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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Alstroemeria yellow spot virus (AYSV) : a new orthotospovirus species within a growing Eurasian clade
Hassani-Mehraban, A. ; Dullemans, A.M. ; Verhoeven, J.Th.J. ; Roenhorst, J.W. ; Peters, D. ; Vlugt, R.A.A. van der; Kormelink, R. - \ 2019
Archives of Virology 164 (2019)1. - ISSN 0304-8608 - p. 117 - 126.

An orthotospovirus distinct from all other orthotospoviruses was isolated from naturally infected alstroemeria plants. Disease symptoms caused by this virus mainly consisted of yellow spots on the leaves based on which the name alstroemeria yellow spot virus (AYSV) was coined. A host range analysis was performed and a polyclonal antiserum was produced against purified AYSV ribonucleoproteins which only reacted with the homologous antigen and not with any other (established or tentative) orthotospovirus from a selection of American and Asian species. Upon thrips transmission assays the virus was successfully transmitted by a population of Thrips tabaci. The entire nucleotide sequence of the M and S RNA segments was elucidated by a conventional cloning and sequencing strategy, and contained 4797 respectively 2734 nucleotides (nt). Simultaneously, a next generation sequencing (NGS) approach (RNAseq) was employed and generated contigs covering the entire viral tripartite RNA genome. In addition to the M and S RNA nucleotide sequences, the L RNA (8865 nt) was obtained. The nucleocapsid (N) gene encoded by the S RNA of this virus consisted of 819 nucleotides with a deduced N protein of 272 amino acids and by comparative sequence alignments to other established orthotospovirus species showed highest homology (69.5% identity) to the N protein of polygonum ringspot virus. The data altogether support the proposal of AYSV as a new orthotospovirus species within a growing clade of orthotospoviruses that seem to share the Middle East basin as a region of origin.

Impact of Positive Selection on Incidence of Different Viruses During Multiple Generations of Potato Seed Tubers in Uganda
Priegnitz, Uta ; Lommen, Willemien J.M. ; Vlugt, René A.A. van der; Struik, Paul C. - \ 2019
Potato Research 62 (2019)1. - ISSN 0014-3065 - p. 1 - 30.
Multi-seasonal trials - Positive selection - Seed degeneration - Seed potatoes - Seed regeneration - Uganda - Viruses

Smallholder farmers in Uganda commonly use seed potato tubers from the informal sector, especially by seed recycling over several generations. Therefore, seed tubers are highly degenerated with viruses and other pathogens, resulting in poor yield and quality of the produce. Over one cycle of multiplication, degeneration management by positive seed selection was found to be efficient in reducing virus diseases compared with the farmers’ method of selection. The objective of this study was to assess to what extent positive selection over several seasons can reduce six different virus incidences in seed lots of different starting quality in southwestern Uganda. Multi-seasonal trials were carried out in three locations, with five seed lots from four sources and three cultivars. Detection of viruses was based on DAS-ELISA and Luminex xMAP technology. Analysis was carried out with analysis of variance (ANOVA) on angular-transformed percentages of virus incidence. Results showed fluctuations in some viruses over seasons with lower Potato leafroll virus (PLRV) and Potato virus X (PVX) incidences in lots from positive selection compared with lots from farmers’ selection. In contrast, some seed lots were initially highly infected with Potato virus S (PVS) and Potato virus M (PVM) and showed no reduction in virus incidence through positive selection. In general, little infection with Potato virus Y (PVY) and Potato virus A (PVA) was found. Based on these results, it is recommended that smallholder farmers are trained in positive selection to opt for less virus-infected plants and tubers, thus increasing potato production.

High-throughput sequencing technologies for plant pest diagnosis: challenges and opportunities
Olmos, A. ; Boonham, N. ; Candresse, T. ; Gentit, P. ; Giovani, B. ; Kutnjak, D. ; Liefting, L. ; Maree, H.J. ; Minafra, A. ; Moreira, A. ; Nakhla, M.K. ; Petter, F. ; Ravnikar, M. ; Rodoni, B.C. ; Roenhorst, J.W. ; Rott, M. ; Ruiz-Garcia, A.B. ; Santala, J. ; Stancanelli, G. ; Vlugt, R.A.A. van der; Varveri, C. ; Westenberg, M. ; Wetzel, T. ; Ziebell, H. ; Massart, S. - \ 2018
EPPO Bulletin 48 (2018)2. - ISSN 0250-8052 - p. 219 - 224.
High‐throughput sequencing (HTS) technologies have revolutionized plant pest research and are now raising interest for plant pest diagnostics, with plant virus diagnostics at the forefront of development. However, the application of HTS in plant pest diagnostics raises important challenges that plant health regulators will have to address. Adapted infrastructures, technical guidelines and training are pivotal for further use and adoption of the HTS technologies in the phytosanitary framework.
Innovative detection methods to support plant health diagnostics
Bonants, P.J.M. ; Houwers, I.M. ; Dullemans, A.M. ; Griekspoor, Y. ; Mendes, O. ; Gent-Pelzer, M.P.E. van; Vlugt, R.A.A. van der; Bergervoet, J.H.W. ; Schoen, C.D. ; Wolf, J.M. van der; Lee, T.A.J. van der - \ 2018
Kunnen we de virussen en de bladluizen nog de baas blijven?
Vlugt, Rene van der - \ 2018
Virus taxonomy and population genetics.
Vlugt, Rene van der - \ 2018
The impact of the viruses' transmission strategies
Verbeek, M. ; Stijger, I. ; Vlugt, R.A.A. van der - \ 2017
Prophyta 2017 (2017). - ISSN 0921-5506
New diagnostic and rapid ‘nextgeneration sequencing’ methods facilitate the
discovery of new plant viruses. However, virus detection or elucidation of the
sequence of its dna/rna is no guarantee for understanding its epidemiology.
In order to develop effective control measures in field crops or in greenhouses,
knowledge of how viruses move from one plant to another is essential.
Grote impact verbod neonicotinoïden
Verbeek, M. ; Vlugt, R.A.A. van der; Raaijmakers, Elma ; Tijink, Frank - \ 2017
Boerderij/Akkerbouw 103 (2017)6. - ISSN 0169-0116 - p. A22 - A24.
Dringend alternatieven nodig voor de beheersing van vergelingsziekte in de suikerbietenteelt. De ziekte kan de opbrengst ernstig schaden.
Schistosome egg antigens, including the glycoprotein IPSE/alpha-1, trigger the development of regulatory B cells
Haeberlein, Simone ; Obieglo, Katja ; Ozir-Fazalalikhan, Arifa ; Chayé, Mathilde A.M. ; Veninga, Henrike ; Vlugt, Luciën E.P.M. van der; Voskamp, Astrid ; Boon, Louis ; Haan, Joke M.M. den; Westerhof, Lotte B. ; Wilbers, Ruud H.P. ; Schots, Arjen ; Schramm, Gabriele ; Hokke, Cornelis H. ; Smits, Hermelijn H. - \ 2017
PLoS Pathogens 13 (2017)7. - ISSN 1553-7366
Infection with the helminth Schistosoma (S.) mansoni drives the development of interleukin (IL)-10-producing regulatory B (Breg) cells in mice and man, which have the capacity to reduce experimental allergic airway inflammation and are thus of high therapeutic interest. However, both the involved antigen and cellular mechanisms that drive Breg cell development remain to be elucidated. Therefore, we investigated whether S. mansoni soluble egg antigens (SEA) directly interact with B cells to enhance their regulatory potential, or act indirectly on B cells via SEA-modulated macrophage subsets. Intraperitoneal injections of S. mansoni eggs or SEA significantly upregulated IL-10 and CD86 expression by marginal zone B cells. Both B cells as well as macrophages of the splenic marginal zone efficiently bound SEA in vivo, but macrophages were dispensable for Breg cell induction as shown by macrophage depletion with clodronate liposomes. SEA was internalized into acidic cell compartments of B cells and induced a 3-fold increase of IL-10, which was dependent on endosomal acidification and further enhanced by CD40 ligation. IPSE/alpha-1, one of the major antigens in SEA, was also capable of inducing IL-10 in naïve B cells, which was reproduced by tobacco plant-derived recombinant IPSE. Other major schistosomal antigens, omega-1 and kappa-5, had no effect. SEA depleted of IPSE/alpha-1 was still able to induce Breg cells indicating that SEA contains more Breg cell-inducing components. Importantly, SEA- and IPSE-induced Breg cells triggered regulatory T cell development in vitro. SEA and recombinant IPSE/alpha-1 also induced IL-10 production in human CD1d+B cells. In conclusion, the mechanism of S. mansoni-induced Breg cell development involves a direct targeting of B cells by SEA components such as the secretory glycoprotein IPSE/alpha-1.
Euphresco project VirusCollect – fulfilling the need for a common collection of plant viruses and viroids for reference
Roenhorst, J.W. ; Lacomme, C. ; Nisbet, C. ; Leichtfried, T. ; Menzel, W. ; Winter, S. ; Vlugt, R.A.A. van der - \ 2017
EPPO Bulletin 47 (2017)1. - ISSN 0250-8052 - p. 41 - 47.

The availability and accessibility of suitably characterized plant virus and viroid isolates for reference is vital for research and diagnostic laboratories. To ensure the long-term availability of isolates and reference materials, there is a need for international collaboration. The Euphresco (European Plant Health Research Coordination) project VirusCollect aimed to establish a platform to link collections of viruses and viroids maintained by individual institutions via Q-bank (http://www.q-bank.eu/), a database on plant pests and diseases. Within the VirusCollect project, standard operating procedures were developed and implemented by the participating laboratories to guarantee the quality of isolates and data. In addition, over 135 virus and viroid isolates of phytosanitary and/or economic importance were added to Q-bank, which now provides links to over 500 virus isolates of almost 100 species, in addition to basic information on many more plant viruses. VirusCollect has enabled the first step in collaboration between curators and standardization of maintenance of virus collections. The project established the basis for improving the quality of individual collections and the layout of Q-bank as a platform to share data and information. The follow-up project, VirusCollect II, enables further international collaboration to ensure future access to reliable collections of plant viruses and viroids.

Aphid transmission of Lettuce necrotic leaf curl virus, a member of atentative new subgroup within the genus Torradovirus
Verbeek, M. ; Dullemans, A.M. ; Vlugt, R.A.A. van der - \ 2017
Virus Research 241 (2017). - ISSN 0168-1702 - p. 125 - 130.
Lettuce necrotic leaf curl virus (LNLCV) was described as the first non-tomato-infecting member of the genus Torradovirus. Until today, the virus was found only in The Netherlands in two different areas in open field crops of lettuce. In 2015, LNLCV was accepted by the ICTV as a new member of the genus Torradovirus. The tomato-infecting (TI) torradoviruses Tomato torrado virus (ToTV), Tomato marchitez virus (ToMarV) and Tomato chocolàte virus (ToChV) are transmitted by at least three whitefly species in a semi-persistent and stylet-borne manner. As LNLCV was transmitted in open fields in The Netherlands, where whiteflies are present only in low incidence, transmission studies were set up to identify the natural vector of LNLCV. Whitefly species which survive Dutch open field conditions during summer, as well as lettuce colonizing aphid species, were tested for their ability to transmit LNLCV. Lengths of acquisition and inoculation periods were chosen in accordance with the conditions for TI torradoviruses. Transmission experiments involving whiteflies were never successful. Transmission with aphids was only successful in case of the lettuce-currant aphid, Nasonovia ribisnigri. Localization of LNLCV virions in N. ribisnigri with a nested RT-PCR indicated the stylets as possible retention sites. The willow-carrot aphid Cavariella aegopodii did not transmit LNLCV in our transmission experiment but the virus could be detected in the stylets of this aphid, leaving C. aegopodii as a possible vector for LNLCV.
Consensus statement : Virus taxonomy in the age of metagenomics
Simmonds, Peter ; Adams, Mike J. ; Benk, Mária ; Breitbart, Mya ; Brister, J.R. ; Carstens, Eric B. ; Davison, Andrew J. ; Delwart, Eric ; Gorbalenya, Alexander E. ; Harrach, Balázs ; Hull, Roger ; King, Andrew M.Q. ; Koonin, Eugene V. ; Krupovic, Mart ; Kuhn, Jens H. ; Lefkowitz, Elliot J. ; Nibert, Max L. ; Orton, Richard ; Roossinck, Marilyn J. ; Sabanadzovic, Sead ; Sullivan, Matthew B. ; Suttle, Curtis A. ; Tesh, Robert B. ; Vlugt, René A. Van Der; Varsani, Arvind ; Murilo Zerbini, F. - \ 2017
Nature Reviews Microbiology 15 (2017)3. - ISSN 1740-1526 - p. 161 - 168.
The number and diversity of viral sequences that are identified in metagenomic data far exceeds that of experimentally characterized virus isolates. In a recent workshop, a panel of experts discussed the proposal that, with appropriate quality control, viruses that are known only from metagenomic data can, and should be, incorporated into the official classification scheme of the International Committee on Taxonomy of Viruses (ICTV). Although a taxonomy that is based on metagenomic sequence data alone represents a substantial departure from the traditional reliance on phenotypic properties, the development of a robust framework for sequence-based virus taxonomy is indispensable for the comprehensive characterization of the global virome. In this Consensus Statement article, we consider the rationale for why metagenomic sequence data should, and how it can, be incorporated into the ICTV taxonomy, and present proposals that have been endorsed by the Executive Committee of the ICTV.
Torradoviruses
Verbeek, M. ; Dullemans, A.M. ; Vlugt, R.A.A. van der - \ 2016
In: Vector-Mediated Transmission of Plant Pathogens / Brown, J.K., APS Press - ISBN 9780890545164 - p. 431 - 434.
The plant virus genus Torradovirus was created to contain two new species of whitefly-transmitted, tomato-infecting plant picorna-like viruses: Tomato torrado virus and Tomato marchitez virus. So far, research on torradoviruses has focused mainly on the description of the viruses and the diseases they cause, the determination of viral properties and nucleic acid sequences, and the development of detection methods. Evidence has been found for the transmission of torradoviruses by three whitefly species in a semipersistent, stylet-borne manner.

Key concepts included in this chapter:

Discovery of Torradoviruses
Properties of Torradoviruses
Transmission
Future Research
Ringspots in Phalaenopsis, is there a role for a putative new virus?
Meekes, E. ; Dullemans, A.M. ; Hooftman, R. ; Gawehns, Fleur ; Ebskamp, M. ; Verbeek, M. ; Vlugt, R.A.A. van der; Lee, T.A.J. van der - \ 2016
Full genome characterisation of 10 tospoviruses by next generation sequencing
Dullemans, A.M. ; Bekkum, P.J. van; Roenhorst, J.W. ; Kormelink, R.J.M. ; Vlugt, R.A.A. van der - \ 2016
Detection of a non-described virus in Dracaena surculosa?
Krom, C.E. de; Verhoeven, J.T.J. ; Dullemans, A.M. ; Vlugt, R.A.A. van der; Roenhorst, J.W. - \ 2016
Full genome characterisation of 10 tospoviruses by next generation sequencing
Dullemans, A.M. ; Bekkum, P.J. van; Roenhorst, J.W. ; Kormelink, R.J.M. ; Vlugt, R.A.A. van der - \ 2016
Down-regulation of Arabidopsis DND1 orthologs in potato and tomato leads to broad-spectrum resistance to late blight and powdery mildew
Sun, K. ; Wolters, A.M.A. ; Loonen, A.E.H.M. ; Huibers, R.P. ; Vlugt, R.A.A. van der; Goverse, A. ; Jacobsen, E. ; Visser, R.G.F. ; Bai, Y. - \ 2016
Transgenic Research 25 (2016). - ISSN 0962-8819 - p. 123 - 138.
Multiple susceptibility genes (S), identified in Arabidopsis, have been shown to be functionally conserved in crop plants. Mutations in these S genes result in resistance to different pathogens, opening a new way to achieve plant disease resistance. The aim of this study was to investigate the role of Defense No Death 1 (DND1) in susceptibility of tomato and potato to late blight (Phytophthora infestans). In Arabidopsis, the dnd1 mutant has broad-spectrum resistance against several fungal, bacterial, and viral pathogens. However this mutation is also associated with a dwarfed phenotype. Using an RNAi approach, we silenced AtDND1 orthologs in potato and tomato. Our results showed that silencing of the DND1 ortholog in both crops resulted in resistance to the pathogenic oomycete P. infestans and to two powdery mildew species, Oidium neolycopersici and Golovinomyces orontii. The resistance to P. infestans in potato was effective to four different isolates although the level of resistance (complete or partial) was dependent on the aggressiveness of the isolate. In tomato, DND1-silenced plants showed a severe dwarf phenotype and autonecrosis, whereas DND1-silenced potato plants were not dwarfed and showed a less pronounced autonecrosis. Our results indicate that S gene function of DND1 is conserved in tomato and potato. We discuss the possibilities of using RNAi silencing or loss-of-function mutations of DND1 orthologs, as well as additional S gene orthologs from Arabidopsis, to breed for resistance to pathogens in crop plants.
NGS applications in plant pathogen diagnostics
Dullemans, Annette - \ 2015
NGS applications in plant pathogen diagnosticsDullemans Annette, Verstappen Els, Houwers Ilse, Verbeek Martin, Van der Lee Theo, Van der Vlugt René and Bonants Peter. Wageningen UR, BU Biointeractions & Plant Health, PO. Box 16, 6700 AA Wageningen, The Netherlands, annette.dullemans@wur.nlRoutine diagnostics of plant pathogens often involve methods such as ELISA and real-time (TaqMan) PCR. These methods only detect known pathogens. Next Generation Sequencing (NGS) is a valuable method to identify new pathogens. We developed a (semi) automated pipeline to use HiSeq Illumina Sequencing to detect pathogens in different hosts. Total DNA or RNA was isolated from symptomatic plant tissue to generate sequence libraries. Individual samples were labelled with tags to pool multiple samples in one run. The sequence reads generated from a single sample were analyzed in a CLC Genomics Work Bench pipeline. Host reads were removed and the remaining reads were used in a de novo assembly. The resulting contig sequences were compared with sequences in public and in-house databases to identify the origin of the non-host sequences. General knowledge on plant pathogens is essential to identify the pathogen contigs. The read coverage of the pathogen genomes expressed as the Reads per Kb per million reads, and therefore the analytical sensitivity, depends on number of reads, genome size, and the abundance of the pathogen in the host. To investigate whether NGS can be a useful tool in routine screening, RNA samples from an inspection service were sequenced. Samples infected with known pathogens, detected by real-time (Taqman) PCR could be confirmed by NGS. Several examples of NGS will be presented.
Screening of the COGEM lists of non-pathogenic bacteria and fungi for postharvest diseases and plant pathogens
Vlugt, R.A.A. van der; Verbeek, M. ; Molhoek, W. ; Stevens, L. - \ 2015
Wageningen : Wageningen UR, Business Unit Biointeractions and Plant Heath (CGM onderzoeksrapport 2016-06) - 109
plantenziekteverwekkers - plantenziekten - bederf na de oogst - plantenziekteverwekkende bacteriën - plantenziekteverwekkende schimmels - screenen - plant pathogens - plant diseases - postharvest decay - plant pathogenic bacteria - plant pathogenic fungi - screening
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