A5026828191- Plant Pathogens and Fungal Diseases
- Plant-Microbe Interactions and Immunity
- Mycorrhizal Fungi and Plant Interactions
- Plant Disease Resistance and Genetics
- Mycotoxins in Agriculture and Food
- Bioinformatics and Genomic Networks
- Plant Pathogens and Resistance
- Protein Structure and Dynamics
- Physics and Engineering Research Articles
- Fungal and yeast genetics research
- Plant and Fungal Interactions Research
- Plant Molecular Biology Research
- Genomics and Phylogenetic Studies
- Flexible and Reconfigurable Manufacturing Systems
- Fungal Biology and Applications
- Data Analysis with R
- Wheat and Barley Genetics and Pathology
- Machine Learning in Bioinformatics
- Genetic Mapping and Diversity in Plants and Animals
- Plant Virus Research Studies
- Microbial Metabolism and Applications
- Plant Stress Responses and Tolerance
- Microbial Metabolic Engineering and Bioproduction
- Plant Parasitism and Resistance
- Genetic diversity and population structure
Wageningen University & Research
2022-2024
University of Amsterdam
2016-2023
Microbiology Institute of Shaanxi
2023
Peking University
2023
Institute of Microbiology
2023
State Key Laboratory of Microbial Resources
2023
Peking University First Hospital
2023
National Clinical Research Center for Digestive Diseases
2023
Netherlands Institute for Neuroscience
2016-2022
Utrecht University
2009-2012
Summary Formae speciales (ff.spp.) of the fungus Fusarium oxysporum are often polyphyletic within species complex, making it impossible to identify them on basis conserved genes. However, sequences that determine host‐specific pathogenicity may be expected similar between strains same forma specialis . Whole genome sequencing was performed from five different ff.spp. ( cucumerinum , niveum melonis radicis‐cucumerinum and lycopersici ). In each genome, genes for putative effectors were...
Abstract The genome of Fusarium oxysporum (Fo) consists a set eleven ‘core’ chromosomes, shared by most strains and responsible for housekeeping, one or several accessory chromosomes. We sequenced strain Fo f.sp. radicis - cucumerinum (Forc) using PacBio SMRT sequencing. All but the core chromosomes were assembled into single contigs, chromosome that shows all hallmarks pathogenicity comprised two contigs. A central part this contains identified candidate effector genes, including homologs...
Horizontal transfer of supernumerary or lineage-specific (LS) chromosomes has been described in a number plant pathogenic filamentous fungi. So far it was not known whether is restricted to certain size properties, 'core' can also undergo horizontal transfer. We combined directed and non-biased approach determine such restrictions exist. Selection genes were integrated into the genome strain Fusarium oxysporum on tomato, either targeted specific by homologous recombination randomly genome....
Natural variation among Arabidopsis accessions is an important genetic resource to identify mechanisms underlying plant development and stress tolerance. To evaluate the natural in salinity tolerance, two large-scale experiments were performed on populations consisting of 160 each. Multiple traits, including projected rosette area, fresh dry weight collected as estimate for Our results reveal a correlation between size under salt conditions developmental differences grown control conditions,...
Increased ambient temperature is inhibitory to plant immunity including auto-immunity. SNC1-dependent auto-immunity is, for example, fully suppressed at 28°C. We found that the Arabidopsis sumoylation mutant siz1 displays 22°C but also 28°C, which was EDS1 dependent both temperatures. This auto-immune phenotype provided enhanced resistance Pseudomonas Moreover, rosette size of recovered only weakly while this rescues growth defects other mutants. thermo-insensitivity correlated with a...
Proteins secreted by pathogens during host colonization largely determine the outcome of pathogen-host interactions and are commonly called 'effectors'. In fungal plant pathogens, coordinated transcriptional up-regulation effector genes is a key feature pathogenesis effectors often encoded in genomic regions with distinct repeat content, histone code rate evolution. tomato pathogen Fusarium oxysporum f. sp. lycopersici (Fol), reside on one four accessory chromosomes, known as 'pathogenicity'...
ABSTRACT Race 1 isolates of Fusarium oxysporum f. sp. lycopersici (FOL) are characterized by the presence AVR1 in their genomes. The product this gene, Avr1, triggers resistance tomato cultivars carrying gene I . In FOL race 2 and 3 isolates, is absent, hence they virulent on study, we analyzed an approximately 100-kb genomic fragment containing locus isolate 004 (FOL004) compared it to sequenced genome 4287 (FOL4287). A 31 kb was found be missing FOL4287. Further analysis suggests that...
Summary In Fusarium oxysporum f.sp. lycopersici , all effector genes reported so far – also called SIX are located on a single accessory chromosome which is required for pathogenicity and can be horizontally transferred to another strain. To narrow down the minimal region virulence, we selected partial deletion strains by fluorescence‐assisted cell sorting of strain in two arms were labelled with GFP RFP respectively. By testing virulence these mutants, show that complete long arm part short...
Abstract Fusarium oxysporum f. sp. radicis ‐ cucumerinum (Forc) causes severe root rot and wilt in several cucurbit species, including cucumber, melon, watermelon. Previously, a pathogenicity chromosome, chr RC , was identified Forc. Strains that were previously nonpathogenic could infect multiple species after obtaining this chromosome via horizontal transfer (HCT). In contrast, F. melonis (Fom) can only cause disease on melon plants, even though Fom contains contigs are largely syntenic...
Abstract Fusarium oxysporum is an economically important pathogen causing wilting or rotting disease symptoms in a large number of crops. It proposed to have structured, “two-speed” genome: i.e. regions containing genes involved pathogenicity cluster with transposons on separate accessory chromosomes. This hypothesized enhance evolvability. Given the continuum adaptation all encoded genome, however, one would expect more complex genome structure. By comparing reference strain Fol4287 those...
Plant pathogens cause widespread yield losses in agriculture. Understanding the drivers of plant-pathogen interactions requires decoding molecular dialog leading to either resistance or disease. However, progress deciphering pathogenicity genes has been severely hampered by suitable model systems and incomplete fungal genome assemblies. Here, we report a significant improvement assembly annotation Fusarium oxysporum (Fo) strain Fo5176. Fo comprises large number serious plant on dozens...
The fungus Fusarium oxysporum (Fo) is widely known for causing wilt disease in over 100 different plant species. Endophytic interactions of Fo with plants are much more common, and strains pathogenic on one species can even be beneficial endophytes another However, endophytic have been less investigated at the molecular level, genetic basis that underlies versus behavior unknown. To investigate this, 44 from non-cultivated Australian soils, grass roots Spain, tomato stems United States were...
Nematophagous fungi employ three distinct predatory strategies: nematode trapping, parasitism of females and eggs, endoparasitism. While endoparasites play key roles in controlling populations nature, their application for integrated pest management is hindered by the limited understanding biology. We present a comparative analysis high quality finished genome assembly Drechmeria coniospora, model endoparasitic nematophagous fungus, with transcriptomic study. Adaptation D. coniospora to its...
Abstract Fungal effectors (small‐secreted proteins) have long been considered as species or even subpopulation‐specific. The increasing availability of high‐quality fungal genomes and annotations has allowed the identification trans‐species trans‐genera families effectors. Two avirulence effectors, AvrLm10A AvrLm10B , Leptosphaeria maculans fungus causing stem canker oilseed rape, are members such a large family neighbouring genes, organized in divergent transcriptional orientation. Sequence...
Ramularia leaf spot has recently emerged as a major threat to barley production world-wide, causing 25% yield loss in many growing regions. Here, we provide new reference genome of the causal agent, Dothideomycete collo-cygni. The assembly 32 Mb consists 78 scaffolds. We used RNA-seq identify 11,622 genes which 1,303 and 282 are coding for predicted secreted proteins putative effectors respectively. pathogen separated from its nearest sequenced relative, Zymoseptoria tritici ∼27 Ma....
The fungus Fusarium oxysporum is infamous for its devastating effects on economically important crops worldwide. F. isolates are grouped into formae speciales based their ability to cause disease different hosts. Assigning strains using non-experimental procedures has proven be challenging due genetic heterogeneity and polyphyletic nature. However, genetically diverse of the same forma specialis encode similar repertoires effectors, proteins that secreted by contribute establishment...
Helitrons are eukaryotic rolling circle transposable elements that can have a large impact on host genomes due to their copy-number and ability capture copy genes regulatory elements. They occur widely in plants animals, thus far been relatively little investigated fungi. Here, we comprehensively survey several completely sequenced representing the F. oxysporum species complex (FOSC). We thoroughly characterize 5 different Helitron subgroups determine genome evolution assembly this complex....
Fusarium wilt of spinach, caused by oxysporum f. sp. spinaciae, is an important disease during warm conditions in production regions with acid soils, yet little known about what confers pathogenicity to spinach F. spinaciae genetically. To identify candidate fungal genes that contribute wilt, each 69 geographically diverse isolates was tested for on three inbreds. Thirty-nine identified as quantitative differences severity among the inbreds revealed two distinct groups spinaciae. Putative...
Abstract Fusarium oxysoporum f. sp. radicis‐cucumerinum (Forc) is able to cause disease in cucumber, melon, and watermelon, while F. oxysporum melonis (Fom) can only infect melon plants. Earlier research showed that mobile chromosomes Forc Fom determine the difference host range between Fom. By closely comparing these pathogenicity combined with RNA‐sequencing data, we selected 11 candidate genes tested for involvement One of candidates a putative effector gene on chromosome has nonidentical...
Although functionally related proteins can be reliably predicted from phylogenetic profiles, many functional modules do not seem to evolve cohesively according case studies and systematic analyses in prokaryotes. In this study we quantify the extent of evolutionary cohesiveness eukaryotes probe biological methodological factors influencing our estimates. We have collected various datasets protein complexes pathways Saccheromyces cerevisiae. define orthologous groups on 34 eukaryotic genomes...
Heterokaryon formation is an essential step in asexual recombination Fusarium oxysporum. Filamentous fungi have elaborate nonself recognition machinery to prevent and proliferation of heterokaryotic cells, called heterokaryon incompatibility (HI). In F. oxysporum the regulation this not well understood. Neurospora crassa, Vib-1, a putative transcription factor p53-like Ndt80 family factors, has been identified as global regulator HI. study we investigated role homolog Suf, vegetative hyphal...
Homology is a crucial concept in comparative genomics. The algorithm probably most widely used for homology detection genomics, BLAST. Usually stringent score cutoff applied to distinguish putative homologs from possible false positive hits. As consequence, some BLAST hits are discarded that fact homologous. Analogous the use of genomics context genome alignments, we test whether conserved functional can be select candidate insignificant We make co-complex network alignment between complex...
The study of biological networks and how they have evolved is fundamental to our understanding the cell. By investigating proteins different ages are connected in protein interaction network, one can infer that network has expanded evolution, without need for explicit reconstruction ancestral networks. Studies implement this approach show often a similar age, suggesting simultaneous emergence interacting proteins. There several theories explaining phenomenon, but despite importance gene...