specific interactions in the population dynamics of X- and Y-chromosomal genes, since otherwise the fittest haplotype would inevitably sweep to fixation. Stable Y-chromosomal polymorphism due one of these factors only seems possible when there are Y-chromosomal distorters of an equal sex ratio, which act by negatively affecting X-gametes, or Y-chromosomal suppressors of a female-biased sex ratio. These sex-ratio (SR) genes modify (suppress) gamete transmission in their own favour at a fitness cost, allowing for stable polymorphism. Results - Here we show temporal correlations between Y-chromosomal haplotype frequencies and foetal sex ratios in the KNP buffalo population, suggesting SR genes. Frequencies varied by a factor of five; too high to be alternatively explained by Y-chromosomal effects on pregnancy loss. Sex ratios were male-biased during wet and female-biased during dry periods (male proportion: 0.47-0.53), seasonally and annually. Both wet and dry periods were associated with a specific haplotype indicating a SR distorter and SR suppressor, respectively. Conclusions - The distinctive properties suggested for explaining Y-chromosomal polymorphism in African buffalo may not be restricted to this species alone. SR genes may play a broader and largely overlooked role in mammalian sex-ratio variation
    Doorbreking van kruisingsbarrières tussen Oriental- en Aziatische hybriden t.b.v. van introgressie van virus, Fusarium en Botrytisresistentie
    Tuyl, J.M. van - \ 2006
    Wageningen : Plant Research International - 36
    siergewassen - bloembollen - lelies - veredelen - commerciële hybriden - diploïdie - mitotische recombinatie - meiotic drive - ziekteresistentie - gewasbescherming - leliemozaïekvirus - fusarium - botrytis - ornamental crops - ornamental bulbs - lilies - breeding - commercial hybrids - diploidy - mitotic recombination - meiotic drive - disease resistance - plant protection - lily mottle virus - fusarium - botrytis
    Dit project heeft als doel om de laatste hindernissen in het gebruik van OA-hybriden voor de lelieveredeling weg te nemen. Dit betekent: Herstel van fertiliteit d.m.v. (geïnduceerde) mitotische en meiotische polyploïdisatie (chromosoomverdubbeling). Selectie van het meest fertiele materiaal en analyse van nakomelingschappen met streven naar maximale introgressie van de diverse genomen. Onderzoek gericht op een combinatie van ziekteresistenties (Lily Mottle Virus, Fusarium en Botrytis).
    Genomic conflicts in Podospora anserina = Genomische conflicten in Podospora anserina
    Gaag, M. van der - \ 2005
    Wageningen University. Promotor(en): Rolf Hoekstra, co-promotor(en): Fons Debets. - s.l. : S.n. - ISBN 9789085042556 - 152
    pezizomycotina - schimmels - genomen - genetica - plasmiden - meiotic drive - meiose - uitkruisen - pezizomycotina - fungi - genomes - genetics - plasmids - meiotic drive - meiosis - outcrossing
    This thesis deals with genomic conflicts raised by selfish elements in the ascomycete fungus Podospora anserina .Genomic conflicts arise when the effects of the selfish elements are opposite to the interests of the other parts of the genome. Two types of selfish elements are studied as well as certain characteristics of Podospora involved in the population dynamics of these elements, such as vegetative and sexual incompatibility, senescence and outcrossing.The natural habitat of Podospora anserina is dung of herbivores where it has an optimum growth temperature of 27 °C. The fungus can only reproduce sexually and the ascospores are the products of meiosis as well as the next generation of the fungus. Perithecia or fruiting bodies contain asci with four linearly arranged ascospores, which provide unique opportunities to analyse abnormal segregation and makes this fungus one of the genetic model organisms. Most ascospores are capable of completing the lifecycle of the fungus, as they contain two nuclei, each with one of the two mating types. This fungal trait is called pseudo or secondairy homothallism, and it allows sexual offspring to be produced by either selfing or outcrossing. Sometimes smaller single mating type ascospores are formed containing one nucleus and less cytoplasmic content and mitochondria. Colonies from these spores must outcross with another isolate to produce offspring. The fungal isolates used in this thesis were sampled from dung around Wageningen, theNetherlandsduring 1990-1997, but also some older French isolates dating from 1937 were used.

    The first selfish elements studied in this thesis are linear plasmids with homology to pAL2-1, a 8.3 kb plasmid previously found in this fungus. Linear plasmids are parasitic autonomous replicating genetic elements. In filamentous fungi they reside in the mitochondria. Most plasmids are cryptic or have a negative fitness effect on the host. However the pAL2 plasmid found in P. anserina has been associated with a longevity phenotype, though recently also negative effects were found. Homologous linear plasmids and plasmid families were present in 21 percent of the population and detected over several years. Half of the plasmid containing isolates possesseda single plasmid and the other half a plasmid family consisting of multiple plasmid copies. The lifespan of the isolates was generally uncorrelated with the presence of the plasmid. One isolate showed an increased lifespan, but noinserted plasmid sequences were detected in the mitochondrial DNA, as was the case for the longevity inducing pAL2-1 plasmid. We have looked at the dynamics of plasmid transmission for these plasmids.Vertical transfer of the plasmids to the ascospores occurs only via the maternal line. This transfer is inefficient as up to 40% lose all plasmids in an outcrossing situation and up to 20% retain only the basic plasmid family member in presence of a plasmid family. No difference in efficiency of plasmid transfer to the dikaryotic and the smaller monokaryotic ascospores was detected. Plasmid transmission was also foundindependent of the genetic background of the strains.Loss of plasmids via the sexual route is compensated by horizontal transmission of the plasmid through hyphal contact between different isolates. Horizontal transfer occurs efficiently in both vegetative compatible and incompatible situations. Vegetative incompatibility can be macroscopically observed as a 'barrage', a contact zone of lysed hyphal cells. Vegetative incompatibility is thought to have evolved as a mechanism to hamper spread of mobile selfish elements and parasites. Our experiments show that vegetative incompatibility is not a perfect barrier against this type of selfish elements.

    The other selfish elements studied in this thesis are meiotic drive factors or segregation distorters. Segregation distorters are transmitted into the progeny in excess of the fair Mendelian proportion of 50 %, by actively destructing the alternative allele. Genomic conflicts arise by hitchhiking of genes with deleterious fitness effects. Meiotic drive in Podospora ischaracterized by the abortion of two of the four spores in the ascus.Seven different groups of meiotic drive elements or Spore killer types were identified and characterized. Among 99 isolates from nature, six of these meiotic drive elements occurred in our local population. All drive elements comprise 23% of the natural population of P. anserina in Wageningen, The Netherlands and most elements can be retrieved over the years. Spore-killer type Psk-7 was also present in a French strain dating from 1937 and exists for more than 60 years. No resistance to meiotic drive was observed and all other isolates found so far are sensitive to spore killing. Each type of Spore killer differs in the percentage of asci that show killing, ranging from 50 to 95% two-spored asci, and in their mutual interactions. The aborted ascospores quickly degrade after spore wall formation, except for the Psk-3 group where they remain visible as tiny shriveled ascospores, indicating different abortion factors or timing for killing. The Psk-3 group also shows a variable percentage of two-spored asci within each perithecium. Spore-killer interactions show either mutual resistance ( i.e. no abortion is found if an allele of either Spore killer is present) or dominant epistasis ( i.e. one killer acts as a sensitive type). Genetic mapping could assign most Spore-killer types to linkage group III where they are not tightly linked to the centromere.

    Several possible models that explain the spore killing mechanism in Podospora anserina were examined. Repeatedbackcrossing of Spore killers to the same sensitive isolate produces strains with the same genetic background. Spore killers that belong to the same killer type or show mutual resistance become vegetative compatible to each other during backcrosses. On the other hand, Spore killers that show dominant epistasis, as well as the sensitive strain remained vegetative incompatible. This suggests a common mechanism for spore killing, possibly related to vegetative incompatibility, although the precise genetic nature of the correlation is not yet clear.The Podospora genome was screened for homologues of genes known to be involved in silencing in fungi. Genes were found for all silencing mechanisms (RIP, MSUD, Quelling) known in the related fungus Neurospora . However, the possible role of silencing by methylation of genes during the killing process was excluded by experiments using the drug 5-azacytidine, which both removes methylation and prevents de-novo methylation. No effect of the 5-azacytidine treatments was found on spore-killing frequency for all Spore-killer types. Also the consequences of formation of dikaryotic ascospores for expression of spore killing were examined. Crosses were used of Spore killers with a marker that increases the number of monokaryotic spores to up to eight. Spore-killer types Psk-2 , Psk-3 (Wa27) and Psk-4 produced some asci containing more than four spores in these crosses. In such asci sensitive nuclei were able to survive and resist the meiotic drive system, indicating incomplete penetrance of the spore-killing mechanism. Spore killing in the other killer types ( Psk-1, Psk-5, Psk-6 and Psk-7 ) were full penetrant; only asci with four or less spores could be detected. Here the killing mechanism works similar on all asci. Furthermore the effect of low temperatures (22 ºC) on spore killing was tested in this Chapter. Psk-2 dramatically decreased the percentage of killing at this temperature to almost zero. Other Spore-killer types were not affected by temperature. Based on all characteristics and interactions of the Spore killers we propose that spore killing in Podospora may be an example of post-segregational killing due to Toxin-Antitoxin mechanisms. A Spore Killer produces both a persisting stable toxin and a less stable antitoxin. In ascospores where the Spore Killer is absent the antitoxin disappears more quickly than the toxin, leading to abortion of the spores. Variable killing percentages can be explained by the strict balance between toxin and antitoxin and the timing of shutdown of the genes involved.

    Meiotic drive is only possible in an outcrossing situation. Podospora is in principle capable of both outcrossing and selfing. However to what extent the fungus outcrosses in nature is unknown. The likelihood of outcrossing was assessed for the secondary homothallic ascomycete Podospora anserina. We examined the extent of vegetative en sexual compatibility between wild type strains. The number of vegetative compatibility groups (VCG's) in the population was estimated based on the incompatibility reactions between isolates in our survey using accumulation curve extrapolation and the non-parametric Chao1 formula. The estimated number of VCG's compared to the maximum number of VCG's based on the currently known vegetative incompatibility genes suggest regular outcrossing in this fungus. Also the difference in sexual compatibility reactions of mating types of the same isolate assumes outcrossing takes place. Options for outcrossing in P. anserina were experimentally verified . Both single mating type monokaryotic and dikaryotic double mating type mycelial cultures proved capable of outcrossing, showing no preference for either genotype. This indicates that fertilization by selfing and outcrossing uses the same pathway. Outcrossing percentages between 1-5 percent were found in unmanipulated natural situations of ascospores on dung. The number of monokaryotic ascospores found in Spore-killer ( Psk ) strains was significantly higher than in other isolates, showing an enhancement to outcrossing in these strains.

    The findings in this thesis contribute to the understanding of the population dynamics and evolution of two types of selfish elements, linear plasmids and segregation distorters, in the ascomycete fungus Podospora anserina. Furthermore it increases the knowledge on genomic conflicts caused by these types of selfish elements in general
    Nonmendelian inheritance of the HET-s prion or HET-s prion domains determines the het-S spore killing system in Podospora anserina
    Dalstra, H.J.P. ; Zee, R.I. van der; Swart, K. ; Hoekstra, R.F. ; Saupe, S.J. ; Debets, A.J.M. - \ 2005
    Fungal Genetics and Biology 42 (2005)10. - ISSN 1087-1845 - p. 836 - 847.
    meiotic drive - heterokaryon incompatibility - vegetative incompatibility - in-vivo - protein - neurospora - fungi - organization - analog - genes
    Two alleles of the het-s/S locus occur naturally in the filamentous fungus Podospora anserina, het-s and het-S. The het-s encoded protein can form a prion that propagates a self-perpetuating amyloid aggregate, resulting in two phenotypes for the het-s strains. The prion-infected [Het-s] shows an antagonistic interaction to het-S whereas the prion-free [Het-s*] is neutral in interaction to het-S. The antagonism between [Het-s] and het-S is seen as heterokaryon incompatibility at the somatic level and as het-S spore killing in the sexual cycle. Two different domains of the HET-s and HET-S proteins have been identified, and a structure-function relationship has been established for interactions at the somatic level. In this study, we correlate accumulation of the HET-s and HET-S proteins (visualized using GFP) during the sexual cycle with timing of het-S spore abortion. Also, we present the structure-function relationship of the HET-s domains for interactions in the sexual cycle. We show that the constructs that ensure het-s incompatibility function in somatic mycelium are also active in het-S spore killing in the sexual cycle. In addition, paternal prion transmission and het-S spore killing has been found with the HET-s(157-289) truncated protein. The consequences of the unique transition from a coenocytic to a cellular state in the sexual phase and the timing, and localization of paternal and maternal HET-s and HET-S expression that are pertinent to prion transmission, and het-S spore killing are elaborated. These data further support our previously proposed model for het-S spore killing.
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