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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    Onderzoek naar een kennisbasis voor natuurgedreven landbouw
    Dijk, J. van; Veer, G. van der; Woestenburg, M. ; Stoop, J. ; Wijdeven, M. ; Veluw, K. van; Schrijver, R. ; Akker, J. van den; Woudenberg, E. van; Kerkhoven, D. ; Slot, M. - \ 2020
    WINK - 52
    Identification of Alternaria spp. as causal agent of dead flower buds disease of pear (Pyrus communis) in the Netherlands and methods for disease control
    Wenneker, Marcel ; Pham, Khanh T.K. ; Woudenberg, Joyce H.C. ; Thomma, Bart P.H.J. - \ 2019
    European Journal of Plant Pathology 155 (2019)3. - ISSN 0929-1873 - p. 967 - 981.
    Alternaria spp - Control - Pear flower buds - Pseudomonas syringae

    The occurrence of dead dormant flower buds is a common phenomenon of economic importance in the major pear production areas of Europe. Thus far, the cause of dead flower buds disease remained unknown. Several causes have been proposed, including insufficient tree chilling, unmet dormancy requirements, incompatibility between scion and cultivar, but also various biotic stress agents such as pathogens and pests. In this study, we tested the relationship between reduction of tree growth and dead flower bud incidences, but found no indication that growth regulation can prevent the occurrence of dead flower buds. It has been proposed that the bacterium Pseudomonas syringae pv. syringae may be the causal agent of dead flower buds of pear. However, although we found the bacterium as epiphyte and even as endophyte on and in flower buds, our findings argue that P. syringae pv. syringae is not the causal agent of dead flower buds disease in the Netherlands. In our research, Alternaria spp. were consistently found in diseased flower buds, and strong correlations between dead dormant flower buds and infection rates of flower buds with Alternaria spp. were recorded. The isolated Alternaria species were identified as A. arborescens SC and A. alternata SC. Field experiments for disease control showed that the disease may be controlled by specific fungicide applications. Thus, we propose that dead flower buds of pear in the Netherlands should be regarded as a fungal disease caused by A. alternata SC and potentially also A. arborescens SC.

    A rapid method to screen wild Solanum for resistance to early blight
    Wolters, Pieter J. ; Vos, Lennard de; Bijsterbosch, Gerard ; Woudenberg, Joyce H.C. ; Visser, Richard G.F. ; Linden, Gerard van der; Vleeshouwers, Vivianne G.A.A. - \ 2019
    European Journal of Plant Pathology 154 (2019)1. - ISSN 0929-1873 - p. 109 - 114.
    A. grandis - A. protenta - A. solani - Alternaria - Disease assay - Wild potato

    Early blight of potato and tomato is caused by Alternaria fungi and negatively impacts crop yields. Environmental factors and plant maturity influence disease development, which is usually kept under control by fungicide applications. Wild tuber-bearing Solanum section Petota species are a promising source of resistance to early blight that could be used to control the disease, for example by crossbreeding or modern breeding approaches. An efficient screening method is a first prerequisite for the identification of resistant genotypes in wild Solanum germplasm. Here, we describe a protocol that can be used to rapidly screen for resistance to early blight in wild Solanum collections. This protocol provides a good starting point for the identification of resistant genotypes and is a step towards breeding for resistance to early blight using wild Solanum species.

    Vergelijking enkele sorghumrassen met snijmaïs op zandgrond : resultaten van éénjarige veldproef 2018
    Kasper, G.J. ; Schilder, H. - \ 2019
    Wageningen : Wageningen Livestock Research (Wageningen Livestock Research rapport 1143) - 32
    The Waterboard Vallei en Veluwe, and LaMi have financed comparative research of five sorghum crops and maize on a sandy soil in Woudenberg. The average yield of the five sorghum crops studied was low and equal to those of maize (11.5 tonnes DM/ha). The most important causes are the dry and warm climate, and the poorer soil structure. It should be noted that the maize variety was sown three to four weeks later than normal. With regard to the feed value most sorghum crops have a relatively low starch content, low DCOM (Digestibility Coefficient of the Organic Matter), a relatively high crude protein content and a relatively high ADL (Acid Detergent Fiber) content, compared to maize. It was concluded that the sorghum crop STH 16149 was not suitable as a high-quality fodder crop. The soil moisture content did not differ between varieties. In the soil layer 0-90 cm, maize had the highest residual-N: 62 kg residual-N/ha, whereas the average value of the five sorghum varieties in this layer was 48 kg residual-N/ha. No significant differences between varieties were observed in residual-N (kg/ha) per soil layer 0-30 cm, 30-60 cm and 60-90 cm.
    First report of Alternaria arborescens species complex causing leaf blotch and associated premature leaf drop of ‘golden delicious’ apple trees in the Netherlands
    Wenneker, M. ; Pham, K.T.K. ; Woudenberg, J.H.C. ; Thomma, B.P.H.J. - \ 2018
    Plant Disease 102 (2018)8. - ISSN 0191-2917 - p. 1654 - 1654.
    First report of Boeremia exigua var. Exigua causing stem and leaf spot on common speedwell in Switzerland
    Michel, V.V. ; Daepp, M. ; Woudenberg, J.H.C. ; Gruyter, J. de; Wit, P.J.G.M. de - \ 2018
    Plant Disease 102 (2018)2. - ISSN 0191-2917 - p. 440 - 440.
    Stemphylium revisited
    Woudenberg, J.H.C. ; Hanse, B. ; Leeuwen, G.C.M. van; Groenewald, J.Z. ; Crous, P.W. - \ 2017
    Studies in Mycology 87 (2017). - ISSN 0166-0616 - p. 77 - 103.
    Morphology - Multi-gene phylogeny - Pleospora

    In 2007 a new Stemphylium leaf spot disease of Beta vulgaris (sugar beet) spread through the Netherlands. Attempts to identify this destructive Stemphylium sp. in sugar beet led to a phylogenetic revision of the genus. The name Stemphylium has been recommended for use over that of its sexual morph, Pleospora, which is polyphyletic. Stemphylium forms a well-defined monophyletic genus in the Pleosporaceae, Pleosporales (Dothideomycetes), but lacks an up-to-date phylogeny. To address this issue, the internal transcribed spacer 1 and 2 and intervening 5.8S nr DNA (ITS) of all available Stemphylium and Pleospora isolates from the CBS culture collection of the Westerdijk Institute (N = 418), and from 23 freshly collected isolates obtained from sugar beet and related hosts, were sequenced to construct an overview phylogeny (N = 350). Based on their phylogenetic informativeness, parts of the protein-coding genes calmodulin and glyceraldehyde-3-phosphate dehydrogenase were also sequenced for a subset of isolates (N = 149). This resulted in a multi-gene phylogeny of the genus Stemphylium containing 28 species-clades, of which five were found to represent new species. The majority of the sugar beet isolates, including isolates from the Netherlands, Germany and the UK, clustered together in a species clade for which the name S. beticola was recently proposed. Morphological studies were performed to describe the new species. Twenty-two names were reduced to synonymy, and two new combinations proposed. Three epitypes, one lectotype and two neotypes were also designated in order to create a uniform taxonomy for Stemphylium.

    Diversity and movement of indoor Alternaria alternata across the mainland USA
    Woudenberg, J.H.C. ; Merwe, N.A. Van Der; Jurjevic, Z. ; Groenewald, J.Z. ; Crous, P.W. - \ 2015
    Fungal Genetics and Biology 81 (2015). - ISSN 1087-1845 - p. 62 - 72.
    Alternaria spp. from sect. Alternaria are frequently associated with hypersensitivity pneumonitis, asthma and allergic fungal rhinitis and sinusitis. Since Alternaria is omnipresent in the outdoor environment, it is thought that the indoor spore concentration is mainly influenced by the outdoor spore concentration. However, few studies have investigated indoor Alternaria isolates, or attempted a phylogeographic or population genetic approach to investigate their movement. Therefore, the aim of the current study was to investigate the molecular diversity of indoor Alternaria isolates in the USA, and to test for recombination, using these approaches. Alternaria isolates collected throughout the USA were identified using ITS, gapdh and endoPG gene sequencing. This was followed by genotyping and population genetic inference of isolates belonging to Alternaria sect. Alternaria together with 37 reference isolates, using five microsatellite markers. Phylogenetic analyses revealed that species of Alternaria sect. Alternaria represented 98% (153 isolates) of the indoor isolates collected throughout the USA, of which 137 isolates could be assigned to A. alternata, 15 to the A. arborescens species complex and a single isolate to A. burnsii. The remaining 2% (3 isolates) represented sect. Infectoriae (single isolate) and sect. Pseudoulocladium (2 isolates). Population assignment analyses of the 137 A. alternata isolates suggested that subpopulations did not exist within the sample. The A. alternata isolates were thus divided into four artificial subpopulations to represent four quadrants of the USA. Forty-four isolates representing the south-western quadrant displayed the highest level of uniqueness based on private alleles, while the highest level of gene flow was detected between the south-eastern (32 isolates) and south-western quadrants. Genotypic diversity was high for all quadrants, and a test for linkage disequilibrium suggested that A. alternata has a cryptic sexual cycle. These statistics could be correlated with environmental factors, suggesting that indoor A. alternata isolates, although extremely diverse, have a continental distribution and high levels of gene flow over the continent.
    Alternaria section Alternaria: Species, formae speciales or pathotypes?
    Woudenberg, J.H.C. ; Seidl, M.F. ; Groenewald, J.Z. ; Vries, M. de; Stielow, J.B. ; Thomma, B. ; Crous, P.W. - \ 2015
    Studies in Mycology 82 (2015). - ISSN 0166-0616 - p. 1 - 21.
    The cosmopolitan fungal genus Alternaria consists of multiple saprophytic and pathogenic species. Based on phylogenetic and morphological studies, the genus is currently divided into 26 sections. Alternaria sect. Alternaria contains most of the small-spored Alternaria species with concatenated conidia, including important plant, human and postharvest pathogens. Species within sect. Alternaria have been mostly described based on morphology and / or host-specificity, yet molecular variation between them is minimal. To investigate whether the described morphospecies within sect. Alternaria are supported by molecular data, whole-genome sequencing of nine Alternaria morphospecies supplemented with transcriptome sequencing of 12 Alternaria morphospecies as well as multi-gene sequencing of 168 Alternaria isolates was performed. The assembled genomes ranged in size from 33.3–35.2 Mb within sect. Alternaria and from 32.0–39.1 Mb for all Alternaria genomes. The number of repetitive sequences differed significantly between the different Alternaria genomes; ranging from 1.4–16.5 %. The repeat content within sect. Alternaria was relatively low with only 1.4–2.7 % of repeats. Whole-genome alignments revealed 96.7–98.2 % genome identity between sect. Alternaria isolates, compared to 85.1–89.3 % genome identity for isolates from other sections to the A. alternata reference genome. Similarly, 1.4–2.8 % and 0.8–1.8 % single nucleotide polymorphisms (SNPs) were observed in genomic and transcriptomic sequences, respectively, between isolates from sect. Alternaria, while the percentage of SNPs found in isolates from different sections compared to the A. alternata reference genome was considerably higher; 8.0–10.3 % and 6.1–8.5 %. The topology of a phylogenetic tree based on the whole-genome and transcriptome reads was congruent with multi-gene phylogenies based on commonly used gene regions. Based on the genome and transcriptome data, a set of core proteins was extracted, and primers were designed on two gene regions with a relatively low degree of conservation within sect. Alternaria (96.8 and 97.3 % conservation). Their potential discriminatory power within sect. Alternaria was tested next to nine commonly used gene regions in sect. Alternaria, namely the SSU, LSU, ITS, gapdh, rpb2, tef1, Alt a 1, endoPG and OPA10-2 gene regions. The phylogenies from the two gene regions with a relatively low conservation, KOG1058 and KOG1077, could not distinguish the described morphospecies within sect. Alternaria more effectively than the phylogenies based on the commonly used gene regions for Alternaria. Based on genome and transcriptome comparisons and molecular phylogenies, Alternaria sect. Alternaria consists of only 11 phylogenetic species and one species complex. Thirty-five morphospecies, which cannot be distinguished based on the multi-gene phylogeny, are synonymised under A. alternata. By providing guidelines for the naming and identification of phylogenetic species in Alternaria sect. Alternaria, this manuscript provides a clear and stable species classification in this section
    Restyling Alternaria
    Woudenberg, J.H.C. - \ 2015
    Wageningen University. Promotor(en): Pedro Crous; Pierre de Wit, co-promotor(en): J.Z. Groenewald. - Wageningen : Wageningen University - ISBN 9789462574106 - 250
    alternaria - taxonomie - fylogenie - moleculaire taxonomie - plantenziekteverwekkende schimmels - alternaria - taxonomy - phylogeny - molecular taxonomy - plant pathogenic fungi

    The omnipresent dematiaceous hyphomycete genus Alternaria is associated with a wide variety of substrates including seeds, plants, agricultural products, humans, soil and even the atmosphere. It includes saprophytic, endophytic and pathogenic species, among which multiple plant pathogens, post-harvest pathogens, and human pathogens (causative agents of phaeohyphomycosis and hypersensitivity reactions). Molecular studies reveal that the Alternaria complex comprises nine genera. Within this complex several genera are non-monophyletic and Alternaria species cluster into multiple distinct species clades, which are not always correlated with species-groups based on morphological characteristics. The most commonly reported species in literature and type species of the genus Alternaria, A. alternata, also comprises one such species-group. The small-spored Alternaria species within this group are mainly described based on morphology and / or host-specificity, but are difficult to distinguish based on molecular techniques alone. As A. alternata is considered as one of the most prolific producers of fungal allergens and is reported as pathogen on over 100 host plants, correct species identification is of utmost importance. The research presented in this thesis discusses the taxonomic status of Alternaria and its related genera, with a further focus on the two biggest and most important species complexes; the large-spored A. porri and small-spored A. alternata species complexes. With the phylogenies and classifications presented in this thesis, more robust and understandable taxonomy and nomenclature in Alternaria and allied genera within the Alternaria complex are created.

    Chapter 1 gives a general introduction to the genus Alternaria and related genera. The history of the genus and its economic importance as plant pathogen, post-harvest pathogen, causative agent of phaeohyphomycosis and common allergen causing hypersensitivity reactions are summarized. The introduction of the morphological species complexes, based on characters of the conidia, the pattern of chain formation, and the nature of the apical extensions of conidia are treated. Molecular studies recognise seven Alternaria species-groups within the Alternaria complex. Besides Alternaria, eight other genera are assigned to the Alternaria complex based on molecular and morphological studies.

    Chapter 2 focusses on the relationship of Alternaria and its closely related genera within the broader Alternaria complex. The phylogenetic lineages within the Alternaria complex are delineated based on nucleotide sequence data of parts of the 18S nrDNA (SSU), 28S nrDNA (LSU), the internal transcribed spacer regions 1 and 2 and intervening 5.8S nrDNA (ITS), glyceraldehyde-3-phosphate dehydrogenase (GAPDH), RNA polymerase second largest subunit (RPB2) and translation elongation factor 1-alpha (TEF1) gene regions. The phylogenetic data reveal a Stemphylium clade sister to Embellisia annulata and a big Alternaria clade. The Alternaria clade contains six monotypic lineages and 24 internal clades, which are treated as sections of Alternaria. In order to create a stable phylogenetic taxonomy, and supported by i) a well-supported phylogenetic node in multiple analyses, ii) a high-similarity of clades within Alternaria based on SSU, LSU and ITS data, and iii) variation in the clade order between the different gene phylogenies, 13 genera are placed into synonymy with Alternaria. Embellisia annulata is synonymized with Dendryphiella salina, and together with D. arenariae placed in the new genus Paradendryphiella. The sexual genera Clathrospora and Comoclathris, with asexual forms linked to Alternaria, cluster within the Pleosporaceae, as does Alternaria, but outside Alternaria s. str. The genus Alternariaster, described to accommodate Alternaria helianthi, clusters within the Leptosphaeriaceae.

    Chapter 3 describes the reappraisal of the genus Alternariaster. Alternaria helianthi, the causal agent of leaf spot on Helianthus annuus (sunflower) was segregated from Alternaria based on conidial morphology, and placed in the new genus Alternariaster. A multi-gene phylogeny of parts of the ITS, LSU, RPB2 and GAPDH gene regions placed a fungal pathogen associated with leaf spot on Bidens sulphurea (yellow cosmos) in Brazil in close relation with Al. helianthi. Based on the close phylogenetic relation to Al. helianthi, but distinct morphological and pathogenicity characters, the fungal pathogen associated with leaf spot on B. sulphurea is newly described as Al. bidentis.

    Chapter 4 treats the Alternaria species which form the largest section of Alternaria, sect. Porri. This section contains almost all Alternaria species with medium to large conidia with long beaks, some of which are important plant pathogens. A multi-gene phylogeny on parts of the ITS, GAPDH, RPB2, TEF1 and Alternaria major allergen (Alt a 1) gene regions, supplemented with morphological and cultural studies, forms the basis for species recognition in this section. The polyphasic data reveal 63 species in sect. Porri, of which 10 are newly described, and 27 names are synonymized.

    Chapter 5 treats the small-spored Alternaria species, which reside in sect. Alternaria. A lot of confusion around the naming of species within this section exists, since the naming is mostly based on morphology and host-specificity, although the molecular variation is minimal. Whole genome sequencing, combined with transcriptome profiling and multi-gene sequencing of nine gene regions, SSU, LSU, ITS, GAPDH, RPB2, TEF1, Alt a 1, endopolygalacturonase (endoPG) and an anonymous gene region (OPA10-2), is used to create a clear and stable species classification in this section. The nine sequenced Alternaria genomes range in size from 32.0 - 39.1 Mb. The number of repetitive sequences varies significantly, with a relative low percentage of repeats within sect. Alternaria. The genome identity within sect. Alternaria is high, compared to the genome identity for isolates from other sections to the A. alternata reference genome. Similarly, a relative low percentage of single nucleotide polymorphisms (SNPs) were observed in genomic and transcriptomic sequences between isolates from sect. Alternaria, compared to the percentage of SNP’s found in isolates from different sections compared to the A. alternata reference genome. A set of core proteins was extracted from the genome and transcriptome data, and primers were designed on two eukaryotic orthologous group (KOG) protein loci with a relatively low degree of conservation within section Alternaria. The phylogenies from these two gene regions, KOG1058 and KOG1077, could not distinguish the described morphospecies within sect. Alternaria better than the phylogenies based on the nine commonly used gene regions for Alternaria. Based on genome and transcriptome comparisons and molecular phylogenies, Alternaria sect. Alternaria consists of only 11 phylogenetic species and one species complex. Thirty-five morphospecies are synonymized under A. alternata. The subclades that are formed by these isolates are incongruent between the different gene regions sequenced; no two genes show the same groupings for any of the over 100 isolates. A sequence-based identification guide is provided for the species which are now recognized in sect. Alternaria. None of the genes sequenced in this study can distinguish all of the species recognized here on its own.

    Chapter 6 investigates the molecular diversity of indoor Alternaria isolates in the USA, with the help of a phylogeographic / population genetic approach. Isolates collected throughout the USA were identified using ITS, GAPDH and endoPG gene sequencing, followed by genotyping and population genetic inference of the sect. Alternaria isolates and 37 reference isolates, using five microsatellite markers. Phylogenetic analyses revealed that 98 % (153 isolates) of the indoor isolates consisted of species from Alternaria sect. Alternaria. The remaining 2 % (three isolates) represented one sect. Infectoriae and two sect. Pseudoulocladium isolates. From the 153 isolates that belonged to sect. Alternaria, one could be assigned to A. burnsii, 15 to the A. arborescens species complex and the remaining 137 isolates were identified as A. alternata. Based on the microsatellite data, no specific indoor population could be distinguished. Population assignment analyses of the A. alternata isolates suggested that subpopulations did not exist within the sample, which we thus divided into four artificial subpopulations to represent four quadrants of the USA. Genotypic diversity was extremely high for all quadrants and a test for linkage disequilibrium suggested that A. alternata has a cryptic sexual cycle. The SouthWest-USA population displayed the highest level of uniqueness, based on private alleles. Intriguingly, the highest amount of gene flow, between SouthWest-USA and SouthEast-USA, correlated with the west-to-east movement of the antitrade winds. This suggests that indoor A. alternata isolates, although extremely diverse, have a continental distribution and high levels of gene flow over the continent.

    Chapter 7 discusses the data presented in this thesis. The implications of the performed studies are placed in a broader context, with a focus on the relation between morphology and the new species classification based on molecular tools and the use of genome data in contrast to multi-gene data.

    Real-time adaptive residual calculation for detecting trend deviations in systems with natural variability
    Woudenberg, Steven P.D. ; Gaag, Linda C. van der; Feelders, Ad ; Elbers, Armin R.W. - \ 2014
    In: Advances in Intelligent DataAnalysis XIII - 13th International Symposium, IDA 2014, Proceedings. - Springer Verlag (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) ) - ISBN 9783319125701 - p. 380 - 392.

    Real-time detection of potential problems from animal production data is challenging, since these data do not just include chance fluctuations but reflect natural variability as well. This variability makes future observations from a specific instance of the production process hard to predict, even though a general trend may be known. Given the importance of well-established residuals for reliable detection of trend deviations, we present a new method for real-time residual calculation which aims at reducing the effects of natural variability and hence results in residuals reflecting chance fluctuations mostly. The basic idea is to exploit prior knowledge about the general expected data trend and to adapt this trend to the instance of the production process at hand as real data becomes available. We study the behavioural performance of our method by means of artificially generated and real-world data, and compare it against Bayesian linear regression.

    Real-time adaptive problem detection in poultry
    Woudenberg, S.P.D. ; Gaag, L.C. van der; Feelders, A. ; Elbers, A.R.W. - \ 2014
    In: 21st European Conference on Artificial Intelligence. - IOS Press - ISBN 9781614994183 - p. 1217 - 1218.
    Real-time identification of unexpected values upon monitoring the production parameters of egg laying hens is quite challenging, as the collected data includes natural variability in addition to chance fluctuation. We present an adaptive method for calculating residuals that reflect the latter type of fluctuation only, and thereby provide for more accurate detection of potential problems. We report on the application of our method to real-world poultry data.
    Large-spored Alternaria pathogens in section Porri disentangled
    Woudenberg, J.H.C. ; Truter, M. ; Groenewald, J.Z. ; Crous, P.W. - \ 2014
    Studies in Mycology 79 (2014). - ISSN 0166-0616 - p. 1 - 47.
    south-africa - solani - themes - disease - blight - diagnostics - tomatophila - phylogeny - potatoes - dauci
    The omnipresent fungal genus Alternaria was recently divided into 24 sections based on molecular and morphological data. Alternaria sect. Porri is the largest section, containing almost all Alternaria species with medium to large conidia and long beaks, some of which are important plant pathogens (e.g. Alternaria porri, A. solani and A. tomatophila). We constructed a multi-gene phylogeny on parts of the ITS, GAPDH, RPB2, TEF1 and Alt a 1 gene regions, which, supplemented with morphological and cultural studies, forms the basis for species recognition in sect. Porri. Our data reveal 63 species, of which 10 are newly described in sect. Porri, and 27 species names are synonymised. The three known Alternaria pathogens causing early blight on tomato all cluster in one clade, and are synonymised under the older name, A. linariae. Alternaria protenta, a species formerly only known as pathogen on Helianthus annuus, is also reported to cause early blight of potato, together with A. solani and A. grandis. Two clades with isolates causing purple blotch of onion are confirmed as A. allii and A. porri, but the two species cannot adequately be distinguished based on the number of beaks and branches as suggested previously. This is also found among the pathogens of Passifloraceae, which are reduced from four to three species. In addition to the known pathogen of sweet potato, A. bataticola, three more species are delineated of which two are newly described. A new Alternaria section is also described, comprising two large-spored Alternaria species with concatenate conidia.
    Een gezond binnenmilieu in de toekomst
    Passchier, W.F. ; Woudenberg, F. ; Berg, M. van den; Erisman, J.W. ; Hazel, P.J. van den; Lebret, E. ; Leemans, R. ; Sluijs, J.P. van der; Vliet, P.W. van - \ 2013
    Den Haag : Gezondheidsraad (Publikatie / Gezondheidsraad 2013/17) - ISBN 9789055499526 - 44 p.
    Development of a clinical decision-support system for early detection of low pathogenic avian influenza outbreaks in poultry
    Woudenberg, S.P.D. ; Gaag, L.C. van der; Elbers, A.R.W. - \ 2013
    In: Proceedings 3rd Annual meeting of AniBioThreat, 5-7 February 2013, Åre, Sweden. - - p. 65 - 65.
    Reappraisal of the genus Alternariaster (Dothideomycetes)
    Alves, J.L. ; Woudenberg, J.H.C. ; Duarte, L.L. ; Crous, P.W. ; Barreto, R.W. - \ 2013
    Persoonia 31 (2013). - ISSN 0031-5850 - p. 77 - 85.
    inference - mrbayes - brazil
    Alternariaster was erected in 2007 to accommodate Alternaria helianthi, a fungal species known to cause leaf spots on Helianthus annuus (sunflower). It was segregated from Alternaria based on conidial morphology. Recently an unknown alternaria-like dematiaceous fungus was found associated with leaf spots on Bidens sulphurea (yellow cosmos) in Brazil. Based on a multi-gene phylogeny of parts of the ITS and LSU genes, this fungus was placed within the Leptosphaeriaceae with Alternariaster helianthi as its closest neighbour. Additional genes sequenced, RPB2 and GAPDH, confirmed this close relationship. The fungus on B. sulphurea has smaller conidia, 50¿97.5 × 12.5¿20 µm, compared to Al. helianthi, 80¿160 × 18¿30 µm, and lacks oblique or transverse septa which can be present in Al. helianthi. Pathogenicity studies on 18 plant species belonging to the Compositae showed that the B. sulphurea fungus only infected B. sulphurea, whereas Al. helianthi infected H. annuus and Galinsoga quadriradiata, a yet unreported host of Al. helianthi. The fungus causing disease on B. sulphurea is hence closely related but phylogenetically, morphologically and pathologically distinct from Al. helianthi, and therefore newly described as Alternariaster bidentis. The collection of a second species in the genus Alternariaster and the multigene phylogenetic analysis of these two species, confirmed Alternariaster to be a well-delimited genus in the Leptosphaeriaceae rather than the Pleosporaceae, to which Alternaria belongs
    Alternaria redefined
    Woudenberg, J.H.C. ; Groenewald, J.Z. ; Binder, M. ; Crous, P.W. - \ 2013
    Studies in Mycology 75 (2013)1. - ISSN 0166-0616 - p. 171 - 212.
    ribosomal dna - phylogenetic-relationships - species-group - ulocladium - embellisia - genus - identification - sequences - taxonomy - nuclear
    Alternaria is a ubiquitous fungal genus that includes saprobic, endophytic and pathogenic species associated with a wide variety of substrates. In recent years, DNA-based studies revealed multiple non-monophyletic genera within the Alternaria complex, and Alternaria species clades that do not always correlate to species-groups based on morphological characteristics. The Alternaria complex currently comprises nine genera and eight Alternaria sections. The aim of this study was to delineate phylogenetic lineages within Alternaria and allied genera based on nucleotide sequence data of parts of the 18S nrDNA, 28S nrDNA, ITS, GAPDH, RPB2 and TEF1-alpha gene regions. Our data reveal a Pleospora/Stemphylium clade sister to Embellisia annulata, and a well-supported Alternaria clade. The Alternaria clade contains 24 internal clades and six monotypic lineages, the assemblage of which we recognise as Alternaria. This puts the genera Allewia, Brachycladium, Chalastospora, Chmelia, Crivellia, Embellisia, Lewia, Nimbya, Sinomyces, Teretispora, Ulocladium, Undifilum and Ybotromyces in synonymy with Alternaria. In this study, we treat the 24 internal clades in the Alternaria complex as sections, which is a continuation of a recent proposal for the taxonomic treatment of lineages in Alternaria. Embellisia annulata is synonymised with Dendryphiella salina, and together with Dendryphiella arenariae, are placed in the new genus Paradendryphiella. The sexual genera Clathrospora and Comoclathris, which were previously associated with Alternaria, cluster within the Pleosporaceae, outside Alternaria s. str., whereas Alternariaster, a genus formerly seen as part of Alternaria, clusters within the Leptosphaeriaceae. Paradendryphiella is newly described, the generic circumscription of Alternaria is emended, and 32 new combinations and 10 new names are proposed. A further 10 names are resurrected, while descriptions are provided for 16 new Alternaria sections
    Redisposition of Phoma-like anamorphs in Pleosporales
    Gruyter, J. de; Woudenberg, J.H.C. ; Aveskamp, M.M. ; Verkley, G.J.M. ; Groenewald, J.Z. ; Crous, P.W. - \ 2013
    Studies in Mycology 75 (2013). - ISSN 0166-0616 - p. 1 - 36.
    ribosomal dna-sequences - winter oilseed rape - 7 mu-m - leptosphaeria-maculans - stem canker - molecular phylogeny - section plenodomus - small conidia - monograph - taxa
    The anamorphic genus Phoma was subdivided into nine sections based on morphological characters, and included teleomorphs in Didymella, Leptosphaeria, Pleospora and Mycosphaerella, suggesting the polyphyly of the genus. Recent molecular, phylogenetic studies led to the conclusion that Phoma should be restricted to Didymellaceae. The present study focuses on the taxonomy of excluded Phoma species, currently classified in Phoma sections Plenodomus, Heterospora and Pilosa. Species of Leptosphaeria and Phoma section Plenodomus are reclassified in Plenodomus, Subplenodomus gen. nov., Leptosphaeria and Paraleptosphaeria gen. nov., based on the phylogeny determined by analysis of sequence data of the large subunit 28S nrDNA (LSU) and Internal Transcribed Spacer regions 1 & 2 and 5.8S nrDNA (ITS). Phoma heteromorphospora, type species of Phoma section Heterospora, and its allied species Phoma dimorphospora, are transferred to the genus Heterospora stat. nov. The Phoma acuta complex (teleomorph Leptosphaeria doliolum), is revised based on a multilocus sequence analysis of the LSU, ITS, small subunit 18S nrDNA (SSU), ß-tubulin (TUB), and chitin synthase 1 (CHS-1) regions. Species of Phoma section Pilosa and allied Ascochyta species were determined to belong to Pleosporaceae based on analysis of actin (ACT) sequence data. Anamorphs that are similar morphologically to Phoma and described in Ascochyta, Asteromella, Coniothyrium, Plectophomella, Pleurophoma and Pyrenochaeta are included in this study. Phoma-like species, which grouped outside the Pleosporineae based on a LSU sequence analysis, are transferred to the genera Aposphaeria, Paraconiothyrium and Westerdykella. The genera Medicopsis gen. nov. and Nigrograna gen. nov. are introduced to accommodate the medically important species formerly known as Pyrenochaeta romeroi and Pyrenochaeta mackinnonii, respectively.
    Voordracht i.s.m. Raad van Beheer: Woudenberg
    Windig, Jack - \ 2012
    Voordracht i.s.m. Raad van Beheer, Woudenberg
    Windig, Jack - \ 2012
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