Biology subjects

Verweij, W.

Publications and source records attributed to Verweij, W..

4 recordsLinked to original sources

bioRxiv2023

Role of the metallo-reductase FADING and vacuolinos in anthocyanin degradation in flowers and fruits.

Anthocyanins are vacuolar pigments that confer red-violet colors to plant tissues. Pigmentation patterns result from spatio-temporally regulated anthocyanin synthesis and degradation. Mutational inactivation of a conserved MYB-bHLH-WDrepeat-WRKY transcriptional complex (MBWW) causes degradation of anthocyanins and fading of flower color via a pathway that involves FADING (FA). Here we show that FA encodes a vacuolar membrane Fe-reductase-oxidase that promotes anthocyanin degradation. In wild type petals anthocyanins in the central vacuole (CV) are stable, because FA-GFP is upheld in small vacuoles (vacuolinos) and kept away from the CV, indicating that vacuolinos act as gatekeepers in protein trafficking. In cells lacking vacuolinos, including mbww- mutant petals, FA-GFP reaches the CV and triggers anthocyanin degradation. Virus-induced gene silencing (VIGS) of an FA-homolog in pepper fruits prevented the "fading" of anthocyanins during fruit maturation. These findings provide new insights to breed ornamental and food crops with increased anthocyanin-content and enhanced nutritional value of edible parts.

plant biology↗

bioRxiv2022

Air-seq: Measuring air metagenomic diversity in an agricultural ecosystem

BackgroundAll species shed DNA into their environment during life or in death providing an opportunity to monitor biodiversity via its environmental DNA. Biodiversity monitoring using environmental DNA based technologies has become an important tool in understanding ecosystems. In recent years promising progress for non-invasive and, more importantly, non-destructive monitoring has been made by combining the retrieval of information transmitted by released environmental DNA with high-throughput sequencing technologies. Important ecosystems under continuous threat by disease but essential for food supplies are agricultural systems, often farmed as large monocultures and so highly vulnerable to disease outbreaks. Pest and pathogen monitoring in agricultural ecosystems is therefore key for efficient and early disease prevention and management. Air is rich in biodiversity, but has the lowest DNA concentration of all environmental media and yet it is required for windborne spread by many of the worlds most damaging crop pathogens. Our work and recent research suggests that ecosystems can be monitored efficiently using airborne nucleic acid information. ResultsHere we show that the airborne DNA of microbes can be recovered, sequenced and taxonomically classified, including down to the species level. Monitoring a field growing key crops we show that Air-seq can identify the presence of agriculturally significant pathogens and quantify their changing abundance over a period of 1.5 months often correlating with weather variables. ConclusionWe add to the evidence that aerial environmental DNA can be used as a source for biomonitoring in agricultural and more general terrestrial ecosystems. The ability to detect fluxes and occurrence patterns of species and strains with high throughput sample processing and analysis technologies highlights the value of airborne environmental DNA in monitoring biodiversity changes and tracking of taxa of human interest or concern.

genomics↗

bioRxiv2019

Spatially resolved transcriptomics reveals plant host responses to pathogens

BackgroundThorough understanding of complex model systems requires the characterisation of processes in different cell types of an organism. This can be achieved with high-throughput spatial transcriptomics at a large scale. However, for plant model systems this is still challenging as suitable transcriptomics methods are sparsely available. Here we present Grid-seq, an easy to adopt, micro-scale spatial-transcriptomics workflow that allows to study expression profiles across small areas of plant tissue at a fraction of the cost of existing sequencing-based methods.\n\nResultsWe compare the Grid-seq method with widely used library preparation methods (Illumina TruSeq). In spatial experiments we show that the Grid-seq method is sensitive enough to identify expression differences across a plant organ. We further assess the spatial transcriptome response of Arabidopsis thaliana leaves exposed to the bacterial molecule flagellin-22.\n\nConclusionWe show that our method can be used to identify known, rapidly flagellin-22 elicited genes, plant immune response pathways to bacterial attack and spatial expression patterns of genes associated with these pathways.

genomics↗

bioRxiv2017

The ash dieback invasion of Europe was founded by two individuals from a native population with huge adaptive potential

Accelerating international trade and climate change make pathogen spread an increasing concern. Hymenoscyphus fraxineus, the causal agent of ash dieback is one such pathogen, moving across continents and hosts from Asian to European ash. Most European common ash (Fraxinus excelsior) trees are highly susceptible to H. fraxineus although a small minority (~5%) evidently have partial resistance to dieback. We have assembled and annotated a draft of the H. fraxineus genome which approaches chromosome scale. Pathogen genetic diversity across Europe, and in Japan, reveals a tight bottleneck into Europe, though a signal of adaptive diversity remains in key host interaction genes (effectors). We find that the European population was founded by two divergent haploid individuals. Divergence between these haplotypes represents the 'shadow' of a large source population and subsequent introduction would greatly increase adaptive potential and the pathogen's threat. Thus, EU wide biological security measures remain an important part of the strategy to manage this disease.

genomics↗