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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    Comparative genomics of plant pathogenic Botrytis species with distinct host specificity
    Valero-Jiménez, Claudio A. ; Veloso, Javier ; Staats, Martijn ; Kan, Jan A.L. van - \ 2019
    BMC Genomics 20 (2019)1. - ISSN 1471-2164
    Effector - Grey mould - Necrotroph - Secondary metabolite - Secretome

    Background: Fungi of the genus Botrytis (presently containing ~ 35 species) are able to infect more than 1400 different plant species and cause losses in a wide range of crops of economic importance. The best studied species is B. cinerea, which has a broad host range and is one of the best studied necrotrophic plant pathogenic fungi. Most other Botrytis spp. have a narrow host range and have been studied in less detail. To characterize genomic variation among different representatives of Botrytis spp., we sequenced and annotated the draft genomes of nine Botrytis species: B. calthae, B. convoluta, B. elliptica, B. galanthina, B. hyacinthi, B. narcissicola, B. paeoniae, B. porri and B. tulipae. Results: Bioinformatics and comparative genomics tools were applied to determine a core of 7668 shared protein families in all Botrytis species, which grouped them in two distinct phylogenetic clades. The secretome of all nine Botrytis spp. was similar in number (ranging from 716 to 784 predicted proteins). A detailed analysis of the molecular functions of the secretome revealed that shared activities were highly similar. Orthologs to effectors functionally studied in B. cinerea were also present in the other Botrytis species. A complex pattern of presence/absence of secondary metabolite biosynthetic key enzymes was observed. Conclusions: Comparative genomics of Botrytis show that overall, species share the main signatures and protein families in the secreted proteins, and of known effectors. Our study provides leads to study host range determinants in the genus Botrytis and provides a stepping stone to elucidate the roles of effector candidates in the infection process of these species.

    Antibacterial prenylated stilbenoids from peanut (Arachis hypogaea)
    Bruijn, Wouter J.C. de; Araya-Cloutier, Carla ; Bijlsma, Judith ; Swart, Anne de; Sanders, Mark G. ; Waard, Pieter de; Gruppen, Harry ; Vincken, Jean Paul - \ 2018
    Phytochemistry Letters 28 (2018). - ISSN 1874-3900 - p. 13 - 18.
    Antimicrobial - Leguminosae - Natural product - Prenylation - Secondary metabolite - Stilbene

    Stilbenoids are a class of secondary metabolites with a stilbene backbone that can be produced by peanut (Arachis hypogaea) as defence metabolites. Six monomeric prenylated stilbenoids, including the compound arachidin-6 (4), were isolated from extracts of fungus-elicited peanuts (Arachis hypogaea) using preparative liquid chromatography. Their structures were confirmed by MSn, HRMS and NMR spectroscopy and their antibacterial activity was evaluated against methicillin-resistant Staphylococcus aureus (MRSA). Similarly to other phenolic compounds, prenylated derivatives of stilbenoids were more active than their non-prenylated precursors piceatannol, resveratrol, and pinosylvin. Chiricanine A (6), a chain-prenylated pinosylvin derivative, was the most potent compound tested, with a minimum inhibitory concentration (MIC) of 12.5 μg mL−1. Arachidin-6 (4), a ring-prenylated piceatannol derivative, had moderate potency (MIC 50–75 μg mL−1). In conclusion, prenylated stilbenoids represent a group of potential natural antibacterials which show promising activity against MRSA.

    Genomic identification and analysis of specialized metabolite biosynthetic gene clusters in plants using plantiSMASH
    Kautsar, Satria A. ; Suarez Duran, Hernando G. ; Medema, Marnix H. - \ 2018
    In: Plant Chemical Genomics / Fauser, Friedrich, Jonikas, Martin, New York : Humana Press Inc. (Methods in Molecular Biology ) - ISBN 9781493978731 - p. 173 - 188.
    Bioinformatics - Biosynthetic gene cluster - Biosynthetic pathway - Genomic - Plant - Secondary metabolite - Specialized metabolite

    Plants produce a vast diversity of specialized metabolites, which play important roles in the interactions with their microbiome, as well as with animals and other plants. Many such molecules have valuable biological activities that render them (potentially) useful as medicines, flavors and fragrances, nutritional ingredients, or cosmetics. Recently, plant scientists have discovered that the genes for many biosynthetic pathways for the production of such specialized metabolites are physically clustered on the chromosome within biosynthetic gene clusters (BGCs). The Plant Secondary Metabolite Analysis Shell (plantiSMASH) allows for the automated identification of such plant BGCs, facilitates comparison of BGCs across genomes, and helps users to predict the functional interactions of pairs of genes within and between BGCs based on coexpression analysis. In this chapter, we provide a detailed protocol on how to install and run plantiSMASH, and how to interpret its results to draw biological conclusions that are supported by the data.

    Pyrrolizidine alkaloid variation in Senecio vulgaris populations from native and invasive ranges
    Cheng, Dandan ; Nguyen, Viet Thang ; Ndihokubwayo, Noel ; Ge, Jiwen ; Mulder, Patrick P.J. - \ 2017
    PeerJ 2017 (2017)8. - ISSN 2167-8359
    Biological invasion - Diversity - Liquid chromatography-tanderm mass spectrometry (LC-MS/MS) - Qualitative defense - Secondary metabolite - Shift Defense Hypothesis (SDH)

    Biological invasion is regarded as one of the greatest environmental problems facilitated by globalization. Some hypotheses about the invasive mechanisms of alien invasive plants consider the plant-herbivore interaction and the role of plant defense in this interaction. For example, the ``Shift Defense Hypothesis'' (SDH) argues that introduced plants evolve higher levels of qualitative defense chemicals and decreased levels of quantitative defense, as they are released of the selective pressures from specialist herbivores but still face attack from generalists. Common groundsel (Senecio vulgaris), originating from Europe, is a cosmopolitan invasive plant in temperate regions. As in other Senecio species, S. vulgaris contains pyrrolizidine alkaloids (PAs) as characteristic qualitative defense compounds. In this study, S. vulgaris plants originating from native and invasive ranges (Europe and China, respectively) were grown under identical conditions and harvested upon flowering. PA composition and concentration in shoot and root samples were determined using Liquid Chromatography-Tandem Mass Spectrometry (LC-MS/MS). We investigated the differences between native and invasive S. vulgaris populations with regard to quantitative and qualitative variation of PAs. We identified 20 PAs, among which senecionine, senecionine N-oxide, integerrimine Noxide and seneciphylline N-oxide were dominant in the roots. In the shoots, in addition to the four PAs dominant in roots, retrorsine N-oxide, spartioidine N-oxide and two non-identified PAs were also prevalent. The roots possessed a lower PA diversity but a higher total PA concentration than the shoots. Most individual PAs as well as the total PA concentration were strongly positively correlated between the roots and shoots. Both native and invasive S. vulgaris populations shared the pattern described above. However, there was a slight trend indicating lower PA diversity and lower total PA concentration in invasive S. vulgaris populations than native populations, which is not consistent with the prediction of SDH.

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