A5039959094- Epigenetics and DNA Methylation
- Plant-Microbe Interactions and Immunity
- Plant Pathogens and Fungal Diseases
- Coastal wetland ecosystem dynamics
- Plant pathogens and resistance mechanisms
- Plant Taxonomy and Phylogenetics
- Plant Molecular Biology Research
- Marine and coastal plant biology
- Plant Virus Research Studies
- Biofuel production and bioconversion
- Peatlands and Wetlands Ecology
- Microbial metabolism and enzyme function
- Botany and Plant Ecology Studies
- Environmental DNA in Biodiversity Studies
- Real-time simulation and control systems
- Bryophyte Studies and Records
- Genomics and Phylogenetic Studies
- Legume Nitrogen Fixing Symbiosis
- Genetic diversity and population structure
- Parasites and Host Interactions
- Mycorrhizal Fungi and Plant Interactions
- Parasite Biology and Host Interactions
- Genetic and Clinical Aspects of Sex Determination and Chromosomal Abnormalities
- Plant Diversity and Evolution
- Nematode management and characterization studies
Netherlands Institute of Ecology
2020-2023
University of Amsterdam
2011-2023
Zero to Three
2023
Netherlands Institute for Neuroscience
2023
Centre for BioSystems Genomics
2012
Plant pathogens secrete effectors to manipulate their host and facilitate colonization. Fusarium oxysporum f. sp. lycopersici is the causal agent of wilt disease in tomato. Upon infection, F. secretes numerous small proteins into xylem sap (Six proteins). Most Six are unique oxysporum, but Six6 an exception; a homolog also present two Colletotrichum spp. SIX6 expression was found require living cells knockout compromised virulence, classifying it as genuine effector. Heterologous did not...
Summary Plant‐invading microbes betray their presence to a plant by exposure of antigenic molecules such as small, secreted proteins called ‘effectors’. In Fusarium oxysporum f. sp . lycopersici ( Fol ) we identified pair effector gene candidates, AVR 2 ‐ SIX 5 , whose expression is controlled shared promoter. The pathogenicity and knockouts was assessed on susceptible resistant tomato Solanum lycopersicum plants carrying I‐2 NB LRR protein confers resistance races Like Avr2, Six5 found be...
Plant pathogens secrete small proteins, of which some are effectors that promote infection. During colonization the tomato xylem vessels fungus Fusarium oxysporum f.sp. lycopersici (Fol) secretes proteins referred to as SIX (Secreted In Xylem) proteins. Of these, Six1 (Avr3), Six3 (Avr2), Six5, and Six6 required for full virulence, denoting them effectors. To investigate their activities in plant, sap proteome plants inoculated with Fol wild-type or either AVR2, AVR3, SIX2, SIX5, SIX6...
Plant nucleotide-binding leucine-rich repeat (NLR) proteins enable cells to respond pathogen attack. Several NLRs act in the nucleus; however, conserved nuclear targets that support their role immunity are unknown. Previously, we noted a structural homology between domain of and DNA replication origin-binding Cdc6/Orc1 proteins. Here show NB-ARC (nucleotide-binding, Apaf-1, R-proteins, CED-4) Rx1 NLR potato binds nucleic acids. induces ATP-dependent bending melting vitro, dependent upon...
Several reduced-representation bisulfite sequencing methods have been developed in recent years to determine cytosine methylation de novo nonmodel species. Here, we present epiGBS2, a laboratory protocol based on epiGBS with revised and user-friendly bioinformatics pipeline for wide range of species or without reference genome. epiGBS2 is cost- time-efficient the computational workflow designed reproducible manner. The library allows flexible choice restriction enzymes double digest. was...
Environmentally induced DNA methylation variants may mediate gene expression responses to environmental changes. If such are transgenerationally stable, there is potential for persist over multiple generations. Our current knowledge in plants, however, almost exclusively based on studies conducted sexually reproducing species where the majority of changes subject resetting germlines, limiting transgenerational epigenetics stress memory. Asexual reproduction circumvents and therefore be more...
Vascular wilt diseases caused by Fusarium oxysporum are a major threat to many agriculturally important crops. Genetic resistance is rare and inevitably overcome the emergence of new races. To identify potentially durable non-race-specific genetic against diseases, we set out effector targets in tomato that mediate susceptibility fungus. For this purpose, used SIX8 protein, an conserved virulence factor present pathogenic F. isolates. Using protein pull-downs yeast two-hybrid assays, was...
Early developmental conditions are known to have life-long effects on an individual’s behavior, physiology and fitness. In altricial birds, a majority of these conditions, such as the number siblings amount food provisioned, controlled by parents. This opens up potential for parents adjust behavior their offspring according local post-natal circumstances. However, mechanisms underlying intergenerational regulation remain largely unknown. A mechanism often proposed possibly explain how...
Abstract The environment experienced during early life is a crucial factor in the of many organisms. This has been shown to have profound effects on morphology, physiology and fitness. However, molecular mechanisms that mediate these are largely unknown, even though they essential for our understanding processes induce phenotypic variation natural populations. DNA methylation an epigenetic mechanism suggested explain such environmentally induced changes life. To investigate whether...
Abstract Background 5-Methylcytosine (5mC) is an important epigenetic mark in eukaryotes. Little information about its role exists for invertebrates. To investigate the contribution of 5mC to phenotypic variation invertebrates, alteration methylation patterns needs be produced. Here, we apply new non-nucleoside DNA methyltransferase inhibitors (DNMTi) introduce aleatory changes into methylome mollusk species. Results Flavanone inhibitor Flv1 was efficient reducing freshwater snails...
Abstract DNA methylation in plant genomes occurs different sequences and genomic contexts that have very properties. CG (mCG) sequence context shows transgenerational stability high epimutation rate, can thus provide genealogical information at short time scales. However, due to meta‐stability because mCG variants may arise other factors than epimutation, such as environmental stress exposure, it is not clear how well captures micro‐evolutionary Here, we analysed variation between accessions...
Synopsis The search for the hereditary mechanisms underlying quantitative traits traditionally focused on identification of genomic polymorphisms such as single-nucleotide polymorphisms. It has now become clear that epigenetic mechanisms, DNA methylation, can consistently alter gene expression over multiple generations. is unclear, however, if and how methylation stably be transferred from one generation to next thereby a component heritable variation trait. In this study, we explore whether...
Abstract The profiling of epigenetic marks like DNA methylation has become a central aspect studies in evolution and ecology. Bisulphite sequencing is commonly used for assessing genome‐wide at single nucleotide resolution but these data can also provide information on genetic variants polymorphisms (SNPs). However, bisulphite conversion causes unmethylated cytosines to appear as thymines, complicating the alignment subsequent SNP calling. Several tools have been developed overcome this...
Ecological genomics approaches have informed us about the structure of genetic diversity in natural populations that might underlie patterns trait variation. However, we still know surprisingly little mechanisms permit organisms to adapt variable environmental conditions. The salt marsh foundation plant Spartina alterniflora exhibits a dramatic range phenotype is associated with pronounced intertidal gradient across narrow spatial scale. Both and non-genetic molecular this phenotypic To...
Abstract epiGBS is an existing reduced representation bisulfite sequencing method to determine cytosine methylation and genetic polymorphisms de novo . Here, we present epiGBS2, improved laboratory protocol user-friendly bioinformatics pipeline for a wide range of species with or without reference genome. epiGBS2 decreases costs time investment increases user-friendliness reproducibility. The library was adjusted allow flexible choice restriction enzymes double digest. Instead fully...
5-methylcytosine (5mC) is an important epigenetic mark in eukaryotes. Little information about its role exists for invertebrates. How 5mC contributes to phenotypic variation invertebrates can be investigated by experimental alteration of methylation patterns. Here, we apply new non-nucleoside DNA methyltransferase inhibitors (DNMTi) introduce global changes into the methylome mollusk species. Flavanone inhibitor Flv1 was highly efficient reducing freshwater snails Biomphalaria glabrata and...
Abstract While some DNA methylation variants are transgenerationally stable in plants, modifications that specifically induced by environmental exposure typically transient and subject to resetting germ lines, limiting the potential for transgenerational epigenetics stress memory. Asexual reproduction circumvents germlines, may be more conducive long-term memory inheritance of epigenetic marks. This, however, has been poorly explored. Taking advantage rapid clonal common duckweed Lemna minor...