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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    Evolution of Hyaloperonospora effectors: ATR1 effector homologs from sister species of the downy mildew pathogen H. arabidopsidis are not recognised by RPP1WsB
    Solovyeva, I. ; Schmuker, A. ; Cano, L.M. ; Damme, M. van; Ploch, S. ; Kamoun, S. ; Thines, M. - \ 2015
    Mycological Progress 14 (2015). - ISSN 1617-416X - 9 p.
    plant immune-system - phylogenetic-relationships - peronospora-parasitica - oomycete effector - resistance gene - proteins - sequences - thaliana - reveals - plasmopara
    Like other plant-pathogenic oomycetes, downy mildew species of the genus Hyaloperonospora manipulate their hosts by secreting effector proteins. Despite intense research efforts devoted to deciphering the virulence and avirulence activities of effectors in the H. arabidopsidis/Arabidopsis thaliana pathosystem, there is only a single study in this pathosystem on the variation of effectors and resistance genes in natural populations, and the evolution of these effectors in the context of pathogen evolution is studied even less. In this work, the identification of A rabidopsis t haliana recognised (ATR)1-homologs is reported in two sister species of H. arabidopsidis, H. thlaspeos-perfoliati, and H. crispula, which are specialized on the host plants Microthlaspi perfoliatum and Reseda lutea, respectively. ATR1-diversity within these sister species of H. arabidopsidis was evaluated, and the ATR1-homologs from different isolates of H. thlaspeos-perfoliati and H. crispula were tested to see if they would be recognised by the previously characterised RPP1-WsB protein from A. thaliana. None of the effectors from the sister species was recognised, suggesting that due to the adaptation to altered or new targets after a host jump, features of variable effectors might vary to a degree that recognition of orthologous Avr-causing effectors is no longer effective and probably does not contribute to non-host immunity.
    Distributions, ex situ conservation priorities, and genetic resource potential of crop wild relatives of sweetpotato [Ipomoea batatas (L.) Lam., I. series Batatas]
    Khoury, C.K. ; Heider, B. ; Castaneda-Alvarez, N.P. ; Achicanoy, H.A. ; Sosa, C.C. ; Miller, R.E. ; Scotland, R.W. ; Wood, J.R.I. ; Rossel, G. ; Eserman, L.A. ; Jarret, R.L. ; Yencho, G.C. ; Bernau, V. ; Juarez, H. ; Sotelo, S. ; Haan, S. de; Struik, P.C. - \ 2015
    Frontiers in Plant Science 6 (2015). - ISSN 1664-462X - 14 p.
    species distribution models - phylogenetic-relationships - beta-carotene - convolvulaceae - sequences - diversity - evolution - bias - challenges - tolerance
    Crop wild relatives of sweetpotato [Ipomoea batatas (L.) Lam., I. series Batatas] have the potential to contribute to breeding objectives for this important root crop. Uncertainty in regard to species boundaries and their phylogenetic relationships, the limited availability of germplasm with which to perform crosses, and the difficulty of introgression of genes from wild species has constrained their utilization. Here, we compile geographic occurrence data on relevant sweetpotato wild relatives and produce potential distribution models for the species. We then assess the comprehensiveness of ex situ germplasm collections, contextualize these results with research and breeding priorities, and use ecogeographic information to identify species with the potential to contribute desirable agronomic traits. The fourteen species that are considered the closest wild relatives of sweetpotato generally occur from the central United States to Argentina, with richness concentrated in Mesoamerica and in the extreme Southeastern United States. Currently designated species differ among themselves and in comparison to the crop in their adaptations to temperature, precipitation, and edaphic characteristics and most species also show considerable intraspecific variation. With 79% of species identified as high priority for further collecting, we find that these crop genetic resources are highly under-represented in ex situ conservation systems and thus their availability to breeders and researchers is inadequate. We prioritize taxa and specific geographic locations for further collecting in order to improve the completeness of germplasm collections. In concert with enhanced conservation of sweetpotato wild relatives, further taxonomic research, characterization and evaluation of germplasm, and improving the techniques to overcome barriers to introgression with wild species are needed in order to mobilize these genetic resources for crop breeding.
    Using RNA-Seq to assemble a rose transcriptome with more than 13,000 full-length expressed genes and to develop the WagRhSNP 68k Axiom SNP array for rose (Rosa L.)
    Koning, C.F.S. ; Esselink, G. ; Vukosavljev, M. ; Westende, W.P.C. van 't; Gitonga, V.W. ; Krens, F.A. ; Voorrips, R.E. ; Weg, W.E. van de; Schulz, D. ; Debener, T. ; Maliepaard, C.A. ; Arens, P.F.P. ; Smulders, M.J.M. - \ 2015
    Frontiers in Plant Science 6 (2015). - ISSN 1664-462X - 10 p.
    powdery mildew - markers - tool - identification - resistance - genome - diversity - sequences - platform - plant
    In order to develop a versatile and large SNP array for rose, we set out to mine ESTs from diverse sets of rose germplasm. For this RNA-Seq libraries containing about 700 million reads were generated from tetraploid cut and garden roses using Illumina paired-end sequencing, and from diploid Rosa multiflora using 454 sequencing. Separate de novo assemblies were performed in order to identify single nucleotide polymorphisms (SNPs) within and between rose varieties. SNPs among tetraploid roses were selected for constructing a genotyping array that can be employed for genetic mapping and marker-trait association discovery in breeding programs based on tetraploid germplasm, both from cut roses and from garden roses. In total 68,893 SNPs were included on the WagRhSNP Axiom array. Next, an orthology-guided assembly was performed for the construction of a non-redundant rose transcriptome database. A total of 21,740 transcripts had significant hits with orthologous genes in the strawberry (Fragaria vesca L.) genome. Of these 13,390 appeared to contain the full-length coding regions. This newly established transcriptome resource adds considerably to the currently available sequence resources for the Rosaceae family in general and the genus Rosa in particular.
    Composition and predicted functional ecology of mussel - associated bacteria in Indonesian marine lakes
    Cleary, D.F.R. ; Becking, L.E. ; Polonia, A. ; Freitas, R.M. ; Gomes, N. - \ 2015
    Antonie van Leeuwenhoek: : Nederlandsch tijdschrift voor hygiëne, microbiologie en serologie 107 (2015)3. - ISSN 0003-6072 - p. 821 - 834.
    microbial communities - brachidontes-exustus - scorched mussel - species complex - mytilidae - bivalvia - mycoplasma - diversity - islands - sequences
    In the present study, we sampled bacterial communities associated with mussels inhabiting two distinct coastal marine ecosystems in Kalimantan, Indonesia, namely, marine lakes and coastal mangroves. We used 16S rRNA gene pyrosequencing and predicted metagenomic analysis to compare microbial composition and function. Marine lakes are small landlocked bodies of seawater isolated to varying degrees from the open sea environment. They contain numerous endemic taxa and represent natural laboratories of speciation. Our primary goals were to (1) use BLAST search to identify closely related organisms to dominant bacterial OTUs in our mussel dataset and (2) to compare bacterial communities and enrichment in the predicted bacterial metagenome among lakes. Our sequencing effort yielded 3553 OTUs belonging to 44 phyla, 99 classes and 121 orders. Mussels in the largest marine lake (Kakaban) and the coastal mangrove habitat were dominated by bacteria belonging to the phylum Proteobacteria whereas smaller lakes, located on the island of Maratua, were dominated by bacteria belonging to the phyla Firmicutes and Tenericutes. The single most abundant OTU overall was assigned to the genus Mycoplasma. There were several significant differences among locations with respect to metabolic pathways. These included enrichment of xenobiotic biodegradation pathways in the largest marine lake and coastal mangrove. These locations were also the most enriched with respect to nitrogen metabolism. The presence of genes related to isoquinoline alkaloids, polyketides, hydrolases, mono and dioxygenases in the predicted analysis of functional pathways is an indication that the bacterial communities of Brachidontes mussels may be potentially important sources of new marine medicines and enzymes of industrial interest. Future work should focus on measuring how mussel microbial communities influence nutrient dynamics within the marine lake environment and isolating microbes with potential biotechnological applications.
    Small Homologous Blocks in Phytophthora Genomes Do Not Point to an Ancient Whole-Genome Duplication
    Hooff, J.J.E. van; Snel, B. ; Seidl, M.F. - \ 2014
    Genome Biology and Evolution 6 (2014)5. - ISSN 1759-6653 - p. 1079 - 1085.
    pathogen phytophthora - maximum-likelihood - evolution - genes - consequences - mechanisms - adaptation - repertoire - sequences - infestans
    Genomes of the plant-pathogenic genus Phytophthora are characterized by small duplicated blocks consisting of two consecutive genes (2HOM blocks) and by an elevated abundance of similarly aged gene duplicates. Both properties, in particular the presence of 2HOM blocks, have been attributed to a whole-genome duplication (WGD) at the last common ancestor of Phytophthora. However, large intraspecies synteny-compelling evidence for a WGD-has not been detected. Here, we revisited the WGD hypothesis by deducing the age of 2HOM blocks. Two independent timing methods reveal that the majority of 2HOM blocks arose after divergence of the Phytophthora lineages. In addition, a large proportion of the 2HOM block copies colocalize on the same scaffold. Therefore, the presence of 2HOM blocks does not support a WGD at the last common ancestor of Phytophthora. Thus, genome evolution of Phytophthora is likely driven by alternative mechanisms, such as bursts of transposon activity.
    The Colletotrichum gigasporum species complex
    Liu, F. ; Cai, L. ; Crous, P.W. ; Damm, U. - \ 2014
    Persoonia 33 (2014). - ISSN 0031-5850 - p. 83 - 97.
    sp-nov - primer sets - endophytes - pathogens - china - gloeosporioides - anthracnose - diversity - sequences - acutatum
    In a preliminary analysis, 21 Colletotrichum strains with large conidia preserved in the CBS culture collection clustered with a recently described species, C. gigasporum, forming a clade distinct from other currently known Colletotrichum species complexes. Multi-locus phylogenetic analyses (ITS, ACT, TUB2, CHS-1, GAPDH) as well as each of the single-locus analyses resolved seven distinct species, one of them being C. gigasporum. Colletotrichum gigasporum and its close allies thus constitute a previously unknown species complex with shared morphological features. Five of the seven species accepted in the C. gigasporum species complex are described here as novel species, namely C. arxii, C. magnisporum, C. pseudomajus, C. radicis and C. vietnamense. A species represented by a single sterile strain, namely CBS 159.50, was not described as novel species, and is treated as Colletotrichum sp. CBS 159.50. Furthermore, C. thailandicum is reduced to synonymy with C. gigasporum.
    Polycistronic expression of a ß-carotene biosynthetic pathway in Saccharomyces cerevisiae coupled to ß-ionone production
    Beekwilder, J. ; Rossum, H.M. ; Koopman, F. ; Sonntag, F. ; Buchhaupt, M. ; Schrader, J. ; Hall, R.D. ; Bosch, H.J. ; Pronk, J.T. ; Maris, A.J.A. van; Daran, J.M. - \ 2014
    Journal of Biotechnology 192 (2014)partB. - ISSN 0168-1656 - p. 383 - 392.
    cleavage dioxygenase - yeast - genes - sequences - transformation - translation - polyprotein - versatile - genome - strain
    The flavour and fragrance compound ß-ionone, which naturally occurs in raspberry and many other fruits and flowers, is currently produced by synthetic chemistry. This study describes a synthetic biology approach for ß-ionone production from glucose by Saccharomyces cerevisiae that is partially based on polycistronic expression. Experiments with model proteins showed that the T2A sequence of the Thosea asigna virus mediated efficient production of individual proteins from a single transcript in S. cerevisiae. Subsequently, three ß-carotene biosynthesis genes from the carotenoid-producing ascomycete Xanthophyllomyces dendrorhous (crtI, crtE and crtYB) were expressed in S. cerevisiae from a single polycistronic construct. In this construct, the individual crt proteins were separated by T2A sequences. Production of the individual proteins from the polycistronic construct was confirmed by Western blot analysis and by measuring the production of ß-carotene. To enable ß-ionone production, a carotenoid-cleavage dioxygenase from raspberry (RiCCD1) was co-expressed in the ß-carotene producing strain. In glucose-grown cultures with a second phase of dodecane, ß-ionone and geranylacetone accumulated in the organic phase. Thus, by introducing a polycistronic construct encoding a fungal carotenoid pathway and an expression cassette encoding a plant dioxygenase, a novel microbial production system has been established for a fruit flavour compound.
    Dynamics of the Microbiota in Response to Host Infection
    Belzer, C. ; Gerber, G.K. ; Roeselers, G. ; Delaney, M. ; DuBois, A. ; Liu, Q. ; Belavusava, V. ; Yeliseyev, V. ; Houseman, A. ; Onderdonk, A. ; Cavanaugh, C. ; Bry, L. - \ 2014
    PLoS ONE 9 (2014)7. - ISSN 1932-6203
    citrobacter-rodentium infection - gene-expression data - mucosal infection - gut microbiome - mice - inflammation - diversity - sequences - pathogen - colitis
    Longitudinal studies of the microbiota are important for discovering changes in microbial communities that affect the host. The complexity of these ecosystems requires rigorous integrated experimental and computational methods to identify temporal signatures that promote physiologic or pathophysiologic responses in vivo. Employing a murine model of infectious colitis with the pathogen Citrobacter rodentium, we generated a 2-month time-series of 16S rDNA gene profiles, and quantitatively cultured commensals, from multiple intestinal sites in infected and uninfected mice. We developed a computational framework to discover time-varying signatures for individual taxa, and to automatically group signatures to identify microbial sub-communities within the larger gut ecosystem that demonstrate common behaviors. Application of this model to the 16S rDNA dataset revealed dynamic alterations in the microbiota at multiple levels of resolution, from effects on systems-level metrics to changes across anatomic sites for individual taxa and species. These analyses revealed unique, time-dependent microbial signatures associated with host responses at different stages of colitis. Signatures included a Mucispirillum OTU associated with early disruption of the colonic surface mucus layer, prior to the onset of symptomatic colitis, and members of the Clostridiales and Lactobacillales that increased with successful resolution of inflammation, after clearance of the pathogen. Quantitative culture data validated findings for predominant species, further refining and strengthening model predictions. These findings provide new insights into the complex behaviors found within host ecosystems, and define several time-dependent microbial signatures that may be leveraged in studies of other infectious or inflammatory conditions.
    Binning metagenomic contigs by coverage and composition
    Alneberg, J. ; Bjarnason, B.S. ; Bruijn, I. de; Schirmer, M. ; Quick, J. ; Ijaz, U.Z. ; Lahti, L.M. ; Loman, N.J. ; Andersson, A.F. ; Quince, C. - \ 2014
    Nature Methods : techniques for life scientists and chemists 11 (2014). - ISSN 1548-7091 - p. 1144 - 1146.
    sequences - genomes
    Shotgun sequencing enables the reconstruction of genomes from complex microbial communities, but because assembly does not reconstruct entire genomes, it is necessary to bin genome fragments. Here we present CONCOCT, a new algorithm that combines sequence composition and coverage across multiple samples, to automatically cluster contigs into genomes. We demonstrate high recall and precision on artificial as well as real human gut metagenome data sets.
    An integrated catalog of reference genes in the human gut microbiome
    Li, J. ; Jia, H. ; Cai, X. ; Zhong, H. ; Feng, Q. ; Sunagawa, S. ; Arumugam, M. ; Kultima, J.R. ; Prifti, E. ; Nielsen, T. ; Juncker, A.S. ; Manichanh, C. ; Chen, B. ; Zhang, W. ; Levenez, F. ; Xu, X. ; Xiao, L. ; Liang, S. ; Zhang, D. ; Zhang, Z. ; Chen, W. ; Zhao, H. ; Al-Aama, J.Y. ; Edris, S. ; Yang, H. ; Hansen, H. ; Nielsen, H.B. ; Brunak, S. ; Kristiansen, K. ; Guarner, F. ; Pedersen, O. ; Doré, J. ; Ehrlich, S.D. ; Bork, P. ; Wang, J. ; Vos, W.M. de; Tims, S. ; Zoetendal, E.G. ; Kleerebezem, M. - \ 2014
    Nature Biotechnology 32 (2014)8. - ISSN 1087-0156 - p. 834 - 841.
    eukaryotic diversity - fecal microbiota - population-size - metagenome - sequences - genomes - tool - alignment - impact - twins
    Many analyses of the human gut microbiome depend on a catalog of reference genes. Existing catalogs for the human gut microbiome are based on samples from single cohorts or on reference genomes or protein sequences, which limits coverage of global microbiome diversity. Here we combined 249 newly sequenced samples of the Metagenomics of the Human Intestinal Tract (MetaHit) project with 1,018 previously sequenced samples to create a cohort from three continents that is at least threefold larger than cohorts used for previous gene catalogs. From this we established the integrated gene catalog (IGC) comprising 9,879,896 genes. The catalog includes close-to-complete sets of genes for most gut microbes, which are also of considerably higher quality than in previous catalogs. Analyses of a group of samples from Chinese and Danish individuals using the catalog revealed country-specific gut microbial signatures. This expanded catalog should facilitate quantitative characterization of metagenomic, metatranscriptomic and metaproteomic data from the gut microbiome to understand its variation across populations in human health and disease.
    BioHackathon series in 2011 and 2012: penetration of ontology and linked data in life science domains
    Katayama, T. ; Wilkinson, M.D. ; Aoki-Kinoshita, K.F. ; Prins, J.C.P. - \ 2014
    Journal of Biomedical Semantics 5 (2014). - ISSN 2041-1480
    genome analysis environment - metabolic pathways - web services - gene - sequences - software - biology - normalization - collection - glycomics
    The application of semantic technologies to the integration of biological data and the interoperability of bioinformatics analysis and visualization tools has been the common theme of a series of annual BioHackathons hosted in Japan for the past five years. Here we provide a review of the activities and outcomes from the BioHackathons held in 2011 in Kyoto and 2012 in Toyama. In order to efficiently implement semantic technologies in the life sciences, participants formed various sub-groups and worked on the following topics: Resource Description Framework (RDF) models for specific domains, text mining of the literature, ontology development, essential metadata for biological databases, platforms to enable efficient Semantic Web technology development and interoperability, and the development of applications for Semantic Web data. In this review, we briefly introduce the themes covered by these sub-groups. The observations made, conclusions drawn, and software development projects that emerged from these activities are discussed.
    Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes
    Nielsen, H.B. ; Almeida, M. ; Sierakowska Juncker, A. ; Rasmussen, S. ; Li, J. ; Sunagawa, S. ; Plichta, D.R. ; Gautier, L. ; Pedersen, A.G. ; Chatelier, E. Le; Pelletier, E. ; Bonde, I. ; Nielsen, T. ; Manichanh, C. ; Arumugam, M. ; Batto, J.M. ; Quintanilha dos Santos, M.B. ; Blom, N. ; Borruel, N. ; Burgdorf, K.S. ; Boumezbeur, F. ; Casellas, F. ; Doré, J. ; Dworzynski, P. ; Guarner, F. ; Hansen, T. ; Hildebrand, F. ; Kaas, R.S. ; Kennedy, S. ; Kristiansen, K. ; Kultima, J.R. ; Leonard, P. ; Levenez, F. ; Lund, O. ; Moumen, B. ; Paslier, D. Le; Pons, N. ; Pedersen, O. ; Prifti, E. ; Qin, J. ; Raes, J. ; Sørensen, S. ; Tap, J. ; Tims, S. ; Ussery, D.W. ; Yamada, T. ; Jamet, A. ; Mérieux, A. ; Cultrone, A. ; Torrejon, A. ; Quinquis, B. ; Brechot, C. ; Delorme, C. ; M'Rini, C. ; Vos, W.M. de; Maguin, E. ; Varela, E. ; Guedon, E. ; Gwen, F. ; Haimet, F. ; Artiguenave, F. ; Vandemeulebrouck, G. ; Denariaz, G. ; Khaci, G. ; Blottière, H. ; Knol, J. ; Weissenbach, J. ; Hylckama Vlieg, J.E. van; Torben, J. ; Parkhil, J. ; Turner, K. ; Guchte, M. van de; Antolin, M. ; Rescigno, M. ; Kleerebezem, M. ; Derrien, M. ; Galleron, N. ; Sanchez, N. ; Grarup, N. ; Veiga, P. ; Oozeer, R. ; Dervyn, R. ; Layec, S. ; Bruls, T. ; Winogradski, Y. ; Zoetendal, E.G. ; Renault, D. ; Sicheritz-Ponten, ; Bork, P. ; Wang, J. ; Brunak, S. ; Ehrlich, S.D. - \ 2014
    Nature Biotechnology 32 (2014). - ISSN 1087-0156 - p. 822 - 828.
    short read alignment - sequences - systems - algorithms - microbiota - protein - life - sets - tree - tool
    Most current approaches for analyzing metagenomic data rely on comparisons to reference genomes, but the microbial diversity of many environments extends far beyond what is covered by reference databases. De novo segregation of complex metagenomic data into specific biological entities, such as particular bacterial strains or viruses, remains a largely unsolved problem. Here we present a method, based on binning co-abundant genes across a series of metagenomic samples, that enables comprehensive discovery of new microbial organisms, viruses and co-inherited genetic entities and aids assembly of microbial genomes without the need for reference sequences. We demonstrate the method on data from 396 human gut microbiome samples and identify 7,381 co-abundance gene groups (CAGs), including 741 metagenomic species (MGS). We use these to assemble 238 high-quality microbial genomes and identify affiliations between MGS and hundreds of viruses or genetic entities. Our method provides the means for comprehensive profiling of the diversity within complex metagenomic samples.
    Introducing Chaetothyriothecium, a new genus of Microthyriales
    Hongsanan, S. ; Chomnunti, P. ; Crous, P.W. ; Chukeatirote, E. ; Hyde, K.D. - \ 2014
    Phytotaxa 161 (2014)2. - ISSN 1179-3155 - p. 157 - 164.
    probability - sequences - bootstrap - inference - alignment - genera - trees - tools
    The order Microthyriales comprises foliar biotrophs, epiphytes, pathogens or saprobes that occur on plant leaves and stems. The order is relatively poorly known due to limited sampling and few in-depth studies. There is also a lack of phylogenetic data for these fungi, which form small black spots on plant host surfaces, but rarely cause any damage to the host. A "Microthyriaceae"-like fungus collected in central Thailand is described as a new genus, Chaetothyriothecium (type species Chaetothyriothecium elegans sp. nov.). Phylogenetic analyses of LSU gene data showed this species to cluster with other members of Microthyriales, where it is related to Microthyrium microscopicum the type of the order. The description of the new species is supplemented by DNA sequence data, which resolves its placement in the order. Little molecular data is available for this order, stressing the need for further collections and molecular data.
    New insights into domestication of carrot from root transcriptome analyses
    Rong, J. ; Lammers, Y. ; Strasburg, J.L. ; Schidlo, N.S. ; Ariyurek, Y. ; Jong, T.J. de; Klinkhamer, P.G.L. ; Smulders, M.J.M. ; Vrieling, K. - \ 2014
    BMC Genomics 15 (2014). - ISSN 1471-2164 - 15 p.
    daucus-carota l. - nucleotide polymorphism - wild - populations - inference - sativus - genome - diversity - sequences - selection
    Background - Understanding the molecular basis of domestication can provide insights into the processes of rapid evolution and crop improvement. Here we demonstrated the processes of carrot domestication and identified genes under selection based on transcriptome analyses. Results - The root transcriptomes of widely differing cultivated and wild carrots were sequenced. A method accounting for sequencing errors was introduced to optimize SNP (single nucleotide polymorphism) discovery. 11,369 SNPs were identified. Of these, 622 (out of 1000 tested SNPs) were validated and used to genotype a large set of cultivated carrot, wild carrot and other wild Daucus carota subspecies, primarily of European origin. Phylogenetic analysis indicated that eastern carrot may originate from Western Asia and western carrot may be selected from eastern carrot. Different wild D. carota subspecies may have contributed to the domestication of cultivated carrot. Genetic diversity was significantly reduced in western cultivars, probably through bottlenecks and selection. However, a high proportion of genetic diversity (more than 85% of the genetic diversity in wild populations) is currently retained in western cultivars. Model simulation indicated high and asymmetric gene flow from wild to cultivated carrots, spontaneously and/or by introgression breeding. Nevertheless, high genetic differentiation exists between cultivated and wild carrots (Fst =0.295) showing the strong effects of selection. Expression patterns differed radically for some genes between cultivated and wild carrot roots which may be related to changes in root traits. The up-regulation of water-channel-protein gene expression in cultivars might be involved in changing water content and transport in roots. The activated expression of carotenoid-binding-protein genes in cultivars could be related to the high carotenoid accumulation in roots. The silencing of allergen-protein-like genes in cultivated carrot roots suggested strong human selection to reduce allergy. These results suggest that regulatory changes of gene expressions may have played a predominant role in domestication. Conclusions - Western carrots may originate from eastern carrots. The reduction in genetic diversity in western cultivars due to domestication bottleneck/selection may have been offset by introgression from wild carrot. Differential gene expression patterns between cultivated and wild carrot roots may be a signature of strong selection for favorable cultivation traits.
    Ercella succinigenes gen. nov., sp. nov., an anaerobic succinate-producing bacterium
    Gelder, A.H. van; Sousa, D.Z. ; Rijpstra, W.I. ; Damsté, J.S. ; Stams, A.J.M. ; Sanchez Andrea, I. - \ 2014
    International Journal of Systematic and Evolutionary Microbiology 64 (2014)7. - ISSN 1466-5026 - p. 2449 - 2454.
    ribosomal-rna genes - acid - heterogeneity - fermentation - sequences - biofuels - glycerol - industry - operons - genomes
    A novel anaerobic succinate-producing bacterium, strain ZWBT, was isolated from sludge collected from a biogas desulfurization bioreactor (Eerbeek, the Netherlands). Cells were non-spore-forming, motile, slightly curved rods (0.4–0.5 µm in diameter and 2–3 µm in length), and stained Gram-negative. The temperature range for growth was 25–40 °C, with an optimum at 37 °C. The pH range for growth was 7.0–9.0, with an optimum at pH 7.5. Strain ZWBT was able to ferment glycerol and several carbohydrates mainly to H2, succinate and acetate. Sulfur and fumarate could be used as electron acceptors by strain ZWBT. The G+C content of the genomic DNA was 37.6 mol%. The most abundant fatty acids were iso-C14¿:¿0 and iso-C16¿:¿0 DMA. On the basis of 16S rRNA gene sequence similarity, strain ZWBT belongs to the family Ruminococcaceae and it is distantly related to Saccharofermentans acetigenes JCM 14006T (92.1¿%). Based on the physiological features and phylogenetic analysis, strain ZWBT represents a novel species of a new genus, for which the name Ercella succinigenes gen. nov., sp. nov. is proposed. The type strain of Ercella succinigenes is ZWBT (¿=¿DSM 27333T¿=¿JCM 19283T).
    Effects of selective digestive decontamination (SDD) on the gut resistome
    Buelow, E. ; Bello Gonzalez, T.D.G. ; Versluis, D. ; Oostdijk, E.A.N. ; Ogilvie, L.A. ; Mourik, M.S.M. van; Oosterink, L. ; Passel, M.W.J. van; Smidt, H. ; D’Andrea, M.M. ; Been, M. de; Jones, B.V. ; Willems, R.J.L. ; Bonten, M.J.M. ; Schaik, W. - \ 2014
    Journal of Antimicrobial Chemotherapy 69 (2014)8. - ISSN 0305-7453 - p. 2215 - 2223.
    intensive-care units - antimicrobial resistance - microbiota - tract - microarray - metagenome - sequences - bacterial - classification - generation
    Objectives Selective digestive decontamination (SDD) is an infection prevention measure for critically ill patients in intensive care units (ICUs) that aims to eradicate opportunistic pathogens from the oropharynx and intestines, while sparing the anaerobic flora, by the application of non-absorbable antibiotics. Selection for antibiotic-resistant bacteria is still a major concern for SDD. We therefore studied the impact of SDD on the reservoir of antibiotic resistance genes (i.e. the resistome) by culture-independent approaches. Methods We evaluated the impact of SDD on the gut microbiota and resistome in a single ICU patient during and after an ICU stay by several metagenomic approaches. We also determined by quantitative PCR the relative abundance of two common aminoglycoside resistance genes in longitudinally collected samples from 12 additional ICU patients who received SDD. Results The patient microbiota was highly dynamic during the hospital stay. The abundance of antibiotic resistance genes more than doubled during SDD use, mainly due to a 6.7-fold increase in aminoglycoside resistance genes, in particular aph(2¿)-Ib and an aadE-like gene. We show that aph(2¿)-Ib is harboured by anaerobic gut commensals and is associated with mobile genetic elements. In longitudinal samples of 12 ICU patients, the dynamics of these two genes ranged from a ~104 fold increase to a ~10-10 fold decrease in relative abundance during SDD. Conclusions ICU hospitalization and the simultaneous application of SDD has large, but highly individualized, effects on the gut resistome of ICU patients. Selection for transferable antibiotic resistance genes in anaerobic commensal bacteria could impact the risk of transfer of antibiotic resistance genes to opportunistic pathogens.
    Development and Validation of a Genotype 3 Recombinant Protein based Immunoassay for Hepatitis E Virus Serology in Swine
    Poel, W.H.M. van der; Pavio, N. ; Goot, J. van der; Es, M. van; Martin, M. ; Engel, B. - \ 2014
    Brazilian Journal of Medical and Biological Research 47 (2014)4. - ISSN 0100-879X - p. 334 - 339.
    sequences - zoonosis
    Hepatitis E virus (HEV) is classified within the family Hepeviridae, genus Hepevirus. HEV genotype 3 (Gt3) infections are endemic in pigs in Western Europe and in North and South America and cause zoonotic infections in humans. Several serological assays to detect HEV antibodies in pigs have been developed, at first mainly based on HEV genotype 1 (Gt1) antigens. To develop a sensitive HEV Gt3 ELISA, a recombinant baculovirus expression product of HEV Gt3 open reading frame-2 was produced and coated onto polystyrene ELISA plates. After incubation of porcine sera, bound HEV antibodies were detected with anti-porcine anti-IgG and anti-IgM conjugates. For primary estimation of sensitivity and specificity of the assay, sets of sera were used from pigs experimentally infected with HEV Gt3. For further validation of the assay and to set the cutoff value, a batch of 1100 pig sera was used. All pig sera were tested using the developed HEV Gt3 assay and two other serologic assays based on HEV Gt1 antigens. Since there is no gold standard available for HEV antibody testing, further validation and a definite setting of the cutoff of the developed HEV Gt3 assay were performed using a statistical approach based on Bayes' theorem. The developed and validated HEV antibody assay showed effective detection of HEV-specific antibodies. This assay can contribute to an improved detection of HEV antibodies and enable more reliable estimates of the prevalence of HEV Gt3 in swine in different regions.
    Comparison of two short DNA barcoding loci (COI and COII) and two longer ribosomal DNA genes (SSU & LSU rRNA) for specimen identification among quarantine root-knot nematodes (Meloidogyne spp.) and their close relatives
    Kiewnick, S. ; Holterman, M.H.M. ; Elsen, S.J.J. van den; Megen, H.H.B. van; Frey, J.E. ; Helder, J. - \ 2014
    European Journal of Plant Pathology 140 (2014)1. - ISSN 0929-1873 - p. 97 - 110.
    small-subunit rdna - molecular characterization - phylogenetic analysis - pellioditis-marina - globodera-pallida - complex nematoda - cyst nematodes - sequences - evolution - morphology
    Root-knot nematodes (Meloidogyne spp.) are important pests of numerous crops worldwide. Some members of this genus have a quarantine status, and accurate species identification is required to prevent further spreading. DNA barcoding is a method for organism identification in non-complex DNA backgrounds based on informative motifs in short DNA stretches (˜600 bp). As part of the EU 7th Framework project QBOL, 15 Meloidogyne species were chosen to compare the resolutions offered by two typical DNA barcoding loci, COI and COII, with the distinguishing signals produced by two ribosomal DNA genes (small and large subunit rDNA; SSU¿˜¿1,700 and LSU¿˜¿3,400 bp). None of the four markers distinguished between the tropical species Meloidogyne incognita, M. javanica and M. arenaria. Taking P ID (Liberal) values =0.93 as a measure for species delimitation, the four mtDNA and rDNA markers performed well for the tropical Meloidogyne species complex, M. enterolobii, M. hapla, and M. maritima. Within cluster III A (Holterman et al. Phytopathology, 99, 227–235, 2009), SSU rDNA did not offer resolution at species level. Both mtDNA loci COI and COII did, whereas for LSU rDNA a longer fragment (=700 bp) is required. The high level of mitochondrial heteroplasmy recently reported for M. chitwoodi (Humphreys-Pereira and Elling Nematology, 15, 315–327, 2013) was not found in the populations under investigation, suggesting this could be a regional phenomenon. For identification of RKNs, we suggest the combined use of SSU rDNA with one of three other markers presented here.
    Towards a new classification system for legumes: Progress report from the 6th International Legume Conference
    Pontes Coelho Borges, L.M. ; Bruneau, A. ; Cardoso, D. ; Crisp, M. ; Delgado-Salinas, A. ; Doyle, J.J. ; Egan, A. ; Herendeen, P.S. ; Hughes, C. ; Kenicer, G. ; Klitgaard, B. ; Koenen, E. ; Lavin, M. ; Lewis, G. ; Luckow, M. ; Mackinder, B. ; Malecot, V. ; Miller, J.T. ; Pennington, R.T. ; Queiroz, L.P. de; Schrire, B. ; Simon, M.F. ; Steele, K. ; Torke, B. ; Wieringa, J.J. ; Wojciechowski, M.F. ; Boatwright, S. ; Estrella, M. de la; Mansano, V.D. ; Prado, D.E. ; Stirton, C. ; Wink, M. - \ 2013
    South African Journal of Botany 89 (2013). - ISSN 0254-6299 - p. 3 - 9.
    caesalpinioid legumes - phylogeny - leguminosae - evolution - diversification - dipsacales - sequences - lineages - gene - rbcl
    Legume systematists have been making great progress in understanding evolutionary relationships within the Leguminosae (Fabaceae), the third largest family of flowering plants. As the phylogenetic picture has become clearer, so too has the need for a revised classification of the family. The organization of the family into three subfamilies and 42 tribes is outdated and evolutionarily misleading. The three traditionally recognized subfamilies, Caesalpinioideae, Mimosoideae, and Papilionoideae, do not adequately represent relationships within the family. The occasion of the Sixth International Legume Conference in Johannesburg, South Africa in January 2013, with its theme "Towards a new classification system for legumes," provided the impetus to move forward with developing a new classification. A draft classification, based on current phylogenetic results and a set of principles and guidelines, was prepared in advance of the conference as the basis for discussion. The principles, guidelines, and draft classification were presented and debated at the conference. The objectives of the discussion were to develop consensus on the principles that should guide the development of the classification, to discuss the draft classification's strengths and weaknesses and make proposals for its revision, and identify and prioritize phylogenetic deficiencies that must be resolved before the classification could be published. This paper describes the collaborative process by a large group of legume systematists, publishing under the name Legume Phylogeny Working Group, to develop a new phylogenetic classification system for the Leguminosae. The goals of this paper are to inform the broader legume community, and others, of the need for a revised classification, and spell out clearly what the alternatives and challenges are for a new classification system for the family. (C) 2013 SAAB. Published by Elsevier B.V. All rights reserved.
    The tropical African legume Scorodophloeus clade includes two undescribed Hymenostegia segregate genera and Micklethwaitia, a rare, monospecific genus from Mozambique.
    Mackinder, B.A. ; Saslis-Lagoudakis, H. ; Wieringa, J.J. ; Devey, D. ; Forest, F. ; Bruneau, A. - \ 2013
    South African Journal of Botany 89 (2013). - ISSN 0254-6299 - p. 156 - 163.
    odd man - leguminosae - caesalpinioideae - detarieae - patterns - phylogeny - sequences - forests
    Legume subfamily Caesalpinioideae accommodates approximately 2250 species in 171 genera which traditionally are placed in four tribes: Caesalpinieae, Cassieae, Cercideae and Detarieae. The monophyletic tribe Detarieae includes the Amherstieae subclade which contains about 55 genera. Our knowledge of the relationships among those genera is good in some cases but for many other genera phylogenetic relationships have been unclear. The non-monophyletic nature of at least two amherstioid genera, Cynometra and Hymenostegia has also complicated the picture. During the course of a multi-disciplinary study of Hymenostegia sensu lato, which includes phylogenetic analyses based on matK and trnL data, we have recovered the “Scorodophloeus clade”, an exclusively tropical African clade of four genera which includes the eponymous genus Scorodophloeus, two undescribed generic segregates of Hymenostegia sensu lato, and the previously unsampled rare monospecific genus Micklethwaitia from Mozambique. Zenkerella is suggested as a possible sister genus to the Scorodophloeus clade. A distribution map is presented of the seven species that belong to the Scorodophloeus clade.
    Comparative Genomics Analysis of Streptococcus Isolates from the Human Small Intestine Reveals their Adaptation to a Highly Dynamic Ecosystem
    Bogert, B. van den; Boekhorst, J. te; Herrmann, R. ; Smid, E.J. ; Zoetendal, E.G. ; Kleerebezem, M. - \ 2013
    PLoS ONE 8 (2013)12. - ISSN 1932-6203
    human gastrointestinal-tract - group-b streptococcus - prokaryotic genomes - lactococcus-lactis - bacterial samples - transport-system - microbiota - pneumoniae - competence - sequences
    The human small-intestinal microbiota is characterised by relatively large and dynamic Streptococcus populations. In this study, genome sequences of small-intestinal streptococci from S. mitis, S. bovis, and S. salivarius species-groups were determined and compared with those from 58 Streptococcus strains in public databases. The Streptococcus pangenome consists of 12,403 orthologous groups of which 574 are shared among all sequenced streptococci and are defined as the Streptococcus core genome. Genome mining of the small-intestinal streptococci focused on functions playing an important role in the interaction of these streptococci in the small-intestinal ecosystem, including natural competence and nutrient-transport and metabolism. Analysis of the small-intestinal Streptococcus genomes predicts a high capacity to synthesize amino acids and various vitamins as well as substantial divergence in their carbohydrate transport and metabolic capacities, which is in agreement with observed physiological differences between these Streptococcus strains. Gene-specific PCR-strategies enabled evaluation of conservation of Streptococcus populations in intestinal samples from different human individuals, revealing that the S. salivarius strains were frequently detected in the small-intestine microbiota, supporting the representative value of the genomes provided in this study. Finally, the Streptococcus genomes allow prediction of the effect of dietary substances on Streptococcus population dynamics in the human small-intestine
    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
    Habitat- and host-related variation in sponge bacterial symbiont communities in Indonesian waters
    Cleary, D.F.R. ; Becking, L.E. ; Voogd, N.J. de; Pires, A.C.C. ; Polonia, A. ; Egas, C. ; Gomes, N. - \ 2013
    FEMS microbiology ecology 85 (2013)3. - ISSN 0168-6496 - p. 465 - 482.
    enso-induced fires - marine sponges - vertical transmission - east kalimantan - kakaban-island - suberites-domuncula - butterfly diversity - microbial community - sp nov. - sequences
    Marine lakes are unique ecosystems that contain isolated populations of marine organisms. Isolated from the surrounding marine habitat, many lakes house numerous endemic species. In this study, microbial communities of sponges inhabiting these lakes were investigated for the first time using barcoded pyrosequencing of 16S rRNA gene amplicons. Our main goals were to compare the bacterial richness and composition of two sponge species (Suberites diversicolor and Cinachyrella australiensis) inhabiting both marine lakes and adjacent open coastal systems. Host species and habitat explained almost 59% of the variation in bacterial composition. There was a significant difference in composition between both host species. Within S. diversicolor, there was little discernible difference between bacterial communities inside and outside lakes. The bacterial community of this species was, furthermore, dominated (63% of all sequences) by three very closely related alphaproteobacterial taxa identified as belonging to the recently described order Kiloniellales. Cinachyrella australiensis, in contrast, hosted markedly different bacterial communities inside and outside lakes with very few shared abundant taxa. Cinachyrella australiensis in open habitat only shared 9.4% of OTUs with C. australiensis in lake habitat. Bacteria were thus both highly species specific and, in the case of C. australiensis, habitat specific.
    Computational protein design with electrostatic focusing: experimental characterization of a conditionally folded helical domain with a reduced amino acid alphabet
    Suarez Diez, M. ; Pujol, M. ; Matzapetakis, M. ; Jaramillo, A. ; Iranzo, O. - \ 2013
    Biotechnology Journal 8 (2013)7. - ISSN 1860-6768 - p. 855 - 864.
    solution nmr structure - structural basis - peptides - recognition - prediction - sequences - dynamics - energy - trifluoroethanol - optimization
    Automated methodologies to design synthetic proteins from first principles use energy computations to estimate the ability of the sequences to adopt a targeted structure. This approach is still far from systematically producing native-like sequences, due, most likely, to inaccuracies when modeling the interactions between the protein and its aqueous environment. This is particularly challenging when engineering small protein domains (with less polar pair interactions than with the solvent). We have re-designed a three-helix bundle, domain B, using a fixed backbone and a four amino acid alphabet. We have enlarged the rotamer library with conformers that increase the weight of electrostatic interactions within the design process without altering the energy function used to compute the folding free energy. Our synthetic sequences show less than 15% similarity to any Swissprot sequence. We have characterized our sequences in different solvents using circular dichroism and nuclear magnetic resonance. The targeted structure achieved is dependent on the solvent used. This method can be readily extended to larger domains. Our method will be useful for the engineering of proteins that become active only in a given solvent and for designing proteins in the context of hydrophobic solvents, an important fraction of the situations in the cell
    Detection and Quantification of Leveillula taurica Growth in Pepper Leaves
    Zheng, Z. ; Nonomura, T. ; Bóka, K. ; Matsuda, Y. ; Visser, R.G.F. ; Toyoda, H. ; Kiss, L. ; Bai, Y. - \ 2013
    Phytopathology 103 (2013)6. - ISSN 0031-949X - p. 623 - 632.
    internal transcribed spacer - powdery-mildew - genus leveillula - capsicum-annuum - resistance - pcr - infections - sequences - fungi - dna
    Leveillula taurica is an obligate fungal pathogen that causes powdery mildew disease on a broad range of plants, including important crops such as pepper, tomato, eggplant, onion, cotton, and so on. The early stage of this disease is difficult to diagnose and the disease can easily spread unobserved; for example, in pepper and tomato production fields and greenhouses. The objective of this study was to develop a detection and quantification method of L. taurica biomass in pepper leaves with special regard to the early stages of infection. We monitored the development of the disease to time the infection process on the leaf surface as well as inside the pepper leaves. The initial and final steps of the infection taking place on the leaf surface were consecutively observed using a dissecting microscope and a scanning electron microscope. The development of the intercellular mycelium in the mesophyll was followed by light and transmission electron microscopy. A pair of L. taurica-specific primers was designed based on the internal transcribed spacer sequence of L. taurica and used in real-time polymerase chain reaction (PCR) assay to quantify the fungal DNA during infection. The specificity of this assay was confirmed by testing the primer pair with DNA from host plants and also from another powdery mildew species, Oidium neolycopersici, infecting tomato. A standard curve was obtained for absolute quantification of L. taurica biomass. In addition, we tested a relative quantification method by using a plant gene as reference and the obtained results were compared with the visual disease index scoring. The real-time PCR assay for L. taurica provides a valuable tool for detection and quantification of this pathogen in breeding activities as well in plant-microbe interaction studies.
    Multi-locus phylogenies of the genus Barteria (Passifloraceae) protray complex patterns in the evolution of myrmecophytism.
    Peccoud, J. ; Piatscheck, F. ; Yockteng, R. ; Garcia, M. ; Sauve, M. ; Djieto-Lordon, C. ; Harris, D.J. ; Wieringa, J.J. ; Breteler, F.J. ; Born, C. ; McKey, D. ; Blatrix, R. - \ 2013
    Molecular Phylogenetics and Evolution 66 (2013)3. - ISSN 1055-7903 - p. 824 - 832.
    chloroplast dna - rain-forest - population - sequences - ants - pseudomyrmecinae - euphorbiaceae - divergence - protection - mutualism
    The four species of the central African genus Barteria show variation in habitat and in degree of association with ants. Whereas B. solida, restricted to submontane forests, attracts opportunistic ants to extrafloral nectar, the three other species, found in lowland rainforests (B. fistulosa, B. dewevrei) and in littoral scrub (B. nigritana), possess stem domatia of varying shapes and degrees of specialisation, hosting either non-specific arboreal ants (B. nigritana, some B. dewevrei) or two large species of ants of the genus Tetraponera Smith, 1852 that are specific to some species of Barteria (B. fistulosa, some B. dewevrei). We aimed to investigate whether this variation represents an evolutionary trend toward increasing specialisation of mutualism or the reduction or loss of myrmecophytic traits. For this, we determined phylogenetic relationships within the genus using DNA sequences (primarily nuclear ITS) and microsatellite genotypes (11 loci) on a large sample of individuals, mostly from Cameroon and Gabon. The two types of markers support an initial dichotomy that groups B. dewevrei with B. nigritana and B. fistulosa with B. solida respectively. Within these pairs, species do not appear reciprocally monophyletic. At microsatellite loci, B. nigritana forms a clade embedded within B. dewevrei; and within both B. solida and B. fistulosa, geographical populations show levels of differentiation similar to that observed between populations of B. solida and B. fistulosa. Geographic distance alone does not account for genetic differentiation between species, which indicates reproductive isolation. Divergence in each of the two pairs implies evolutionary transitions in habitat and in myrmecophytism. Specialised mutualism with specific ant species of the genus Tetraponera has been lost in species found in more marginal habitats.
    Pyrosequencing as a tool for the detection of Phytophthora species: error rate and risk of false Molecular Operational Taxonomic Units
    Vettraino, A.M. ; Bonants, P.J.M. ; Tomassini, A. ; Bruni, N. ; Vannini, A. - \ 2012
    Letters in Applied Microbiology 55 (2012)5. - ISSN 0266-8254 - p. 390 - 396.
    fungal communities - identification - phylogeny - diversity - sequences - reveals
    Aims: To evaluate the accuracy of pyrosequencing for the description of Phytophthora communities in terms of taxa identification and risk of assignment for false Molecular Operational Taxonomic Units (MOTUs). Methods and Results: Pyrosequencing of Internal Transcribed Spacer 1 (ITS1) amplicons was used to describe the structure of a DNA mixture comprising eight Phytophthora spp. and Pythium vexans. Pyrosequencing resulted in 16 965 reads, detecting all species in the template DNA mixture. Reducing the ITS1 sequence identity threshold resulted in a decrease in numbers of unmatched reads but a concomitant increase in the numbers of false MOTUs. The total error rate was 0_63% and comprised mainly mismatches (0_25%) Conclusions: Pyrosequencing of ITS1 region is an efficient and accurate technique for the detection and identification of Phytophthora spp. In environmental samples. However, the risk of allocating false MOTUs, even when demonstrated to be low, may require additional validation with alternative detection methods. Significance and Impact of the Study: Phytophthora spp. are considered among the most destructive groups of invasive plant pathogens, affecting thousands of cultivated and wild plants worldwide. Simultaneous early detection of Phytophthora complexes in environmental samples offers an unique opportunity for the interception of known and unknown species along pathways of introduction, along with the identification of these organisms in invaded environments.
    Genome-Wide Prediction and Validation of Sigma70 Promoters in Lactobacillus plantarum WCFS1
    Todt, T.J. ; Wels, M. ; Bongers, R.S. ; Siezen, R.J. ; Hijum, S.A.F.T. van; Kleerebezem, M. - \ 2012
    PLoS ONE 7 (2012)9. - ISSN 1932-6203
    transcription start sites - escherichia-coli - rna-polymerase - sequences - identification - dna - conservation - compilation - metabolism - initiation
    Background - In prokaryotes, sigma factors are essential for directing the transcription machinery towards promoters. Various sigma factors have been described that recognize, and bind to specific DNA sequence motifs in promoter sequences. The canonical sigma factor s70 is commonly involved in transcription of the cell's housekeeping genes, which is mediated by the conserved s70 promoter sequence motifs. In this study the s70-promoter sequences in Lactobacillus plantarum WCFS1 were predicted using a genome-wide analysis. The accuracy of the transcriptionally-active part of this promoter prediction was subsequently evaluated by correlating locations of predicted promoters with transcription start sites inferred from the 5'-ends of transcripts detected by high-resolution tiling array transcriptome datasets. Results - To identify s70-related promoter sequences, we performed a genome-wide sequence motif scan of the L. plantarum WCFS1 genome focussing on the regions upstream of protein-encoding genes. We obtained several highly conserved motifs including those resembling the conserved s70-promoter consensus. Position weight matrices-based models of the recovered s70-promoter sequence motif were employed to identify 3874 motifs with significant similarity (p-value
    Stagonosporopsis spp. associated with ray blight disease of Asteraceae
    Vaghefi, N. ; Pethybridge, S.J. ; Ford, R. ; Nicolas, M.E. ; Crous, P.W. ; Taylor, P.W.J. - \ 2012
    Australasian Plant Pathology 41 (2012)6. - ISSN 0815-3191 - p. 675 - 686.
    phoma-ligulicola - phylogenetic analyses - ribosomal dna - mixed models - host-range - pyrethrum - sequences - complex - genera - taxa
    Ray blight disease of pyrethrum (Tanacetum cinerariifolium) is shown to be caused by more than one species of Stagonosporopsis. The Australian pathogen, previously identified as Phoma ligulicola var. inoxydabilis, represents a new species described as Stagonosporopsis tanaceti based on morphological characters and a five-gene phylogeny employing partial sequences of the actin, translation elongation factor 1-alpha, internal transcribed spacers and 5.8S of the nrDNA, 28S large subunit and beta-tubulin 2 gene sequences. Furthermore, the two varieties of Stagonosporopsis ligulicola are elevated to species level as S. chrysanthemi and S. inoxydabilis based on their DNA phylogeny and morphology.
    Prediction of Altered 3'- UTR miRNA-Binding Sites from RNA-Seq Data: The Swine Leukocyte Antigen Complex (SLA) as a Model Region
    Endale, M.L. ; Fritz, E.R. ; Estelle, J. ; Hu, Z.L. ; Madsen, O. ; Groenen, M.A.M. - \ 2012
    PLoS ONE 7 (2012)11. - ISSN 1932-6203
    microrna target recognition - mediated gene-regulation - phenotypic variation - expression - accessibility - principles - sequences - evolution - disease - genome
    The SLA (swine leukocyte antigen, MHC: SLA) genes are the most important determinants of immune, infectious disease and vaccine response in pigs; several genetic associations with immunity and swine production traits have been reported. However, most of the current knowledge on SLA is limited to gene coding regions. MicroRNAs (miRNAs) are small molecules that post-transcriptionally regulate the expression of a large number of protein-coding genes in metazoans, and are suggested to play important roles in fine-tuning immune mechanisms and disease responses. Polymorphisms in either miRNAs or their gene targets may have a significant impact on gene expression by abolishing, weakening or creating miRNA target sites, possibly leading to phenotypic variation. We explored the impact of variants in the 3'-UTR miRNA target sites of genes within the whole SLA region. The combined predictions by TargetScan, PACMIT and TargetSpy, based on different biological parameters, empowered the identification of miRNA target sites and the discovery of polymorphic miRNA target sites (poly-miRTSs). Predictions for three SLA genes characterized by a different range of sequence variation provided proof of principle for the analysis of poly-miRTSs from a total of 144 M RNA-Seq reads collected from different porcine tissues. Twenty-four novel SNPs were predicted to affect miRNA-binding sites in 19 genes of the SLA region. Seven of these genes (SLA-1, SLA-6, SLA-DQA, SLA-DQB1, SLA-DOA, SLA-DOB and TAP1) are linked to antigen processing and presentation functions, which is reminiscent of associations with disease traits reported for altered miRNA binding to MHC genes in humans. An inverse correlation in expression levels was demonstrated between miRNAs and co-expressed SLA targets by exploiting a published dataset (RNA-Seq and small RNA-Seq) of three porcine tissues. Our results support the resource value of RNA-Seq collections to identify SNPs that may lead to altered miRNA regulation patterns.
    Cloning and characterization of a tuberous root-specific promoter from cassava (Manihot esculenta Crantz)
    Koehorst-van Putten, H.J.J. ; Wolters, A.M.A. ; Pereira-Bertram, I.J. ; Berg, H. ; Krol, A.R. van der; Visser, R.G.F. - \ 2012
    Planta 236 (2012)6. - ISSN 0032-0935 - p. 1955 - 1965.
    bound-starch-synthase - storage roots - transformation - expression - gene - agrobacterium - elements - sequences - database - program
    In order to obtain a tuberous root-specific promoter to be used in the transformation of cassava, a 1,728 bp sequence containing the cassava granule-bound starch synthase (GBSSI) promoter was isolated. The sequence proved to contain light- and sugar-responsive cis elements. Part of this sequence (1,167 bp) was cloned into binary vectors to drive expression of the firefly luciferase gene. Cassava cultivar Adira 4 was transformed with this construct or a control construct in which the luciferase gene was cloned behind the 35S promoter. Luciferase activity was measured in leaves, stems, roots and tuberous roots. As expected, the 35S promoter induced luciferase activity in all organs at similar levels, whereas the GBSSI promoter showed very low expression in leaves, stems and roots, but very high expression in tuberous roots. These results show that the cassava GBSSI promoter is an excellent candidate to achieve tuberous root-specific expression in cassava.
    Phyllosticta species associated with freckle disease of banana
    Wong, M.H. ; Crous, P.W. ; Henderson, J. ; Groenewald, J.Z. ; Drenth, A. - \ 2012
    Fungal Diversity 56 (2012)1. - ISSN 1560-2745 - p. 173 - 187.
    citrus black spot - ribosomal dna - mycosphaerella - sequences - musarum - plants
    The identity of the casual agent of freckle disease of banana was investigated. The pathogen is generally referred to in literature under its teleomorphic name, Guignardia musae, or that of its purported anamorph, Phyllosticta musarum. Based on morphological and molecular data from a global set of banana specimens, several species were found associated with freckle disease. Phyllosticta maculata (from Southeast Asia and Oceania) is introduced as a new name for Guignardia musae, and an epitype is designated from Australia. Phyllosticta musarum (from India and Thailand) is shown to represent a distinct species, and the name is fixed by designation of an epitype from India. Guignardia stevensii is confirmed as distinct species from Hawaii, while Guignardia musicola from northern Thailand is shown to contain different taxa and is regarded as nomen confusum. Phyllosticta cavendishii is described as a new, widely distributed species, appearing primarily on Cavendish, but also on non-Cavendish banana cultivars.
    A phylogenetic and taxonomic re-evaluation of the Bipolaris - Cochliobolus - Curvularia Complex
    Manamgoda, D.S. ; Cai, L. ; McKenzie, E.H.C. ; Crous, P.W. ; Madrid, H. ; Chukeatirote, E. ; Shivas, R.G. ; Tan, Y.P. ; Hyde, K.D. - \ 2012
    Fungal Diversity 56 (2012)1. - ISSN 1560-2745 - p. 131 - 144.
    species concepts - sequences - pseudocochliobolus - helminthosporium - pathogens - alignment - genes - fungi - genus - rdna
    Three genera, Cochliobolus, Bipolaris and Curvularia form a complex that contains many plant pathogens, mostly on grasses (Poaceae) with a worldwide distribution. The taxonomy of this complex is confusing as frequent nomenclatural changes and refinements have occurred. There is no clear morphological boundary between the asexual genera Bipolaris and Curvularia, and some species show intermediate morphology. We investigated this complex based on a set of ex-type cultures and collections from northern Thailand. Combined gene analysis of rDNA ITS (internal transcribed spacer), GPDH (glyceraldehyde 3-phosphate dehydrogenase), LSU (large subunit) and EF1-a (translation elongation factor 1-a) shows that this generic complex divides into two groups. Bipolaris and Cochliobolus species clustered in Group 1 along with their type species, whereas Curvularia species (including species named as Bipolaris, Cochliobolus and Curvularia) clustered in Group 2, with its generic type. The nomenclatural conflict in this complex is resolved giving priority to the more commonly used established generic names Bipolaris and Curvularia. Modern descriptions of the genera Bipolaris and Curvularia are provided and species resolved in this study are transferred to one of these genera based on their phylogeny.
    The development of a validated real-time (TaqMan) PCR for detection of Stagonosporopsis andigena and S. crystalliniformis in infected leaves of potato and tomato
    Gruyter, J. de; Gent-Pelzer, M.P.E. van; Woudenberg, J.H.C. ; Rijswick, P.C.J. van; Meekes, E.T.M. ; Crous, P.W. ; Bonants, P.J.M. - \ 2012
    European Journal of Plant Pathology 134 (2012)2. - ISSN 0929-1873 - p. 301 - 313.
    polymerase-chain-reaction - phoma-tracheiphila - didymella-bryoniae - complex - foveata - differentiation - phylogeny - multiplex - sequences - disease
    Stagonosporopsis andigena and S. crystalliniformis are serious foliage pathogens on potato (Solanum tuberosum) and tomato (Solanum lycopersicum). As both species have been recorded only in the Andes area, S. andigena is listed as an A1 quarantine organism in Europe. The actin region of isolates of Stagonosporopsis and allied species of Boeremia, Didymella, Peyronellaea and Phoma was amplified using generic primers. DNA sequence differences of the actin gene were utilised to develop species-specific real-time (TaqMan) PCR assays for the detection of S. andigena and S. crystalliniformis in leaves of potato or tomato. The specificity of the TaqMan PCR assays was determined on genomic DNA extracted from two S. andigena and two S. crystalliniformis isolates and 16 selected isolates of Stagonosporopsis, Phoma and Boeremia, which are the closest relatives. The validation of the methods developed included the DNA extraction and the TaqMan PCR assays. The performance criteria specificity, analytical sensitivity, reproducibility, repeatability and robustness of the TaqMan PCR assays demonstrated the reliability of both methods for the detection of S. andigena and S. crystalliniformis in leaf material. The TaqMan PCR assays were tested on symptomatic leaves of potato and tomato that were obtained after artificial inoculation of detached leaves with both pathogens under quarantine conditions. In the artificial inoculation experiments both S. andigena and S. crystalliniformis caused leaf infections on potato and tomato.
    Characterization of Hubera (Annonaceae), a new genus segregated from Polyalthia and allied to Miliusa.
    Chaowasku, T. ; Johnson, D.M. ; Ham, R.W.J.M. van der; Chatrou, L.W. - \ 2012
    Phytotaxa 69 (2012). - ISSN 1179-3155 - p. 33 - 56.
    molecular phylogenetics - uvaria annonaceae - pollen morphology - chloroplast dna - evolution - genera - reconstruction - hypotheses - sequences - revision
    On the basis of molecular phylogenetics, pollen morphology and macromorphology, a new genus of the tribe Miliuseae, Hubera, segregrated from Polyalthia and allied to Miliusa, is established and described. It is characterized by the combination of reticulate tertiary venation of the leaves, axillary inflorescences, a single ovule per ovary and therefore single-seeded monocarps, seeds with a flat to slightly raised raphe, spiniform(-flattened peg) ruminations of the endosperm, and pollen with a finely and densely granular infratectum. Twenty-seven species are accordingly transferred to this new genus.
    Efficiency of Agrobacterium rhizogenes-mediated root transformation of Parasponia and Trema is temperature dependent
    Cao, Q. ; Camp, R. Op den; Seifi Kalhor, M. ; Bisseling, T. ; Geurts, R. - \ 2012
    Plant Growth Regulation 68 (2012)3. - ISSN 0167-6903 - p. 459 - 465.
    medicago-truncatula - gene-transfer - non-legume - plants - nitrogen - andersonii - nodulation - rhizobium - phaseolus - sequences
    Parasponia trees are the only non-legume species that form nitrogen-fixing root nodules with rhizobium. Based on its taxonomic position in relation to legumes (Fabaceae), it is most likely that both lineages have gained this symbiotic capacity independently. Therefore, Parasponia forms a bridging species to understand the evolutionary constraints underlying this symbiosis. However, absence of key technologies to genetically modify Parasponia seriously impeded studies on these species. We employed Agrobacterium rhizogenes to create composite Parasponia andersonii plants that harbour transgenic roots. Here, we provide an optimized protocol to infect P. andersonii as well as its non-symbiotic sister species Trema tomentosa with A. rhizogenes. We show that the transformation efficiency is temperature dependent. Whereas the optimal growth temperature for both these species is 28 °C, the transformation is most efficient when co-cultivation with A. rhizogenes occurs at 21 °C. Using this optimized protocol up to 80 % transformation efficiency can be obtained. These robust transformation platforms will provide a strong tool to unravel the Parasponia–rhizobium symbiosis
    Scenario Analysis of Nutrient Removal from Municipal Wastewater by Microalgal Biofilms
    Boelee, N.C. ; Temmink, H. ; Janssen, M. ; Buisman, C.J.N. ; Wijffels, R.H. - \ 2012
    Water 4 (2012)2. - ISSN 2073-4441 - p. 460 - 473.
    afvalwaterbehandeling - biofilms - algen - biologische waterzuiveringsinstallaties - vergelijkend onderzoek - volgorden - haalbaarheidsstudies - heterotrofe micro-organismen - stikstof - fosfor - verwijdering - biomassa productie - biobased economy - waste water treatment - biofilms - algae - biological water treatment plants - comparative research - sequences - feasibility studies - heterotrophic microorganisms - nitrogen - phosphorus - removal - biomass production - biobased economy - marine-phytoplankton - chemical-composition - chlorella-vulgaris - nitrate uptake - algal biofilm - growth - photobioreactor - photosynthesis
    Microalgae can be used for the treatment of municipal wastewater. The application of microalgal biofilms in wastewater treatment systems seems attractive, being able to remove nitrogen, phosphorus and COD from wastewater at a short hydraulic retention time. This study therefore investigates the area requirement, achieved effluent concentrations and biomass production of a hypothetical large-scale microalgal biofilm system treating municipal wastewater. Three scenarios were defined: using microalgal biofilms: (1) as a post-treatment; (2) as a second stage of wastewater treatment, after a first stage in which COD is removed by activated sludge; and (3) in a symbiotic microalgal/heterotrophic system. The analysis showed that in the Netherlands, the area requirements for these three scenarios range from 0.32 to 2.1 m2 per person equivalent. Moreover, it was found that it was not possible to simultaneously remove all nitrogen and phosphorus from the wastewater, because of the nitrogen:phosphorus ratio in the wastewater. Phosphorus was limiting in the post-treatment scenario, while nitrogen was limiting in the two other scenarios. Furthermore, a substantial amount of microalgal biomass was produced, ranging from 13 to 59 g per person equivalent per day. These findings show that microalgal biofilm systems hold large potential as seasonal wastewater treatment systems and that it is worthwhile to investigate these systems further
    Promoter propagation in prokaryotes
    Matus-Garcia, M. ; Nijveen, H. ; Passel, M.W.J. van - \ 2012
    Nucleic acids research 40 (2012)20. - ISSN 0305-1048 - p. 10032 - 10040.
    horizontal gene-transfer - escherichia-coli - adaptive evolution - lactococcus-lactis - sequences - genomes - networks - identification - mutations - families
    Transcriptional activation or 'rewiring' of silent genes is an important, yet poorly understood, phenomenon in prokaryotic genomes. Anecdotal evidence coming from experimental evolution studies in bacterial systems has shown the promptness of adaptation upon appropriate selective pressure. In many cases, a partial or complete promoter is mobilized to silent genes from elsewhere in the genome. We term hereafter such recruited regulatory sequences as Putative Mobile Promoters (PMPs) and we hypothesize they have a large impact on rapid adaptation of novel or cryptic functions. Querying all publicly available prokaryotic genomes (1362) uncovered >4000 families of highly conserved PMPs (50 to 100 long with =80% nt identity) in 1043 genomes from 424 different genera. The genomes with the largest number of PMP families are Anabaena variabilis (28 families), Geobacter uraniireducens (27 families) and Cyanothece PCC7424 (25 families). Family size varied from 2 to 93 homologous promoters (in Desulfurivibrio alkaliphilus). Some PMPs are present in particular species, but some are conserved across distant genera. The identified PMPs represent a conservative dataset of very recent or conserved events of mobilization of non-coding DNA and thus they constitute evidence of an extensive reservoir of recyclable regulatory sequences for rapid transcriptional rewiring
    Relative entropy differences in bacterial chromosomes, plasmids, phages and genomic islands
    Bohlin, J. ; Passel, M.W.J. van - \ 2012
    BMC Genomics 13 (2012). - ISSN 1471-2164 - 35 p.
    usage patterns - sequences - prokaryotes - communication - reduction - diversity - ancestor
    Background: We sought to assess whether the concept of relative entropy (information capacity), could aid our understanding of the process of horizontal gene transfer in microbes. We analyzed the differences in information capacity between prokaryotic chromosomes, genomic islands (GI), phages, and plasmids. Relative entropy was estimated using the Kullback-Leibler measure. Results: Relative entropy was highest in bacterial chromosomes and had the sequence chromosomes >GI>phage>plasmid. There was an association between relative entropy and AT content in chromosomes, phages, plasmids and GIs with the strongest association being in phages. Relative entropy was also found to be lower in the obligate intracellular Mycobacterium leprae than in the related M. tuberculosis when measured on a shared set of highly conserved genes. Conclusions: We argue that relative entropy differences reflect how plasmids, phages and GIs interact with microbial host chromosomes and that all these biological entities are, or have been, subjected to different selective pressures. The rate at which amelioration of horizontally acquired DNA occurs within the chromosome is likely to account for the small differences between chromosomes and stably incorporated GIs compared to the transient or independent replicons such as phages and plasmids
    Analysis of the mating-type loci of co-occurring and phylogenetically related species of Ascochyta and Phoma
    Woudenberg, J.H.C. ; Gruyter, J. de; Crous, P.W. ; Zwiers, L.H. - \ 2012
    Molecular Plant Pathology 13 (2012)4. - ISSN 1464-6722 - p. 350 - 362.
    evolutionary relationships - sexual development - pyrenophora-teres - pisum-sativum - complex - genes - teleomorph - phylogeny - sequences - cloning
    Ascochyta and Phoma are fungal genera containing several important plant pathogenic species. These genera are morphologically similar, and recent molecular studies performed to unravel their phylogeny have resulted in the establishment of several new genera within the newly erected Didymellaceae family. An analysis of the structure of fungal mating-type genes can contribute to a better understanding of the taxonomic relationships of these plant pathogens, and may shed some light on their evolution and on differences in sexual strategy and pathogenicity. We analysed the mating-type loci of phylogenetically closely related Ascochyta and Phoma species (Phoma clematidina, Didymella vitalbina, Didymella clematidis, Peyronellaea pinodes and Peyronellaea pinodella) that co-occur on the same hosts, either on Clematis or Pisum. The results confirm that the mating-type genes provide the information to distinguish between the homothallic Pey. pinodes (formerly Ascochyta pinodes) and the heterothallic Pey. pinodella (formerly Phoma pinodella), and indicate the close phylogenetic relationship between these two species that are part of the disease complex responsible for Ascochyta blight on pea. Furthermore, our analysis of the mating-type genes of the fungal species responsible for causing wilt of Clematis sp. revealed that the heterothallic D. vitalbina (Phoma anamorph) is more closely related to the homothallic D. clematidis (Ascochyta anamorph) than to the heterothallic P. clematidina. Finally, our results indicate that homothallism in D. clematidis resulted from a single crossover between MAT1-1 and MAT1-2 sequences of heterothallic ancestors, whereas a single crossover event followed by an inversion of a fused MAT1/2 locus resulted in homothallism in Pey. pinodes.
    ProRepeat: an integrated repository for studying amino acid tandem repeats in proteins
    Luo, H. ; Lin, K. ; David, A. ; Nijveen, H. ; Leunissen, J.A.M. - \ 2012
    Nucleic acids research 40 (2012)D1. - ISSN 0305-1048 - p. D394 - D399.
    annotation resource - codon usage - sequences - database - evolution - genomes - selection - alanine - algorithm - proteomes
    ProRepeat ( is an integrated curated repository and analysis platform for in-depth research on the biological characteristics of amino acid tandem repeats. ProRepeat collects repeats from all proteins included in the UniProt knowledgebase, together with 85 completely sequenced eukaryotic proteomes contained within the RefSeq collection. It contains non-redundant perfect tandem repeats, approximate tandem repeats and simple, low-complexity sequences, covering the majority of the amino acid tandem repeat patterns found in proteins. The ProRepeat web interface allows querying the repeat database using repeat characteristics like repeat unit and length, number of repetitions of the repeat unit and position of the repeat in the protein. Users can also search for repeats by the characteristics of repeat containing proteins, such as entry ID, protein description, sequence length, gene name and taxon. ProRepeat offers powerful analysis tools for finding biological interesting properties of repeats, such as the strong position bias of leucine repeats in the N-terminus of eukaryotic protein sequences, the differences of repeat abundance among proteomes, the functional classification of repeat containing proteins and GC content constrains of repeats’ corresponding codons.
    Use of rbcL and trnL-F as a two-locus DNA barcode for identification of NW-European ferns: an ecological perspective
    Groot, G.A. de; During, H.J. ; Maas, J.W. ; Schneider, H. ; Erkens, R.H.J. - \ 2011
    PLoS ONE 6 (2011)1. - ISSN 1932-6203
    dryopteris-affinis group - land plants - noncoding regions - chloroplast dna - mononucleotide repeats - sequences - phylogeny - taxonomy - pcr - amplification
    Although consensus has now been reached on a general two-locus DNA barcode for land plants, the selected combination of markers (rbcL + matK) is not applicable for ferns at the moment. Yet especially for ferns, DNA barcoding is potentially of great value since fern gametophytes—while playing an essential role in fern colonization and reproduction—generally lack the morphological complexity for morphology-based identification and have therefore been underappreciated in ecological studies. We evaluated the potential of a combination of rbcL with a noncoding plastid marker, trnL-F, to obtain DNAidentifications for fern species. A regional approach was adopted, by creating a reference database of trusted rbcL and trnL-F sequences for the wild-occurring homosporous ferns of NW-Europe. A combination of parsimony analyses and distancebased analyses was performed to evaluate the discriminatory power of the two-region barcode. DNA was successfully extracted from 86 tiny fern gametophytes and was used as a test case for the performance of DNA-based identification. Primer universality proved high for both markers. Based on the combined rbcL + trnL-F dataset, all genera as well as all species with non-equal chloroplast genomes formed their own well supported monophyletic clade, indicating a high discriminatory power. Interspecific distances were larger than intraspecific distances for all tested taxa. Identification tests on gametophytes showed a comparable result. All test samples could be identified to genus level, species identification was well possible unless they belonged to a pair of Dryopteris species with completely identical chloroplast genomes. Our results suggest a high potential of the combined use of rbcL and trnL-F as a two-locus cpDNA barcode for identification of fern species. A regional approach may be preferred for ecological tests. We here offer such a ready-to-use barcoding approach for ferns, which opens the way for answering a whole range of questions previously unaddressed in fern gametophyte ecology
    First isolation of Hepatitis E virus genotype 4 in Europe through swine surveillance in the Netherlands and Belgium.
    Honing-Hakze, R.W. van der; Coillie, E. Van; Antonis, A.F.G. ; Poel, W.H.M. van der - \ 2011
    PLoS ONE 6 (2011)8. - ISSN 1932-6203 - 6 p.
    cross-species infection - united-states - rt-pcr - prevalence - hev - epidemiology - transmission - antibodies - sequences - humans
    Hepatitis E virus (HEV) genotypes 3 and 4 are a cause of human hepatitis and swine are considered the main reservoir. To study the HEV prevalence and characterize circulating HEV strains, fecal samples from swine in the Netherlands and Belgium were tested by RT-PCR. HEV prevalence in swine was 7–15%. The Dutch strains were characterized as genotype 3, subgroups 3a, 3c and 3f, closely related to sequences found in humans and swine earlier. The HEV strains found in Belgium belonged to genotypes 3f and 4b. The HEV genotype 4 strain was the first ever reported in swine in Europe and an experimental infection in pigs was performed to isolate the virus. The genotype 4 strain readily infected piglets and caused fever and virus shedding. Since HEV4 infections have been reported to run a more severe clinical course in humans this observation may have public health implications
    Investigation of Cyprinidherpesvirus-3 genetic diversity by a multi-locus variable number of tandem repeats analysis.
    Avarre, J.C. ; Madeira, J.P. ; Santika, A. ; Zainunb, Z. ; Baud, M. ; Cabon, J. ; Caruso, D. ; Castric, J. ; Bigarré, L. ; Engelsma, M.Y. ; Maskur, M. - \ 2011
    Journal of Virological Methods 173 (2011)2. - ISSN 0166-0934 - p. 320 - 327.
    mediated isothermal amplification - koi-herpesvirus - common carp - r-package - virus - khv - sequences - pcr - dna - mortality
    Cyprinid herpesvirus-3 (CyHV-3), or koi herpesvirus (KHV), is responsible for high mortalities in aquaculture of both common carp (Cyprinus carpio carpio) and koi carp (Cyprinus carpio koi) worldwide. The complete genomes of three CyHV-3 isolates showed more than 99% of DNA sequence identity, with the majority of differences located in short tandem repeats, also called VNTR (variable number of tandem repeats). By targeting these variations, eight loci were selected for genotyping CyHV-3 by multiple locus VNTR analysis (MLVA). CyHV-3 strains obtained after sequential in vivo infections exhibited identical MLVA profiles, whereas samples originating from a single isolate passaged 6 and 82 times in vitro exhibited mutations in two of the eight loci, suggesting a relatively slow genetic evolution rate of the VNTRs. The method was subsequently applied on 38 samples collected in Indonesia, France and the Netherlands. Globally, the isolates grouped in two main genetic clusters, each one divided in two subgroups including either CyHV-3-U/I or CyHV3-J. Interestingly, Indonesian strains were rather distant from CyHV-3-J isolate. The results of the present study indicate that these VNTR molecular markers are efficient in estimating the genetic diversity among CyHV-3 isolates and are therefore suitable for further molecular epidemiological studies.
    DNA damage in plant herbarium tissue.
    Staats, M. ; Cuenca, A. ; Richardson, J.E. ; Ginkel, R.V. ; Petersen, G. ; Seberg, O. ; Bakker, F.T. - \ 2011
    PLoS ONE 6 (2011)12. - ISSN 1932-6203 - 9 p.
    programmed cell-death - ancient dna - miscoding lesions - enzymatic amplification - specimens - repair - preservation - extraction - sequences - reveals
    Dried plant herbarium specimens are potentially a valuable source of DNA. Efforts to obtain genetic information from this source are often hindered by an inability to obtain amplifiable DNA as herbarium DNA is typically highly degraded. DNA post-mortem damage may not only reduce the number of amplifiable template molecules, but may also lead to the generation of erroneous sequence information. A qualitative and quantitative assessment of DNA post-mortem damage is essential to determine the accuracy of molecular data from herbarium specimens. In this study we present an assessment of DNA damage as miscoding lesions in herbarium specimens using 454-sequencing of amplicons derived from plastid, mitochondrial, and nuclear DNA. In addition, we assess DNA degradation as a result of strand breaks and other types of polymerase non-bypassable damage by quantitative real-time PCR. Comparing four pairs of fresh and herbarium specimens of the same individuals we quantitatively assess post-mortem DNA damage, directly after specimen preparation, as well as after long-term herbarium storage. After specimen preparation we estimate the proportion of gene copy numbers of plastid, mitochondrial, and nuclear DNA to be 2.4–3.8% of fresh control DNA and 1.0–1.3% after long-term herbarium storage, indicating that nearly all DNA damage occurs on specimen preparation. In addition, there is no evidence of preferential degradation of organelle versus nuclear genomes. Increased levels of C¿T/G¿A transitions were observed in old herbarium plastid DNA, representing 21.8% of observed miscoding lesions. We interpret this type of post-mortem DNA damage-derived modification to have arisen from the hydrolytic deamination of cytosine during long-term herbarium storage. Our results suggest that reliable sequence data can be obtained from herbarium specimens.
    Host status of false brome grass to the leaf rust fungus Puccinia brachypodii and the stripe rust fungus P. Striiformis
    Barbieri, M. ; Marcel, T.C. ; Niks, R.E. - \ 2011
    Plant Disease 95 (2011)11. - ISSN 0191-2917 - p. 1339 - 1345.
    agrobacterium-mediated transformation - model system - distachyon - genome - rice - nonhost - specificity - resistance - morphology - sequences
    Purple false brome grass (Brachypodium distachyon) has recently emerged as a model system for temperate grasses and is also a potential model plant to investigate plant interactions with economically important pathogens such as rust fungi. We determined the host status of five Brachypodium species to three isolates of Puccinia brachypodii, the prevalent rust species on Brachypodium sylvaticum in nature, and to one isolate each of three formae speciales of the stripe rust fungus P. striiformis. Two P. striiformis isolates produced sporulating lesions, both in only one of the tested interactions, suggesting a marginal host status of B. distachyon. P. brachypodii formed sporulating uredinia on the five Brachypodium species tested, and a range of reactions was observed. Surprisingly, the B. sylvaticum–derived rust isolates were more frequently pathogenic to B. distachyon than to their original host species. The B. distachyon diploid inbred lines, developed and distributed as reference material to the Brachypodium research community, include susceptible and resistant genotypes to at least three of the four P. brachypodii isolates tested. This creates the opportunity to use B. distachyon/P. brachypodii as a model pathosystem. In one B. distachyon accession, heavy infection by the loose smut fungus Ustilago bromivora occurred. That pathogen could also serve as a model pathogen of Brachypodium.
    A quantitative account of genomic island acquisitions in prokaryotes
    Roos, T.E. ; Passel, M.W.J. van - \ 2011
    BMC Genomics 12 (2011). - ISSN 1471-2164 - 34 p.
    art. no. 163 - pathogenicity islands - bacterial genomes - signature - sequences - dna - identification - amelioration - evolution - virulence
    BACKGROUND: Microbial genomes do not merely evolve through the slow accumulation of mutations, but also, and often more dramatically, by taking up new DNA in a process called horizontal gene transfer. These innovation leaps in the acquisition of new traits can take place via the introgression of single genes, but also through the acquisition of large gene clusters, which are termed Genomic Islands. Since only a small proportion of all the DNA diversity has been sequenced, it can be hard to find the appropriate donors for acquired genes via sequence alignments from databases. In contrast, relative oligonucleotide frequencies represent a remarkably stable genomic signature in prokaryotes, which facilitates compositional comparisons as an alignment-free alternative for phylogenetic relatedness. In this project, we test whether Genomic Islands identified in individual bacterial genomes have a similar genomic signature, in terms of relative dinucleotide frequencies, and can therefore be expected to originate from a common donor species. RESULTS: When multiple Genomic Islands are present within a single genome, we find that up to 28% of these are compositionally very similar to each other, indicative of frequent recurring acquisitions from the same donor to the same acceptor. CONCLUSIONS: This represents the first quantitative assessment of common directional transfer events in prokaryotic evolutionary history. We suggest that many of the resident Genomic Islands per prokaryotic genome originated from the same source, which may have implications with respect to their regulatory interactions, and for the elucidation of the common origins of these acquired gene clusters
    Base-pairing promotes leader selection to prime in vitro influenza genome transcription
    Geerts-Dimitriadou, C. ; Zwart, M.P. ; Goldbach, R.W. ; Kormelink, R.J.M. - \ 2011
    Virology 409 (2011)1. - ISSN 0042-6822 - p. 17 - 26.
    messenger-rna synthesis - cap-snatching mechanism - mosaic-virus rnas - viral-rna - 5' ends - complementary rna - a virus - polymerase - endonuclease - sequences
    The requirements for alignment of capped leader sequences along the viral genome during influenza transcription initiation (cap-snatching) have long been an enigma. In this study, competition experiments using an in vitro transcription assay revealed that influenza virus transcriptase prefers leader sequences with base complementarity to the 3'-ultimate residues of the viral template, 10 or 11 nt from the 5' cap. Internal priming at the 3'-penultimate residue, as well as prime-and-realign was observed. The nucleotide identity immediately 5' of the base-pairing residues also affected cap donor usage. Application to the in vitro system of RNA molecules with increased base complementarity to the viral RNA template showed stronger reduction of globin RNA leader initiated influenza transcription compared to those with a single base-pairing possibility. Altogether the results indicated an optimal cap donor consensus sequence of 7mG-(N)7–8-(A/U/G)-(A/U)-AGC-3'.
    Bivariate colour maps for visualizing climate data
    Teuling, A.J. ; Stöckli, R. ; Seneviratne, S.I. - \ 2011
    International Journal of Climatology 31 (2011)9. - ISSN 0899-8418 - p. 1408 - 1412.
    univariate - sequences
    The increasing availability of gridded, high-resolution, multivariate climatological data sets calls for innovative approaches to visualize inter-variable relations. In this study, we present a methodology, based on properties of common colour schemes, to plot two variables in a single colour map by using a two-dimensional colour legend for both sequential and diverging data. This is especially suited for climate data as the spatial distribution of the relation between different variables is often as important as the distribution of variables individually. Two example applications are given to illustrate the use of the method: one that shows the global distribution of climate based on observed temperature and relative humidity, and the other showing the distribution of recent changes in observed temperature and precipitation over Europe. A flexible and easy-to-implement method is provided to construct different colour legends for sequential and diverging data.
    Functional analysis and expression of HcrVf1 and HcrVf2 for development of scab resistant cisgenic and intragenic apples
    Joshi, S.G. ; Schaart, J. ; Groenwold, R. ; Jacobsen, E. ; Schouten, H.J. ; Krens, F.A. - \ 2011
    Plant Molecular Biology 75 (2011)6. - ISSN 0167-4412 - p. 579 - 591.
    receptor-like genes - real-time pcr - venturia-inaequalis - vf gene - plants - sequences - agrobacterium - promoters - linkage - cluster
    Apple scab resistance genes, HcrVf1 and HcrVf2, were isolated including their native promoter, coding and terminator sequences. Two fragment lengths (short and long) of the native gene promoters and the strong apple rubisco gene promoter (PMdRbc) were used for both HcrVf genes to test their effect on expression and phenotype. The scab susceptible cultivar ‘Gala’ was used for plant transformations and after selection of transformants, they were micrografted onto apple seedling rootstocks for scab disease tests. Apple transformants were also tested for HcrVf expression by quantitative RT-PCR (qRTPCR). For HcrVf1 the long native promoter gave significantly higher expression that the short one; in case of HcrVf2 the difference between the two was not significant. The apple rubisco gene promoter proved to give the highest expression of both HcrVf1 and HcrVf2. The top four expanding leaves were used initially for inoculation with monoconidial isolate EU-B05 which belongs to race 1 of V. inaequalis. Later six other V. inaequalis isolates were used to study the resistance spectra of the individual HcrVf genes. The scab disease assays showed that HcrVf1 did not give resistance against any of the isolates tested regardless of the expression level. The HcrVf2 gene appeared to be the only functional gene for resistance against Vf avirulent isolates of V. inaequalis. HcrVf2 did not provide any resistance to Vf virulent strains, even not in case of overexpression. In conclusion, transformants carrying the apple-derived HcrVf2 gene in a cisgenic as well as in an intragenic configuration were able to reach scab resistance levels comparable to the Vf resistant control cultivar obtained by classical breeding, cv. ‘Santana’.
    Hoe ver en hoeveel? Verspreiding en infecties van koolluis in Nederland, Thema: Functionele biodiversiteit BO-12.03-004-001a
    Belder, E. den; Smulders, M.J.M. ; Esselink, D. ; Elderson, J. - \ 2011
    brevicoryne brassicae - gewasbescherming - verkeerde liggingen - volgorden - gewasmengsels - gewassen - koolsoorten - brevicoryne brassicae - plant protection - malpositions - sequences - crop mixtures - crops - cabbages
    Informatieposter met de titel "Hoe ver en hoeveel? Verspreiding en infecties van koolluis in Nederland", thema functionele biodiversiteit. De frequenties van bladluisinfecties worden beïnvloed door de ruimtelijke ligging en de opvolging van gewassen. Kan er door wijzigingen in bouwplan en gewasrotatie worden bijgedragen aan bladluisbeheersing?
    SLIDER: A Generic Metaheuristic for the Discovery of Correlated Motifs in Protein-Protein Interaction Networks
    Boyen, P. ; Dyck, D. van; Neven, F. ; Ham, R.C.H.J. van; Dijk, A.D.J. van - \ 2011
    IEEE/ACM Transactions on Computational Biology and Bioinformatics 8 (2011)5. - ISSN 1545-5963 - p. 1344 - 1357.
    sequences - scale - pairs
    Correlated motif mining (CMM) is the problem of finding overrepresented pairs of patterns, called motifs, in sequences of interacting proteins. Algorithmic solutions for CMM thereby provide a computational method for predicting binding sites for protein interaction. In this paper, we adopt a motif-driven approach where the support of candidate motif pairs is evaluated in the network. We experimentally establish the superiority of the Chi-square-based support measure over other support measures. Furthermore, we obtain that CMM is an NP-hard problem for a large class of support measures (including Chi-square) and reformulate the search for correlated motifs as a combinatorial optimization problem. We then present the generic metaheuristic SLIDER which uses steepest ascent with a neighborhood function based on sliding motifs and employs the Chi-square-based support measure. We show that SLIDER outperforms existing motif-driven CMM methods and scales to large protein-protein interaction networks. The SLIDER-implementation and the data used in the experiments are available on
    Genetic Basis of Tetracycline Resistance in Bifidobacterium animalis subsp lactis
    Gueimonde, M. ; Florez, A.B. ; Hoek, A.H.A.M. van; Stuer-Lauridsen, B. ; Stroman, P. ; Reyes-Gavilan, C.G. de los; Margolles, A. - \ 2010
    Applied and Environmental Microbiology 76 (2010)10. - ISSN 0099-2240 - p. 3364 - 3369.
    antibiotic susceptibility - probiotic products - tet(w) - bacteria - bile - lactobacillus - sequences - strains - humans - thermophilum
    All strains of Bifidobacterium animalis subsp. lactis described to date show medium level resistance to tetracycline. Screening of 26 strains from a variety of sources revealed the presence of tet(W) in all isolates. A transposase gene upstream of tet(W) was found in all strains, and both genes were cotranscribed in strain IPLAIC4. Mutants with increased tetracycline resistance as well as tetracycline-sensitive mutants of IPLAIC4 were isolated and genetically characterized. The native tet(W) gene was able to restore the resistance phenotype to a mutant with an alteration in tet(W) by functional complementation, indicating that tet(W) is necessary and sufficient for the tetracycline resistance seen in B. animalis subsp. lactis.
    Novel fungal genera and species associated with the sooty blotch and flyspeck complex on apple in China and the USA
    Yang, H.L. ; Sun, G.Y. ; Batzer, J.C. ; Crous, P.W. ; Groenewald, J.Z. ; Gleason, M.L. - \ 2010
    Persoonia (2010)24. - ISSN 0031-5850 - p. 29 - 37.
    ribosomal dna - sp-nov - sporidesmium - sequences - disease
    Fungi in the sooty blotch and flyspeck (SBFS) complex cause blemishes on apple and pear fruit that result in economic losses for growers. The SBFS fungi colonise the epicuticular wax layer of pomaceous fruit but do not invade the cuticle. Fungi causing fuliginous and punctate mycelial types on apple are particularly difficult to identify based on morphological criteria because many species in the SBFS complex share the same mycelial phenotypes. We compared the morphology and nuclear ribosomal DNA phylogeny (ITS, LSU) of 11 fungal strains isolated from SBFS blemishes on apple obtained from two provinces in China and five states in the USA. Parsimony analysis, supported by cultural characteristics and morphology in vitro, provided support to delimit the isolates into three novel genera, representing five new species. Phaeothecoidiella, with two species, P. missouriensis and P. illinoisensis, is introduced as a new genus with pigmented endoconidia in the Dothideomycetes. Houjia (Capnodiales) is introduced for H. pomigena and H. yanglingensis. Although morphologically similar to Stanjehughesia (Chaetosphaeriaceae), Houjia is distinct in having solitary conidiogenous cells. Sporidesmajora (Capnodiales), based on S. pennsylvaniensis, is distinguished from Sporidesmium (Sordariomycetes) in having long, multiseptate conidiophores that frequently have a subconical, darkly pigmented apical cell, and very long, multi-euseptate conidia
    Microcyclospora and Microcyclosporella: novel genera accommodating epiphytic fungi causing sooty blotch on apple
    Frank, J. ; Crous, P.W. ; Groenewald, J.Z. ; Oertel, B. ; Hyde, K.D. ; Phengsintham, P. ; Schroers, H.J. - \ 2010
    Persoonia 24 (2010). - ISSN 0031-5850 - p. 93 - 105.
    flyspeck complex - ribosomal dna - mycosphaerella - anamorphs - phylogeny - disease - teratosphaeria - proteaceae - morphology - sequences
    Recent studies have found a wide range of ascomycetes to be associated with sooty blotch and flyspeck (SBFS) blemishes on the surfaces of pomaceous fruits, specifically apples. Based on collections of such fungi from apple orchards in Germany and Slovenia we introduce two novel genera according to analyses of morphological characters and nuclear ribosomal DNA sequences (large subunit and internal transcribed spacer regions). Microcyclosporella is represented by a single species, M. mali, and is presently known from Germany and Slovenia. Microcyclosporella is Pseudocercosporella-like in morphology, but genetically and morphologically distinct from Pseudocercosporella s.str., for which an epitype is designated based on a fresh collection of P. bakeri from Laos. Furthermore, Pseudocercosporella is shown to be paraphyletic within the Capnodiales. Microcyclospora gen. nov. is Pseudocercospora-like in morphology, but is genetically and morphologically distinct from Pseudocercospora s.str., which is based on P. vitis. Three species, Microcyclospora malicola, M. pomicola (both collected in Germany), and M. tardicrescens (collected in Slovenia) are described. Finally, a new species of Devriesia, D. pseudoamericana, is described from pome fruit surfaces collected in Germany. Devriesia is shown to be paraphyletic, and to represent several lineages of which only Devriesia s.str. is thermotolerant. Further collections are required, however, before the latter generic complex can be resolved.
    Biochemical and genetical analysis reveal a new clade of biovar 3 Dickeya spp. strains isolated from potato in Europe
    Slawiak, M. ; Beckhoven, J.R.C.M. van; Speksnijder, A.G.C.L. ; Czajkowski, R.L. ; Grabe, G. ; Wolf, J.M. van der - \ 2009
    European Journal of Plant Pathology 125 (2009)2. - ISSN 0929-1873 - p. 245 - 261.
    erwinia-chrysanthemi - xanthomonas - pcr - sequences - hosts - water - fingerprints - genomes - plants
    Sixty-five potato strains of the soft rot-causing plant pathogenic bacterium Dickeya spp., and two strains from hyacinth, were characterised using biochemical assays, REP-PCR genomic finger printing, 16S rDNA and dnaX sequence analysis. These methods were compared with nineteen strains representing six Dickeya species which included the type strains. A group of twenty-two potato strains isolated between 2005-2007 in the Netherlands, Poland, Finland and Israel were characterised as belonging to biovar 3. They were 100% identical in REP-PCR, dnaX and 16S rDNA sequence analysis. In a polyphasic analysis they formed a new clade different from the six Dickeya species previously described, and may therefore constitute a new species. The strains were very similar to a Dutch strain from hyacinth. On the basis of dnaX sequences and biochemical assays, all other potato strains isolated in Europe between 1979 and 1994 were identified as D. dianthicola (biovar 1 and 7), with the exception of two German strains classified as D. dieffenbachia (biovar 2) and D. dadantii (biovar 3), respectively. Potato strains from Peru were classified as D. dadantii, from Australia as D. zeae and from Taiwan as D. chrysanthemi bv. parthenii, indicating that different Dickeya species are found in association with potato.
    Base composition, selection, and phylogenetic significance of indels in the recombination activating gene-1 in vertebrates
    Chiari, Y. ; Meijden, A. van der; Madsen, O. ; Vences, M. ; Meyer, A. - \ 2009
    Frontiers in Zoology 6 (2009). - ISSN 1742-9994 - 15 p.
    nuclear rag-1 gene - v(d)j recombination - mitochondrial-dna - evolution - sequences - diversification - patterns - frogs - amphibians - inference
    Background: The Recombination Activating Proteins, RAG1 and RAG2, play a crucial role in the immune response in vertebrates. Among the nuclear markers currently used for phylogenetic purposes, Rag1 has especially enjoyed enormous popularity, since it successfully contributed to elucidating the relationships among and within a large variety of vertebrate lineages. We here report on a comparative investigation of the genetic variation, base composition, presence of indels, and selection in Rag1 in different vertebrate lineages (Actinopterygii, Amphibia, Aves, Chondrichthyes, Crocodylia, Lepidosauria, Mammalia, and Testudines) through the analysis of 582 sequences obtained from Genbank. We also analyze possible differences between distinct parts of the gene with different type of protein functions. Results: In the vertebrate lineages studied, Rag1 is over 3 kb long. We observed a high level of heterogeneity in base composition at the 3(rd) codon position in some of the studied vertebrate lineages and in some specific taxa. This result is also paralleled by taxonomic differences in the GC content at the same codon position. Moreover, positive selection occurs at some sites in Aves, Lepidosauria and Testudines. Indels, which are often used as phylogenetic characters, are more informative across vertebrates in the 5' than in the 3'-end of the gene. When the entire gene is considered, the use of indels as phylogenetic character only recovers one major vertebrate clade, the Actinopterygii. However, in numerous cases insertions or deletions are specific to a monophyletic group. Conclusions: Rag1 is a phylogenetic marker of undoubted quality. Our study points to the need of carrying out a preliminary investigation on the base composition and the possible existence of sites under selection of this gene within the groups studied to avoid misleading resolution. The gene shows highly heterogeneous base composition, which affects some taxa in particular and contains sites under positive selection in some vertebrate lineages in the 5'-end. The first part of the gene (5'-end) is more variable than the second (3'-end), and less affected by a heterogeneous base composition. However, in some vertebrate lineages the 5'-end of the gene is not yet widely used for phylogenetic studies
    Eukaryotic transcriptomics in silico: Optimizing cDNA-AFLP efficiency
    Stölting, K.N. ; Gort, G. ; Wüst, C. ; Wilson, A.B. - \ 2009
    BMC Genomics 10 (2009). - ISSN 1471-2164 - 15 p.
    full-length cdnas - differential gene-expression - identification - distributions - resistance - sequences - resources - markers - library - plant
    Background - Complementary-DNA based amplified fragment length polymorphism (cDNA-AFLP) is a commonly used tool for assessing the genetic regulation of traits through the correlation of trait expression with cDNA expression profiles. In spite of the frequent application of this method, studies on the optimization of the cDNA-AFLP assay design are rare and have typically been taxonomically restricted. Here, we model cDNA-AFLPs on all 92 eukaryotic species for which cDNA pools are currently available, using all combinations of eight restriction enzymes standard in cDNA-AFLP screens. Results - In silco simulations reveal that cDNA pool coverage is largely determined by the choice of individual restriction enzymes and that, through the choice of optimal enzyme combinations, coverage can be increased from
    Towards a phylogenetic clarification of Lophiostoma / Massarina and morphologically similar genera in the Pleosporales
    Zhang, Y. ; Wang, H.K. ; Fournier, J. ; Crous, P.W. ; Jeewon, R. ; Pointing, S.B. ; Hyde, K.D. - \ 2009
    Fungal Diversity 38 (2009). - ISSN 1560-2745 - p. 225 - 251.
    submerged wood - ribosomal dna - fresh-water - hong-kong - fungi - ascomycota - revision - epitypification - teleomorph - sequences
    Lophiostoma, Lophiotrema and Massarina are similar genera that are difficult to distinguish morphologically. In order to obtain a better understanding of these genera, lectotype material of the generic types, Lophiostoma macrostomun, Lophiotrema nucula and Massarina eburnea were examined and are re-described. The phylogeny of these genera is investigated based oil the analysis of 26 Lophiostoma- and Massarina-like taxa and three genes - 18S, 28S rDNA and RPB2. These taxa formed five well-supported sub-clades in Pleosporales. This Study confirms that both Lophiostoma and Massarina are polyphyletic. Massarina-like taxa can presently be differentiated into two groups - the Lentithecium group and the Massarina group. Of these, the type species M. eburnea together with the Massarina group represents Massarina sensu stricto. Lophiostoma taxa Clustered in two groups - one group, including the type species L. macrostomum, is characterized by fusiform, hyaline one-septate ascospores which are pigmented and 3-septate when senescent, clavate asci, and apical structures which are highly variable, being crest-like in L. macrostomum, all umbilicate pore surrounded by 4-6 radial ridges in L. rugulosum, or papillate in L. glabrotunicatum. The second group comprises Lophiostoma species with heavily pigmented multi-septate ascospores and compressed crests. Lophiotrema species including the type species L. nucula form a monophyletic group. One new genus - Lentithecium with five new species - Lentithecium aquaticum, Lophiostoma glabrotunicatum, L. rugulosum, Lophiotrema brunneosporum and L. lignicola and three new combinations - Lentithecium arundinaceum, L. fluviatile and L. lineare are introduced in this paper.
    Quest for ion–ion correlations in electric double layers and overcharging phenomena
    Lyklema, J. - \ 2009
    Advances in Colloid and Interface Science 147-148 (2009). - ISSN 0001-8686 - p. 205 - 213.
    charge inversion - silver-iodide - adsorption - interface - sequences - stability - reversal - systems - anatase - water
    A discussion is given of the experimental evidence for overcharging, also known as charge reversal. The phenomenon is very common. The most general explanation is specific chemical adsorption. However, overcharging can also be explained on the basis of ion-ion correlations, which is rather a physical type of interpretation, and which can also be specific. Several theories have been developed for that. So, there is the luxury problem that two alternative explanations are available for the same observation. The purpose of this paper is to consider the various approaches critically and try to devise experimental options to discriminate between the two interpretations
    Identification of an ortholog of the eukaryotic RNA polymerase III subunit RPC34 in Crenarchaeota and Thaumarchaeota suggests specialization of RNA polymerases for coding and non-coding RNAs in Archaea
    Blombach, F. ; Makarova, K.S. ; Marrero, J. ; Siebers, B. ; Koonin, E.V. ; Oost, J. van der - \ 2009
    Biology Direct 4 (2009). - ISSN 1745-6150 - p. 39 - 39.
    transcription initiation - structure prediction - evolution - sequences - complexes - proteins - database - search - origin - server
    One of the hallmarks of eukaryotic information processing is the co-existence of 3 distinct, multi-subunit RNA polymerase complexes that are dedicated to the transcription of specific classes of coding or non-coding RNAs. Archaea encode only one RNA polymerase that resembles the eukaryotic RNA polymerase II with respect to the subunit composition. Here we identify archaeal orthologs of the eukaryotic RNA polymerase III subunit RPC34. Genome context analysis supports a function of this archaeal protein in the transcription of non-coding RNAs. These findings suggest that functional separation of RNA polymerases for protein-coding genes and non-coding RNAs might predate the origin of the Eukaryotes
    Phylogenetic relationships in Betula (Betulaceae) based on AFLP markers
    Schenk, M.F. ; Thienpont, C.N. ; Koopman, W.J.M. ; Gilissen, L.J.W.J. ; Smulders, M.J.M. - \ 2008
    Tree Genetics and Genomes 4 (2008)4. - ISSN 1614-2942 - p. 911 - 924.
    multilocus genotype data - birch pollen allergen - population-structure - major allergen - b-pubescens - dna - sequences - inference - evolution - isoforms
    The genus Betula comprises various species in boreal and temperate climate zones of the Northern Hemisphere. The taxonomy of Betula is controversial and complicated by parallel evolution of morphological traits, polyploidization events, and extensive hybridization and introgression among species. Multilocus molecular data from AFLPs were used to provide phylogenetic information. A large number of polymorphic markers (321 variable bands) were produced in 107 Betula accessions from 23 species and 11 hybrids. The AFLP results were largely congruent with the results from previously examined nuclear DNA markers. Four distinct subgenera were identified within the genus Betula. These subgenera were partly in disagreement with the traditional (but disputed) division of the genus. In addition, the results indicated several groups of conspecific taxa. The majority of the species fell within subgenus Betula and shared a high degree of similarity with B. pendula. All hybrids were associated with this group, and the AFLP data contained signals on putative parents for some of the interspecific hybrids. Subgenus Chamaebetula and part of the Neurobetula species should be merged with Betula. The subgenera Betulenta, Betulaster, and the remaining part of Neurobetula are distinct and well supported. Although our results indicate that four major taxonomic groups can be recognized within the genus Betula, the relationship between them remains unclear. This may be due to the occurrence of hybridization and introgression, which would have a homogenizing effect on the relationships between species. Naturally occurring Betula species of hybrid origin may explain the low bootstrap values within the Betula clade.
    HaploSNPer: a web-based allele and SNP detection tool
    Tang, J. ; Leunissen, J.A.M. ; Voorrips, R.E. ; Linden, C.G. van der; Vosman, B. - \ 2008
    BMC Genetics 9 (2008). - ISSN 1471-2156 - 7 p.
    discovery - polymorphisms - sequences - database - genomes
    Background - Single nucleotide polymorphisms (SNPs) and small insertions or deletions (indels) are the most common type of polymorphisms and are frequently used for molecular marker development. Such markers have become very popular for all kinds of genetic analysis, including haplotype reconstruction. Haplotypes can be reconstructed for whole chromosomes but also for specific genes, based on the SNPs present. Haplotypes in the latter context represent the different alleles of a gene. The computational approach to SNP mining is becoming increasingly popular because of the continuously increasing number of sequences deposited in databases, which allows a more accurate identification of SNPs. Several software packages have been developed for SNP mining from databases. From these, QualitySNP is the only tool that combines SNP detection with the reconstruction of alleles, which results in a lower number of false positive SNPs and also works much faster than other programs. We have build a web-based SNP discovery and allele detection tool (HaploSNPer) based on QualitySNP. Results - HaploSNPer is a flexible web-based tool for detecting SNPs and alleles in user-specified input sequences from both diploid and polyploid species. It includes BLAST for finding homologous sequences in public EST databases, CAP3 or PHRAP for aligning them, and QualitySNP for discovering reliable allelic sequences and SNPs. All possible and reliable alleles are detected by a mathematical algorithm using potential SNP information. Reliable SNPs are then identified based on the reconstructed alleles and on sequence redundancy. Conclusion - Thorough testing of HaploSNPer (and the underlying QualitySNP algorithm) has shown that EST information alone is sufficient for the identification of alleles and that reliable SNPs can be found efficiently. Furthermore, HaploSNPer supplies a user friendly interface for visualization of SNP and alleles.
    Conversion of chromosome-specific RAPDs into SCAR-based anchor markers for onion linkage maps and its application to genetic analyses inother Allium species
    Masuzaki, S. ; Miyazaki, T. ; McCallum, J. ; Heusden, A.W. van; Kik, C. ; Yamashita, K. ; Tashiro, Y. - \ 2008
    Scientia Horticulturae 115 (2008)4. - ISSN 0304-4238 - p. 323 - 328.
    amplified polymorphic dna - monosomic addition lines - l. aggregatum group - cepa l. - construction - assignment - sequences - aflp - locations - reveals
    Integration of previously developed Allium cepa linkage maps requires the availability of anchor markers for each of the eight chromosomes of shallot (A. cepa L. common group Aggregatum). To this end, eight RAPD markers originating from our previous research were converted into SCAR markers via cloning and sequencing of RAPD amplicons and designing of 24-mer oligonucleotide primers. Of the eight pairs of SCAR primers, seven resulted in the amplification of single bands of the original RAPDs, and the remaining primer set amplified an additional band. The results of Southern hybridization using RAPD amplicons from genomic DNA of Japanese bunching onion (Allium fistulosum L.)¿shallot monosomic addition lines indicated that five SCAR markers were single shallot chromosome-specific markers and were not detected in genomic DNA of A. fistulosum. The eight SCAR primer pairs were applied to other Allium species and exhibited three types of amplification profiles, namely RAPD amplicons observed only in shallot, in shallot and Allium vavilovii, and in several Allium species. A mapping study using 65 F2 plants generated by the selfing of one interspecific cross A. cepa × Allium roylei individual integrated the SCAR marker SAOE17500 into chromosome 5 as expected. The results of the present study show that the eight SCAR primer sets specific to shallot can facilitate the mapping in A. cepa and can also serve as anchor points between maps of different Allium species
    A ribosomal DNA-based framework for the detection and quantification of stress-sensitive nematode families in terrestrial habitats
    Holterman, M.H.M. ; Rybarczyk-Mydlowska, K.D. ; Elsen, S.J.J. van den; Megen, H.H.B. van; Mooijman, P.J.W. ; Santiago, R.P. ; Bongers, A.M.T. ; Bakker, J. ; Helder, J. - \ 2008
    Molecular Ecology Resources 8 (2008). - ISSN 1755-098X - p. 23 - 34.
    phylogenetic-relationships - maturity index - rna gene - sequences - classification - dorylaimida - evolution - reveals
    Indigenous communities of soil-resident nematodes have a high potential for soil health assessment as nematodes are diverse, abundant, trophically heterogeneous and easily extractable from soil. The conserved morphology of nematodes is the main operational reason for their under-exploitation as soil health indicators, and a user-friendly biosensor system should preferably be based on nonmorphological traits. More than 80% of the most environmental stress-sensitive nematode families belong to the orders Mononchida and Dorylaimida. The phylogenetic resolution offered by full-length small subunit ribosomal DNA (SSU rDNA) sequences within these two orders is highly different. Notwithstanding several discrepancies between morphology and SSU rDNA-based systematics, Mononchida families (indicated here as M1¿M5) are relatively well-supported and, consequently, family-specific DNA sequences signatures could be defined. Apart from Nygolaimidae and Longidoridae, the resolution among Dorylaimida families was poor. Therefore, a part of the more variable large subunit rDNA (¿ 1000 bp from the 5'-end) was sequenced for 72 Dorylaimida species. Sequence analysis revealed a subclade division among Dorylaimida (here defined as D1¿D9, PP1¿PP3) that shows only distant similarity with `classical¿ Dorylaimid systematics. Most subclades were trophically homogeneous, and ¿ in most cases ¿ specific morphological characteristics could be pinpointed that support the proposed division. To illustrate the practicability of the proposed molecular framework, we designed primers for the detection of individual subclades within the order Mononchida in a complex DNA background (viz. in terrestrial or freshwater nematode communities) and tested them in quantitative assays (real-time polymerase chain reaction). Our results constitute proof-of-principle for the concept of DNA sequence signatures-based monitoring of stress sensitive nematode families in environmental samples
    Sonnenberg, A.S.M. - \ 2007
    Paddestoelen : onafhankelijk vakblad voor Nederland en België 2007 (2007)6. - ISSN 1380-359X - p. 8 - 8.
    genetica - genomen - dna - paddestoelen - agaricus bisporus - volgorden - genen - toepassing - onderzoek - genetics - genomes - dna - mushrooms - agaricus bisporus - sequences - genes - application - research
    Eind 2007 zal een begin gemaakt worden met de ontrafeling van het hele genoom van de champignon (Agaricus bisporus). Het karwei zal waarschijnlijk in 2009 geklaard zijn. Dan zal de volgorde van alle 34 miljoen bouwstenen in het DNA (sequentie) van deze paddenstoel bekend zijn en tevens de locatie van alle genen
    Molecular and biological characterization of Tomato chlorotic mottle virus suggests that recombination underlies the evolution and diversity of Brazilian tomato begomoviruses
    Ribeiro, S.G. ; Martin, D.P. ; Lacorte, C. ; Simoes, I.C. ; Orlandini, D.R.S. ; Inoue-Nagata, A.K. - \ 2007
    Phytopathology 97 (2007)6. - ISSN 0031-949X - p. 702 - 711.
    whitefly-transmitted geminiviruses - leaf-curl-virus - abutilon-mosaic-virus - dna-b - nicotiana-benthamiana - replication - emergence - sequences - disease - origin
    Tomato chlorotic mottle virus (ToCMoV) is an emerging begomovirus species widely distributed throughout tomato-growing regions of Brazil. ToCMoV appears to have expanded its geographic range recently, invading tomato-growing areas that were free of begomovirus infection before 2004. We have determined the first complete genome sequence of an infectious ToCMoV genome (isolate BA-Se1), which is the first begomovirus species isolated in the northeast of Brazil. When introduced by particle bombardment into tomato, the cloned ToCMoV-[BA-Se1] DNA-A and DNA-B components caused typical chlorotic mottle symptoms. The cloned virus was whitefly-transmissible and, although it was infectious in hosts such as Nicotiana benthamiana, pepper, tobacco, and Nicandra physaloides, it was unable to infect Arabidopsis thaliana, bean, N. glutinosa, and Datura metel. Sequence and biological analyses indicate that ToCMoV-[BA-Se1] is a typical New World begomovirus sp. requiring both DNA-A and DNA-B components to establish systemic infections. Although evidence of multiple recombination events was detected within the ToCMoV-[BA-Se1] DNA-A, they apparently occurred relatively long ago, implying that recombination probably has not contributed to the recent emergence of this species.
    A new robust diagnostic polymerase chain reaction for determining the mating status of female Anopheles gambiae mosquitoes
    Ng'habi, K.R. ; Horton, A. ; Knols, B.G.J. ; Lanzaro, G.C. - \ 2007
    American Journal of Tropical Medicine and Hygiene 77 (2007)3. - ISSN 0002-9637 - p. 485 - 487.
    y-chromosome - drosophila-melanogaster - neo-y - malaria - genome - degeneration - sequences - evolution - miranda - sex
    The principal malaria vector in Africa, Anopheles gambiae, contains two pairs of autosomes and one pair of sex chromosomes. The Y chromosome is only associated with males and other Y chromosome¿specific DNA sequences, which are transferred to women during mating. A reliable tool to determine the mating status of dried wild An. gambiae females is currently lacking. DNA was extracted from dried virgin and mated females and used to test whether Y chromosome¿specific polymerase chain reaction (PCR) markers can be successfully amplified and used as a predictor of mating. Here we report a new PCR-based method to determine the mating status among successfully inseminated and virgin wild An. gambiae females, using three male-specific primers. This dissection-free method has the potential to facilitate studies of both population demographics and gene flow from dried mosquito samples routinely collected in epidemiologic monitoring and aid existing and new malaria-vector control approaches.
    Hybrid Mitochondrial Plasmids From Senescence Suppressor Isolates of Neurospora intermedia
    Maas, M.F.P.M. ; Hoekstra, R.F. ; Debets, A.J.M. - \ 2007
    Genetics 175 (2007). - ISSN 0016-6731 - p. 785 - 794.
    reverse-transcriptase - podospora-anserina - transfer-rnas - dna - sequences - identification - recombination - evolution - insertion - strains
    We analyzed several natural suppressor isolates of the pKalilo-based fungal senescence syndrome of Neurospora intermedia. The pKalilo plasmid did not increase in titer in these isolates. Nor did it show integration "de novo." In at least two of the senescence suppressor isolates, pKalilo had formed stable recombinants with other mitochondrial elements. pKalilo/mtDNA recombination junctions were complete and appeared to have been formed via a nonhomologous recombination mechanism. Further analysis revealed that pKalilo had recombined a novel, 2.6-kb cryptic mitochondrial retroplasmid, similar to the mitochondrial retroplasmid pTHR1 from Trichoderma harzianum and retroplasmids of the "Varkud" homology group. The recombinant molecules consisted of pKalilo, the novel element, and short intervening stretches of mtDNA. The latter stretches clearly corresponded to "in vivo" mitochondrial cDNA, suggesting that the molecules had formed via the action of a template-switching reverse transcriptase. We discuss how different types of mitochondrial plasmids interact and how their detrimental effect on the host may be suppressed.
    A Natural infrageneric classification for Cicer (Leguminoseae, Cicereae)
    Davies, A.M.R. ; Maxted, N. ; Maesen, L.J.G. van der - \ 2007
    Blumea 52 (2007)2. - ISSN 0006-5196 - p. 379 - 400.
    genetic-relationships - genus cicer - phylogenetic-relationships - isozyme polymorphism - sequences - turkey - rapd - dna - morphology - diversity
    A comprehensive morphological survey and analysis of all taxonomically recognised wild species of Cicer L. (Leguminosae, Cicereae) is presented. The data (104 characters from 152 herbarium specimens representing 34 of the 44 recognised taxa in the genus Cicer with supplementary data for the remaining taxa taken from the literature) were analysed using multivariate statistics (cluster analysis, factor analysis and ordination techniques). The results are discussed in the context of extant classifications and the re-organisation of a novel infrageneric classification also incorporating information from published genetic data. A revised classification with 3 subgenera, 5 sections and 2 series is proposed.
    Hepatitis E Virus RNA in Commercial Porcine Livers in The Netherlands
    Bouwknegt, M. ; Lodder-Verschoor, F. ; Poel, W.H.M. van der; Rutjes, S.A. ; Roda Husman, A.M. de - \ 2007
    Journal of Food Protection 70 (2007)12. - ISSN 0362-028X - p. 2889 - 2895.
    cross-species infection - united-states - phylogenetic analysis - genetic diversity - wild boar - swine - transmission - prevalence - sequences - japan
    Human hepatitis E virus (HEV) infections by genotype 3 strains in industrialized countries are hypothesized to be caused by pigs. To examine this hypothesis, the potential health risks of transmission routes should be examined. Possible foodborne transmission was studied by quantifying the presence and infectivity of HEV in commercial porcine livers in The Netherlands. A comparison of four tissue disruption and seven RNA extraction methods revealed that mechanical disruption followed by silica-based RNA extraction gave the highest RNA yields and was therefore employed on commercial porcine livers. Four (6.5%) of 62 porcine livers were HEV RNA positive by reverse transcriptase PCR and Southern blot hybridization. Each positive liver was estimated to contain ~65 PCR-detectable units per g. Sequences were obtained for three of four positive livers and classified as HEV genotype 3. Ninety-three percent similarity to Dutch human HEV sequences and 97% similarity to Dutch swine HEV sequences were observed. To determine whether positive livers contained infectious HEV particles, extracts from livers with known HEV RNA sequences were inoculated intravenously in pigs. Two control pigs were included: one was inoculated with a high dose known to result in infection (104 PCR-detectable units of HEV RNA), and the other was inoculated with a lower concentration of virus that equaled the concentration of PCR-detectable units in commercial livers (~20 PCR-detectable units). Infection was observed in the high-dose control, but not in other pigs, suggesting a dose-dependent response in pigs. Hence, the implications of HEV RNA in commercial porcine livers in The Netherlands are unknown. However, HEV RNA is present in commercial porcine livers, and sufficient heating of porcine livers before consumption as precautionary measure is recommended.
    Distribution and diversity of root-lesion nematodes (Pratylenchus spp.) associated with Ammophila arenaria in coastal dunes of Western Europe
    Peña, E. de la; Karssen, G. ; Moens, M. - \ 2007
    Nematology 9 (2007)6. - ISSN 1388-5545 - p. 881 - 901.
    ribosomal-rna gene - morphological characterization - molecular characterization - phylogenetic analysis - cyst-nematode - clonal grass - d3 expansion - sequences - rdna - region
    The distribution and diversity of Pratylenchus species associated with Ammophila arenaria was investigated in its natural range of distribution. Twelve localities with vigorous stands of A. arenaria along the European Atlantic and Mediterranean coasts were sampled. The populations were identified based on morphology and morphometrics, and further characterised based on sequences of the rDNA D2D3 region. Pratylenchus spp. were present in all of the sampled sites. A total of 19 populations were detected belonging to Pratylenchus dunensis, P. brzeskii, P. pratensis or P. penetrans. Pratylenchus dunensis was widely distributed from Blakeney Point (UK) to Comporta (Portugal). Pratylenchus brzeskii was found in South European localities along the Atlantic coast and also in the Mediterranean region. Pratylenchus pratensis was found associated with A. arenaria for the first time and occurred at different locations along the Atlantic coast. Pratylenchus penetrans was only detected in Biarritz (France). The P. dunensis populations from the south west Iberian Peninsula differed from the original P. dunensis description and showed two incisures on the lip region instead of one. Pratylenchus brzeskii populations did not vary morphologically from the original descriptions; however, the range of their morphometrical characters was wider than that of the type population. The D2D3 rDNA region revealed large interspecific and low intraspecific variation, supporting the morphological identification. The phylogenetic relationships of the populations with respect to other species of the genus were inferred from partial sequences of the rDNA and positioned P. dunensis within the same group as P. convallariae, P. penetrans and P. fallax.
    Phylogeographic patterns in Leccinum sect. Scabra and the status of the arctic/alpine species L. rotundifoliae
    Bakker, H.C. den; Zuccarello, G.C. ; Kuyper, T.W. ; Noordeloos, M.E. - \ 2007
    Mycological Research 111 (2007)6. - ISSN 0953-7562 - p. 663 - 672.
    evolution - substitutions - phylogeny - sequences - muscaria - region - model - dna
    We investigated inter- and intraspecific phylogenetic relationships in the ectomycorrhizal fungal genus Leccinum section Scabra. Species of this section are exclusively associated with Betula and occur throughout the Northern Hemisphere. We compared the phylogenetic relationships of arctic, alpine, boreal and temperate accessions of section Scabra based on DNA sequences of the single-copy nuclear gene Gapdh and the multiple-copy nuclear region 5.8S-ITS2. Exclusively arctic lineages were not detected in species that occur both in arctic-alpine or boreal regions, except in L. rotundifoliae that was restricted to cold climates. L. scabrum and L. holopus showed an intercontinental phylogeographic pattern, and L. variicolor showed a pattern unrelated to geographical distribution. Molecular clock estimates indicated that L. rotundifoliae is as old as other species in section Scabra. Individual gene trees suggest that interspecific hybridisation occurred several times in the evolution of section Scabra.
    Investigation of microbial communities on reverse osmosis membranes used for process water production
    Bereschenko, L.A. ; Stams, A.J.M. ; Heilig, G.H.J. ; Euverink, G.J.W. ; Nederlof, M.M. ; Loosdrecht, M.C.M. - \ 2007
    Water Science and Technology 55 (2007)8-9. - ISSN 0273-1223 - p. 181 - 190.
    16s ribosomal-rna - systems - sequences - biofilms - genes
    In the present study, the diversity and the phylogenetic affiliation of bacteria in a biofouling layer on reverse osmosis (RO) membranes were determined. Fresh surface water was used as a feed in a membrane-based water purification process. Total DNA was extracted from attached cells from feed spacer, RO membrane and product spacer. Universal primers were used to amplify the bacterial 16S rRNA genes. The biofilm community was analysed by 16S rRNA-gene-targeted denaturing gradient gel electrophoresis (DGGE) and the phylogenetic affiliation was determined by sequence analyses of individual 16S rDNA clones. Using this approach, we found that five distinct bacterial genotypes (Sphingomonas, Beta proteobacterium, Flavobacterium, Nitrosomonas and Sphingobacterium) were dominant genera on surfaces of fouled RO membranes. Moreover, the finding that all five ¿key players¿ could be recovered from the cartridge filters of this RO system, which cartridge filters are positioned before the RO membrane, together with literature information where these bacteria are normally encountered, suggests that these microorganisms originate from the feed water rather than from the RO system itself, and represent the fresh water bacteria present in the feed water, despite the fact that the feed water passes an ultrafiltration (UF) membrane (pore size approximately 40 nm), which is able to remove microorganisms to a large extent.
    Microgeographic evolution of snail shell shape and predator behavior
    Schilthuizen, M. ; Til, A. Van; Salverda, M. ; Liew, T.S. ; James, S. ; Elahan, B. Bin; Vermeulen, J.J. - \ 2006
    Evolution 60 (2006)9. - ISSN 0014-3820 - p. 1851 - 1858.
    land-snails - sexual selection - gene flow - speciation - dna - diversification - biodiversity - population - diversity - sequences
    AbstractGenetic divergence in geographically isolated populations is a prerequisite for allopatric speciation, one of the most common modes of speciation. In ecologically equivalent populations existing within a small, environmentally homogeneous area, an important role for environmentally neutral divergence is often found or inferred. We studied a species complex of conspicuously shaped Opisthostoma land snails on scattered limestone outcrops within a small area of lowland rainforest in Borneo. We used shell morphometrics, mitochondrial and nuclear DNA sequences, and marks of predation to study the factors involved in allopatric divergence. We found that a striking geographic divergence exists in shell morphology, which is partly associated with neutral genetic divergence. We also found geographic differentiation in the behavior of the snails' invertebrate predator and evidence of an evolutionary interaction between aspects of shell shape and predator behavior. Our study shows that adaptation to biotic aspects of the environment may play a more important role in allopatric speciation than previously suspected, even on a geographically very small scale.
    Presumptive horizontal symbiont transmission in the fungus-growing termite Macrotermes natalensis
    Fine Licht, H.H. de; Boomsma, J.J. ; Aanen, D.K. - \ 2006
    Molecular Ecology 15 (2006)11. - ISSN 0962-1083 - p. 3131 - 3138.
    odontotermes-formosanus - phylogenetic inference - population-genetics - isoptera - recombination - comb - sequences - colonies - basidiomycota - establishment
    All colonies of the fungus-growing termite Macrotermes natalensis studied so far are associated with a single genetically variable lineage of Termitomyces symbionts. Such limited genetic variation of symbionts and the absence of sexual fruiting bodies (mushrooms) on M. natalensis mounds would be compatible with clonal vertical transmission, as is known to occur in Macrotermes bellicosus. We investigated this hypothesis by analysing DNA sequence polymorphisms as codominant SNP markers of four single-copy gene fragments of Termitomyces isolates from 31 colonies of M. natalensis. A signature of free recombination was found, indicative of frequent sexual horizontal transmission. First, all 31 strains had unique multilocus genotypes. Second, SNP markers (n = 55) were largely in Hardy-Weinberg equilibrium (90.9%) and almost all possible pairs of SNPs between genetically unlinked loci were in linkage equilibrium (96.7%). Finally, extensive intragenic recombination was found, especially in the EF1 alpha fragment. Substantial genetic variation and a freely recombining population structure can only be explained by frequent horizontal and sexual transmission of Termitomyces. The apparent variation in symbiont transmission mode among Macrotermes species implies that vertical symbiont transmission can evolve rapidly. The unexpected finding of horizontal transmission makes the apparent absence of Termitomyces mushrooms on M. natalensis mounds puzzling. To our knowledge, this is the first detailed study of the genetic population structure of a single lineage of Termitomyces.
    Natural occurence of Wolbachia-infected and uninfected Trichogramma species in tomato fields in Portugal
    Gonçalves, C.I. ; Huigens, M.E. ; Verbaarschot, P.G.H. ; Duarte, S. ; Mexia, A. ; Tavares, J. - \ 2006
    Biological Control 37 (2006)3. - ISSN 1049-9644 - p. 375 - 381.
    sex-ratio chromosome - biological-control - parthenogenesis - sequences - wasps - gene - mass
    Minute egg parasitoids of the genus Trichogramma (Hymenoptera; Trichogrammatidae) are promising candidates for biological control of lepidopteran pests in tomato in Portugal. This certainly applies to native Trichogramma strains that have thelytokous reproduction, i.e., produce only daughters. In Trichogramma wasps, thelytoky is mostly induced by the intracellular bacterium Wolbachia. In this study, we carried out a field survey of native Trichogramma species in four locations in Ribatejo, the main processing tomato region of Portugal, and determined the prevalence of Wolbachia in those species. Five Trichogramma species were found to emerge from lepidopteran eggs collected in the field, namely Trichogramma bourarache, Trichogramma cordubensis, Trichogramma evanescens, Trichogramma pintoi, and Trichogramma turkestanica. T. evanescens and T. pintoi were by far the dominating species representing, respectively, 64.9 and 26.4% of the trichogrammatids collected. Total natural parasitism rates of the collected lepidopteran eggs by Trichogramma wasps ranged from 28.2 to 64.6%. Three Trichogramma species were found to be infected with Wolbachia, namely T. cordubensis, T. evanescens, and T. turkestanica. All the wasp broods belonging to T. cordubensis were infected, whereas low infection rates were found in T. evanescens (0.9% of the broods) and T. turkestanica (4.5% of the broods). The latter represents the first record of a Wolbachia infection in T. turkestanica. Sequencing of the Wolbachia surface protein, wsp, revealed this Wolbachia infection to be related to other Wolbachia infections in Trichogramma wasps. As Wolbachia-infected thelytokous strains exist for T. evanescens, the most abundant Trichogramma species naturally occurring in the tomato fields of the Ribatejo region, this species offers interesting and powerful options for biological control of lepidopteran pests in processing tomato in this region.
    Phylum-wide analysis of SSU rDNA reveals deep phylogenetic relationships among nematodes and accelerated evolution toward Crown Clades
    Holterman, M.H.M. ; Wurff, A.W.G. van der; Elsen, S.J.J. van den; Megen, H.H.B. van; Bongers, A.M.T. ; Holovachov, O.V. ; Bakker, J. ; Helder, J. - \ 2006
    Molecular Biology and Evolution 23 (2006)9. - ISSN 0737-4038 - p. 1792 - 1800.
    relative-rate test - ribosomal-rna - sequences - ultrastructure - confidence - bootstrap
    Inference of evolutionary relationships between nematodes is severely hampered by their conserved morphology, the high frequency of homoplasy, and the scarcity of phylum-wide molecular data. To study the origin of nematode radiation and to unravel the phylogenetic relationships between distantly related species, 339 nearly full-length small-subunit rDNA sequences were analyzed from a diverse range of nematodes. Bayesian inference revealed a backbone comprising 12 consecutive dichotomies that subdivided the phylum Nematoda into 12 clades. The most basal clade is dominated by the subclass Enoplia, and members of the order Triplonchida occupy positions most close to the common ancestor of the nematodes. Crown Clades 8¿12, a group formerly indicated as "Secernentea" that includes Caenorhabditis elegans and virtually all major plant and animal parasites, show significantly higher nucleotide substitution rates than the more basal Clades 1¿7. Accelerated substitution rates are associated with parasitic lifestyles (Clades 8 and 12) or short generation times (Clades 9¿11). The relatively high substitution rates in the distal clades resulted in numerous autapomorphies that allow in most cases DNA barcode¿based species identification. Teratocephalus, a genus comprising terrestrial bacterivores, was shown to be most close to the starting point of Secernentean radiation. Notably, fungal feeding nematodes were exclusively found basal to or as sister taxon next to the 3 groups of plant parasitic nematodes, namely, Trichodoridae, Longidoridae, and Tylenchomorpha. The exclusive common presence of fungivorous and plant parasitic nematodes supports a long-standing hypothesis that states that plant parasitic nematodes arose from fungivorous ancestors
    Plant host range of Verticillium longisporum and microsclerotia density in Swedisch soils
    Johansson, A. ; Goud, J.C. ; Dixelius, C. - \ 2006
    European Journal of Plant Pathology 114 (2006)2. - ISSN 0929-1873 - p. 139 - 149.
    molecular characterization - oilseed rape - dahliae - wilt - sequences - identification - nuclear - barley - crops
    Verticillium longisporum is a soil-borne fungal pathogen causing vascular wilt of Brassica crops. This study was conducted to enhance our knowledge on the host range of V. longisporum. Seven crop species (barley, oat, oilseed rape, pea, red clover, sugar beet and wheat) and five weed species (barren brome, black-grass, charlock, cleavers and scentless mayweed) all common in southern Sweden were evaluated for infection by response to V. longisporum. Oat, spring wheat, oilseed rape, scentless mayweed and charlock inoculated with V. longisporum in a greenhouse showed stunting to various degrees close to the fully ripe stage. Based on the extent of microsclerotia formation, explants were separated into four groups: for pea and wheat, 80%. The results suggest that plant species outside the Brassicaceae can act as reservoirs of V. longisporum inoculum. Soil inoculum densities in nine fields were monitored over a period of 12 months, which ranged from 1 to 48 cfu g¿1 soil. Density of microsclerotia was lowest just after harvest, reaching its maximum six months later. No significant correlation between inoculum density in soil and disease incidence on oilseed rape plants was found. However, the data suggest that a threshold of 1 cfu g¿1 soil is needed to cause disease on oilseed rape. Species identification based on microsclerotia morphology and PCR analysis showed that V. longisporum dominated in soil of seven, and V. dahliae in two of the nine fields studied.
    Reconstructing the early evolution of the fungi using a six gene phylogeny
    James, T.Y. ; Kauff, F. ; Schoch, C.L. ; Matheny, P.B. ; Hofstetter, V. ; Cox, C.J. ; Celio, G. ; Gueidan, C. ; Fraker, E. ; Miadlikowska, J. ; Lumbsch, H.T. ; Rauhut, A. ; Reeb, V. ; Arnold, A.E. ; Amtoft, A. ; Stajich, J.E. ; Hosaka, K. ; Sung, G.H. ; Johnson, D. ; O'Rourke, B. ; Binder, M. ; Curtis, J.M. ; Slot, J.C. ; Wang, Z. ; Wilson, A.W. ; Schüßler, A. ; Longcore, J.E. ; O'Donnell, K. ; Mozley-Standridge, S. ; Porter, D. ; Letcher, P.M. ; Powell, M.J. ; Taylor, J.W. ; White, M.M. ; Griffith, G.W. ; Davies, D.R. ; Sugiyama, J. ; Rossman, A.Y. ; Rogers, J.D. ; Pfister, D.H. ; Hewitt, D. ; Hansen, K. ; Hambleton, S. ; Shoemaker, R.A. ; Kohlmeyer, J. ; Volkmann-Kohlmeyer, B. ; Spotts, R.A. ; Serdani, M. ; Crous, P.W. ; Hughes, K.W. ; Matsuura, K. ; Langer, E. ; Langer, G. ; Untereiner, W.A. ; Lücking, R. ; Büdel, B. ; Geiser, D.M. ; Aptroot, A. ; Diederich, P. ; Schmitt, I. ; Schultz, M. ; Yahr, R. ; Hibbett, D.S. ; Lutzoni, F. ; McLaughlin, D.J. ; Spatafora, J.W. ; Vilgalys, R. - \ 2006
    Nature 443 (2006)7113. - ISSN 0028-0836 - p. 818 - 822.
    arbuscular mycorrhizal fungi - molecular phylogeny - maximum-likelihood - land plants - tree - microsporidia - sequences - animals - chytridiomycota - glomeromycota
    The ancestors of fungi are believed to be simple aquatic forms with flagellated spores, similar to members of the extant phylum Chytridiomycota (chytrids). Current classifications assume that chytrids form an early-diverging clade within the kingdom Fungi and imply a single loss of the spore flagellum, leading to the diversification of terrestrial fungi. Here we develop phylogenetic hypotheses for Fungi using data from six gene regions and nearly 200 species. Our results indicate that there may have been at least four independent losses of the flagellum in the kingdom Fungi. These losses of swimming spores coincided with the evolution of new mechanisms of spore dispersal, such as aerial dispersal in mycelial groups and polar tube eversion in the microsporidia (unicellular forms that lack mitochondria). The enigmatic microsporidia seem to be derived from an endoparasitic chytrid ancestor similar to Rozella allomycis, on the earliest diverging branch of the fungal phylogenetic tree
    Analysis of the SHP2 enhancer for the use of tissue specific activation tagging in Arabidopsis thaliana
    Chalfun Junior, A. ; Mes, J.J. ; Busscher, M. ; Angenent, G.C. - \ 2006
    Genetics and Molecular Biology 29 (2006)2. - ISSN 1415-4757 - p. 401 - 407.
    mads-box genes - transformation - biosynthesis - growth - plants - fruit - transcription - regulator - sequences - promoter
    Activation tagging is a powerful tool to identify new mutants and to obtain information about possible biological functions of the overexpressed genes. The quadruple cauliflower mosaic virus (CaMV) 35S enhancer fragment is a strong enhancer, which is most commonly used for this purpose. However, the constitutive nature of this enhancer may generate lethal mutations or aberrations in different plant organs by the same overexpressed gene. A tissue-specific activation tagging approach may overcome these drawbacks and may also lead more efficiently to the desired phenotype. For this reason the SHATTERPROOF2 (SHP2) promoter fragment was analysed for enhancer activity. The SHP2 gene is involved in dehiscence zone development and expressed during silique development. The aim of the experiments described here was to identify a dehiscence zone specific enhancer that could be used for tissue-specific activation tagging. The chosen SHP2 enhancer fragment was found to be expressed predominantly in the dehiscence zone and showed enhancer activity as well as ectopic expression activity. This activity was not influenced by its orientation towards the promoter and it was still functional at the largest tested distance of 2.0 kb. Based on these results, the SHP2 enhancer fragment can potentially be used in a tissue-specific activation tagging approach to identify new Arabidopsis mutants with an altered dehiscence zone formation.
    Lectin receptor kinases participate in protein-protein interactions to mediate plasma membrane-cell wall adhesions in Arabidopsis
    Gouget, A. ; Senchou, V. ; Govers, F. ; Sanson, A. ; Barre, A. ; Rougé, P. ; Pont-Lezica, R. ; Canut, H. - \ 2006
    Plant Physiology 140 (2006)1. - ISSN 0032-0889 - p. 81 - 90.
    signal-transduction - lathyrus-ochrus - isolectin-i - sequences - binding - plants - expression - alignment - families - database
    Interactions between plant cell walls and plasma membranes are essential for cells to function properly, but the molecules that mediate the structural continuity between wall and membrane are unknown. Some of these interactions, which are visualized upon tissue plasmolysis in Arabidopsis (Arabidopsis thaliana), are disrupted by the RGD (arginine-glycine-aspartic acid) tripeptide sequence, a characteristic cell adhesion motif in mammals. In planta induced-O (IPI-O) is an RGD-containing protein from the plant pathogen Phytophthora infestans that can disrupt cell wall-plasma membrane adhesions through its RGD motif. To identify peptide sequences that specifically bind the RGD motif of the IPI-O protein and potentially play a role in receptor recognition, we screened a heptamer peptide library displayed in a filamentous phage and selected two peptides acting as inhibitors of the plasma membrane RGD-binding activity of Arabidopsis. Moreover, the two peptides also disrupted cell wall-plasma membrane adhesions. Sequence comparison of the RGD-binding peptides with the Arabidopsis proteome revealed 12 proteins containing amino acid sequences in their extracellular domains common with the two RGD-binding peptides. Eight belong to the receptor-like kinase family, four of which have a lectin-like extracellular domain. The lectin domain of one of these, At5g60300, recognized the RGD motif both in peptides and proteins. These results imply that lectin receptor kinases are involved in protein-protein interactions with RGD-containing proteins as potential ligands, and play a structural and signaling role at the plant cell surfaces.
    Phylogeography, population dynamics, and molecular evolution of European bat lyssaviruses
    Davis, P.L. ; Holmes, E.C. ; Larrous, F. ; Poel, W.H.M. van der; Tjornehoj, K. ; Alonso, W.J. ; Bourhy, H. - \ 2005
    Journal of Virology 79 (2005)16. - ISSN 0022-538X - p. 10487 - 10497.
    pteropus-giganteus - immune-response - rabies virus - rna viruses - infection - epidemiology - substitution - chiroptera - diversity - sequences
    European bat lyssaviruses types 1 and 2 (EBLV-1 and EBLV-2) are widespread in Europe, although little is known of their evolutionary history. We undertook a comprehensive sequence analysis to infer the selection pressures, rates of nucleotide substitution, age of genetic diversity, geographical origin, and population growth rates of EBLV-1. Our study encompassed data from 12 countries collected over a time span of 35 years and focused on the glycoprotein (G) and nucleoprotein (N) genes. We show that although the two subtypes of EBLV-1¿EBLV-1a and EBLV-1b¿have both grown at a low exponential rate since their introduction into Europe, they have differing population structures and dispersal patterns. Furthermore, there were strong constraints against amino acid change in both EBLV-1 and EBLV-2, as reflected in a low ratio of nonsynonymous to synonymous substitutions per site, particularly in EBLV-1b. Our inferred rate of nucleotide substitution in EBLV-1, approximately 5 x 10¿5 substitutions per site per year, was also one of the lowest recorded for RNA viruses and implied that the current genetic diversity in the virus arose 500 to 750 years ago. We propose that the slow evolution of EBLVs reflects their distinctive epidemiology in bats, where they occupy a relatively stable fitness peak.
    An obliquity-controlled Early Pleistocene river terrace record from Western Turkey?
    Maddy, D. ; Demir, T. ; Bridgeland, D. ; Veldkamp, A. ; Stemerdink, C. ; Schriek, T. van der; Westaway, R. - \ 2005
    Quaternary Research 63 (2005)3. - ISSN 0033-5894 - p. 339 - 346.
    2-stage extension - gediz graben - uplift - stratigraphy - evolution - sequences - selendi - basins - model
    Investigation of the Pleistocene sequence of the Gediz River, Western Turkey, has revealed a record of Early Pleistocene river terraces. Eleven terraces spanning the interval from 1.67 to 1.245 million years ago (MIS 59-37) are preserved beneath basaltic lava flows. The high number of terraces over this short time period reflects high-frequency sedimentation/incision cycles preserved due to the fortuitous combination of relatively high uplift rates (0.16 mm yr¿1) and progressive southwards valley migration. Comparison of this record with ODP967 from the Eastern Mediterranean Basin suggests a link between the production of terraces and obliquity-driven 41,000 year climate cycles in the Early Pleistocene.
    Preliminary studies on Botryosphaeria species from Southern Hemisphere conifers in Australasia and South Africa
    Slippers, B. ; Summerbell, B.A. ; Crous, P.W. ; Coutinho, T.A. ; Wingfield, B.D. ; Wingfield, M.J. - \ 2005
    Australasian Plant Pathology 34 (2005)2. - ISSN 0815-3191 - p. 213 - 220.
    wollemia-nobilis - genetic-variation - sp-nov - eucalyptus - dothidea - characters - pathogens - sequences - cankers - ribis
    Wollemia nobilis is an ancient coniferous tree species that was recently discovered in eastern Australia. This tree is highly threatened due to its limited distribution. No genetic variation has been detected within the wild populations of ~100 adult plants. A recent study has revealed that a species of Botryosphaeria is highly pathogenic to W. nobilis. The aim of the present study was to identify this fungus, as well as Botryosphaeria isolates of unknown identity from other Southern Hemisphere coniferous hosts, Araucaria from New Zealand and Widdringtonia from South Africa. To facilitate their identification, sequence data for the ITS rDNA, as well as the ß-tubulin and translation elongation factor 1-¿ genes were combined to determine the phylogenetic relationship of these isolates with those of known Botryosphaeria spp. Isolates from W. nobilis included two Botryosphaeria spp. The first is closely related to B. ribis, but also shares some unique sequence polymorphisms with B. parva. One isolate grouped with B. australis, but also varied slightly from this taxon in the gene regions analysed. Additional isolates will be needed to determine whether these sequence variations represent speciation events or merely variation within populations of B. ribis and B. australis. In addition to this, B. parva was identified from Araucaria in New Zealand, and B. australis was found on Widdringtonia trees in South Africa. All three reports of these fungi are new records for their various hosts and could represent important pathogens of these trees
    Phylogenetic and morphological re-evaluation of the Botryosphaeria species causing diseases of Mangifera indica
    Slippers, B. ; Johnson, G.I. ; Crous, P.W. ; Coutinho, T.A. ; Wingfield, B.D. ; Wingfield, M.J. - \ 2005
    Mycologia 97 (2005)1. - ISSN 0027-5514 - p. 99 - 110.
    end rot pathogens - new-zealand - mango - dothidea - fungi - characters - anamorphs - infection - sequences - avocado
    Species of Botryosphaeria are among the most serious pathogens that affect mango trees and fruit. Several species occur on mangoes, and these are identified mainly on the morpholopy of the anamorphs. Common taxa include Dothiorella dominicana, D. mangiferae (= Natrassia mangiferae), D. aromatica and an unidentified species, Dothiorella 'long'. The genus name Dothiorella, however, is acknowledged as a synonym of Diplodia. This study aimed to characterize and name the Botryosphaeria spp. associated with disease symptoms on mangoes. To achieve this isolates representing all four Dothiorella slip. mentioned above were compared with the anamorphs of known Botryosphaeria spp., based on conidial morphology and DNA sequence data. Two genomic regions were analyzed, namely the ITS rDNA and beta-tubulin regions. The morphological and molecular results confirmed that the fungi previously identified front mango as species of Dothiorella belong to Fusicoccum. Dothiorella dominicana isolates were identical to isolates of F. parvum (teleomorph = B. Parva). A new epithet, namely F. mangiferum, is proposed for isolates previously treated as D. maugiferae or N. maugiferae. Isolates of D. aromatica were identified as F. aesculi (telcomorph = B. dothidea). A fourth Fusicoccum sp. also was identified as those isolates previously known as Dothiorella 'long'. A key is provided to distinguish these species based on anamorph morphology in culture. This study provides a basis for the identification of Botryosphaeria species front mango, which is important for disease control and to uphold quarantine regulations.
    Alle genen van Phytophthora op een rij: verschillen, overeenkomsten en gastheerspecificiteit
    Meijer, H.J.G. ; Govers, F. ; Jiang, R.H.Y. - \ 2005
    Gewasbescherming 36 (2005)6. - ISSN 0166-6495 - p. 271 - 271.
    gewasbescherming - genoomanalyse - volgorden - schimmels - phytophthora - phytophthora sojae - plantenziekteverwekkers - waardplanten - eiwitten - enzymen - plantensecreties - plantenziektekunde - genexpressieanalyse - plant protection - genome analysis - sequences - fungi - phytophthora - phytophthora sojae - plant pathogens - host plants - proteins - enzymes - plant secretions - plant pathology - genomics
    Samenvatting van de voordracht te houden op 30 november 2005 tijdens de Najaarsvergadering van de KNPV (Koninklijke Nederlandse Plantenziektekundige Vereniging).
    A transmembrane phospholipase D in Phytophthora; a novel PLD subfamily
    Meijer, H.J.G. ; Latijnhouwers, M. ; Ligterink, W. ; Govers, F. - \ 2005
    Gene 350 (2005)2. - ISSN 0378-1119 - p. 173 - 182.
    phosphatidic-acid - infestans - yeast - motif - phosphoinositides - activation - sequences - beta
    Phospholipase D (PLD) is a ubiquitous enzyme in eukaryotes that participates in various cellular processes. Its catalytic domain is characterized by two HKD motifs in the C-terminal part. Until now, two subfamilies were recognized based on their N-terminal domain structure. The first has a PX domain in combination with a PH domain and is designated as PXPH-PLD. Members of the second subfamily, named C2-PLD, have a C2 domain and have, so far, only been found in plants. Here we describe a novel PLD subfamily that we identified in Phytophthora, a genus belonging to the class oomycetes and comprising many important plant pathogens. We cloned Pipld1 from Phytophthora infestans and retrieved full-length sequences of its homologues from Phytophthora sojae and Phytophthora ramorum genome databases. Their promoters contain two putative regulatory elements, one of which is highly conserved in all three genes. The three Phytophthora pld1 genes encode nearly identical proteins of around 1807 amino acids, with the two characteristic HKD motifs in the C-terminal part. Homology of the predicted proteins with known PLDs however is restricted to the two catalytic HKD motifs and adjacent domains. In the N-terminal part Phytophthora PLD1 has a PX-like domain, but it lacks a PH domain. Instead the N-terminal region contains five putative membrane spanning domains suggesting that Phytophthora PLD1 is a transmembrane protein. Since Phytophthora PLD1 cannot be categorized in one of the two existing subfamilies we propose to create a novel subfamily named PXTM-PLD
    Phylogeny, morphological evolution, and speciation of endemic brassicaceae genera in the cape flora of southern Africa
    Mummenhoff, K. ; Al-Shehbaz, I.A. ; Bakker, F.T. ; Linder, H.P. ; Mühlhausen, A. - \ 2005
    Annals of the Missouri Botanical Garden 92 (2005)3. - ISSN 0026-6493 - p. 400 - 424.
    molecular systematics - family brassicaceae - dna - cruciferae - biogeography - arabidopsis - dispersal - radiation - sequences - regions
    Heliophila (ca. 73 spp.), the ditypic Cycloptychis and Thlaspeocarpa, and the monotypic Schlechteria, Silicularia, Brachycarpaea, and Chamira are endemic to the Cape region of South Africa, where they are the dominant genera of Brassicaceae. They may be regarded as the most diversified Brassicaceae lineage in every aspect of habit, leaf, flower, and fruit morphology. The characters used in the separation of these genera and their species, especially fruit type (silique vs. silicle), dehiscence (dehiscent vs. indehiscent), compression (latiseptate vs. angustiseptate), and cotyledonary type (spirolobal, diplecolobal, twice conduplicate), have been used extensively in the delimitation of tribes. The relationship and taxonomic limits among these genera are unclear and controversial. The present ITS study demonstrates the monophyly of tribe Heliophileae, with Chamira as sister clade. The other five smaller genera above are nested within two of the three main lineages of Heliophila, to which they should be reduced to synonymy. The current study reveals parallel evolution of fruit characters often used heavily in the traditional classification schemes of the family. However, the arrangement of species into three main clades largely corresponds with the distribution of morphological characters (e.g., habit, leaf shape, seed structure, inflorescence type, and presence/absence of basal appendages on the pedicels, petals, and staminal filaments) not adequately accounted for in previous studies. Estimation of divergence times of the main lineages of Heliophila is in agreement with recent estimations in other plant groups, all of which date the diversification against a background of aridification in the Pliocene and Pleistocene. Species of one main clade are perennial, microphyllous shrubs/subshrubs typically restricted to poor sandstone soils in the southwestern and western parts of the Cape Floristic Region of South Africa. Species of the other two clades are predominantly annuals that grow in more arid regions of Namibia and Namaqualand, as well as in the above sandstone areas of the Cape Region. The adaptive significance of various floral structures is discussed in terms of their possible role in the rapid diversification within Heliophila.
    PRECISE: software for prediction of cis-acting regulatory elements
    Trindade, L.M. ; Berloo, R. van; Fiers, M.W.E.J. ; Visser, R.G.F. - \ 2005
    Journal of Heredity 96 (2005)5. - ISSN 0022-1503 - p. 618 - 622.
    abscisic-acid - expression - promoter - discovery - regions - genes - sequences - sites - water
    The regulation of gene expression at the transcription initiation level is highly complex and requires the presence of multiple transcription factors. These transcription factors are often proteins or peptides that bind to the so-called cis-acting elements, which are present in the promoter regions and conserved among different species. In order to predict these cis-acting elements, a computer program called PRECISE (Prediction of REgulatory CIS-acting Elements) was developed. The power of the tool lies in its user-friendly interface and in the possibility of using empirical motif frequency tables to filter through the many discovered motifs. The tools to create the empirical motif frequency table (e.g., from a whole genome sequence) are included in the package. In the first case study, the upstream regions of all the genes in the Arabidopsis genome were used to create an empirical motif frequency table and a set of 64 upstream sequences of genes known to be involved in starch metabolism was subjected to analysis by PRECISE. The 20 motifs with the highest specificity in the selected set were analyzed in more detail. Of these 20 motifs, 15 showed a very high or complete homology to the sequences of known cis-acting elements. These cis-acting elements are regulated by light, auxin, and abscisic acid, and confer specific expression in sink organs such as leaves and seeds. All these factors have been shown to play an important role in starch biosynthesis. In the second case study, the upstream regions of 16 genes whose transcription is induced by gibberellins (GA) in Arabidopsis were analyzed with PRECISE and compared to the motifs present in the PLACE database. Among the most promising motifs found by PRECISE were 6 of the 17 known GA motifs. These results indicate the power of the PRECISE software package in the prediction of regulatory elements
    Genetic spatial structure of European common hamsters (Cricetus cricetus) - a result of repeated range expansion and demographic bottlenecks
    Neumann, K. ; Michaux, R. ; Maak, S. ; Jansman, H.A.H. ; Kayser, A. ; Mundt, G. ; Gattermann, R. - \ 2005
    Molecular Ecology 14 (2005)5. - ISSN 0962-1083 - p. 1473 - 1483.
    voles microtus-agrestis - mitochondrial-dna - postglacial colonization - phylogeography - populations - microsatellites - consequences - evolution - oeconomus - sequences
    The spatial genetic structure of common hamsters (Cricetus cricetus) was investigated using three partial mitochondrial (mt) genes and 11 nuclear microsatellite loci. All marker systems revealed significant population differentiation across Europe. Hamsters in central and western Europe belong largely to two allopatric mitochondrial lineages south and northwest of the Carpathian and Sudetes. The southern group, 'Pannonia', comprises populations inside the Carpathian basin (Czech Republic, Hungary) while the second group, 'North', includes hamsters from Belgium, the Netherlands, France, and Germany. Isolation of the lineages is maintained by a combination of geographical and ecological barriers. Both main phylogeographical groups show signs of further subdivision. North is separated into highly polymorphic central German and less polymorphic western populations, which most likely split during late glacial expansion (15 00010 000 bp). Clock estimates based on haplotype distributions predict a divergence of the two major lineages 85 000147 000 bp. Expansion times fall during the last glaciation (115 00010 000 bp) corroborating fossil data, which identify Cricetus cricetus as characteristic of colder climatic phases. Despite the allopatry of mt haplotypes, there is an overlap of nuclear microsatellite alleles between phylogeographical units. Although there are strong evidence that Pannonian hamsters have persisted inside the Carpathian basin over the last 50 000 years, genetic differentiation among European hamsters has mainly been caused by immigration from different eastern refugia. Possible source populations are likely to be found in the Ukrainian and the southern Russian plains core areas of hamster distribution. From there, hamsters have repeatedly expanded during the Quaternary.
    The highly pathogenic avian influenza A (H7N7) virus epidemic in the Netherlands in 2003 - lessons learned from the first five outbreaks
    Elbers, A.R.W. ; Fabri, T. ; Vries, T.S. ; Wit, J.J. de; Pijpers, A. ; Koch, G. - \ 2004
    Avian Diseases 48 (2004)3. - ISSN 0005-2086 - p. 691 - 705.
    poultry - sequences - birds
    Clinical signs and gross lesions observed in poultry submitted for postmortem examination (PME) from the first five infected poultry flocks preceding the detection of the primary outbreak of highly pathogenic avian influenza (HPAI) of subtype H7N7 during the 2003 epidemic in the Netherlands are described. The absence of HPAI from the Netherlands for more than 75 yr created a situation in which poultry farmers and veterinary practitioners did not think of AI in the differential diagnosis as a possible cause of the clinical problems seen. Increased and progressive mortality was not reported to the governmental authorities by farmers or veterinary practitioners. It took 4 days from the first entry of postmortem material to notify the governmental authorities of a strong suspicion of an AI outbreak on the basis of a positive immunofluoresence test result. The gross lesions observed at PME did not comply with the descriptions in literature, especially the lack of hemorrhagic changes in tissues, and the lack of edema and cyanosis in comb and wattles is noted. The following lessons are learned from this epidemic: a) in the future, increased and progressive mortality should be a signal to exclude AI as cause of disease problems on poultry farms; b) intensive contact between the veterinary practitioner in the field and the veterinarian executing PME is necessary to have all relevant data and developments at one's disposal to come to a conclusive diagnosis; c) in an anamnesis, reporting of high or increased mortality should be quantified in the future (number of dead birds in relation to the number of birds brought to the farm to start production, together with the timing within the production cycle), or else this mortality cannot be interpreted properly; d) if clinical findings such as high mortality indicate the possibility of HPAI, the pathologist should submit clinical samples to the reference laboratory, even if PME gives no specific indications for HPAI; e) the best way to facilitate early detection of an HPAI outbreak is to have the poultry farmer and/or veterinary practitioner immediately report to the syndrome-reporting system currently in operation the occurrence of high mortality, a large decrease in feed or water intake, or a considerable drop in egg production; f) in order to detect low pathogenic avian influenza infections that could possibly change to HPAI, a continuous serologic monitoring system has been set up, in which commercial poultry flocks are screened for antibodies against AI virus of subtypes H5 and H7.
    Speciation and distribution of Botryosphaeria spp. on native and introduced Eucalyptus trees in Australia and South Africa
    Slippers, B. ; Fourie, G. ; Crous, P.W. ; Coutinho, T.A. ; Wingfield, B.D. ; Carnegie, A.J. ; Wingfield, M.J. - \ 2004
    Studies in Mycology 50 (2004)2. - ISSN 0166-0616 - p. 343 - 358.
    multiple gene genealogies - sphaeropsis-sapinea - primer sets - sp-nov - fungi - dothidea - sequences - cankers - ribis - characters
    Botryosphaeria spp. are important canker and die-back pathogens that affect Eucalyptus spp. They also occur endophytically in Eucalyptus leaves and stems. For the purpose of this study, Botryosphaeria strains were isolated from diseased and symptomless Eucalyptus material from Australia and South Africa. These isolates were induced to sporulate in culture, and compared with known species of Botryosphaeria. Selected isolates were also compared with authentic isolates of known Botryosphaeria spp. based on nuclear DNA sequence data of the ITS rDNA, P-tubulin and elongation factor l-alpha regions. Five Botryosphaeria spp. were identified from Eucalyptus plants. The ITS rDNA sequence data were then used to develop a PCR RFLP technique that could distinguish these species. Botryosphaeria eucalyptorum and a new species, B. eucalypticola, were the most common species on Eucalyptus in eastern Australia. These species also occur on Eucalyptus in South Africa, where they have most likely been introduced. Botryosphaeria parva was common on Eucalyptus in exotic environments, but rare on this host in Australia. Although B. dothidea was previously thought to be common on eucalypts, only one isolate of each of B. dothidea and B. australis were found in all the areas surveyed. No isolates of B. ribis, which was also commonly reported from Eucalyptus, were identified during this survey from Eucalyptus. Data from the present study provide the first holistic overview of the species of Botryosphaeria associated with Eucalyptus in both native and exotic environments.
    DNA phylogeny, morphology and pathogenicity of Botryosphaeria species on grapevines
    Niekerk, J.M. van; Crous, P.W. ; Groenewald, J.Z. ; Fourie, P.H. ; Halleen, F. - \ 2004
    Mycologia 96 (2004)4. - ISSN 0027-5514 - p. 781 - 798.
    multiple gene genealogies - fusicoccum - characters - sequences - dothidea - zealand - dieback
    Several species of Botr yosphaeria are known to occur on grapevines, causing a wide range of disorders including bud mortality, dieback, brown wood streaking and bunch rot. In this study the 11 Botryosphaeria spp. associated with grapevines growing in various parts of the world, but primarily in South Africa, are distinguished based on morphology, DNA sequences (ITS-1, 5.8S, ITS-2 and EF1-) and pathological data. Botryosphaeria australis, B. lutea, B. obtusa, B. parva, B. rhodina and a Diplodia sp. are confirmed from grapevines in South Africa, while Diplodia porosum, Fusicoccum viticlavatum and F. vitifusiforme are described as new. Although isolates of B. dothidea and B. stevensii are confirmed from grapevines in Portugal, neither of these species occurred in South Africa, nor were any isolates of B. ribis confirmed from grapevines. All grapevine isolates from Portugal, formerly presumed to be B. ribis, are identified as B. parva based on their EF1- equence data. From artificial inoculations on grapevine shoots, we conclude that B. australis, B. parva, B. ribis and B. stevensii are more virulent than the other species studied. The Diplodia sp. collected from grapevine canes is morphologically similar but phylogenetically distinct from D. sarmentorum. Diplodia sarmentorum is confirmed as anamorph of Otthia spiraeae, the type species of the genus Otthia (Botryosphaeriaceae). A culture identified as O. spiraeae clustered within Botryosphaeria and thus is regarded as probable synonym. These findings confirm earlier suggestions that the generic concept of Botryosphaeria should be expanded to include genera with septate ascospores and Diplodia anamorphs.
    Combined multiple gene genealogies and phenotypic characters differentiate several species previously identified as Botryosphaeria dothidea
    Slippers, B. ; Crous, P.W. ; Denman, S. ; Coutinho, T.A. ; Wingfield, B.D. ; Wingfield, M.J. - \ 2004
    Mycologia 96 (2004)1. - ISSN 0027-5514 - p. 83 - 101.
    south-africa - fusicoccum anamorph - primer sets - fungi - eucalyptus - canker - rdna - reassessment - sequences - zealand
    Botryosphaeria dothidea is one of the most commonly reported species in a genus of important pathogens of woody plants. This taxon generally is accepted to represent a species complex, and hence its identity remains unclear. Previous studies either have treated B. dothidea as the valid name for B. ribis and B. berengeriana or argued for them to be separate entities. To add to the confusion, no ex-type cultures are available for either B. dothidea or B. ribis. The aim of the present study, therefore, was to recollect and characterize these fungi and designate a set of reference cultures that can be used in future studies. To this end, morphological, cultural and multi-allelic DNA sequence datasets from the rDNA (ITS 1, 5.8S, and ITS 2), ß-tubulin and EF1- genes were used to fully characterize these species. Botryosphaeria dothidea was found to be distinct from B. ribis, while B. berengeriana was retained as synonym of the former name. Furthermore, Fusicoccum aesculi is accepted as anamorph of B. dothidea, while the anamorph of B. ribis is newly described as F. ribis sp. nov. Botryosphaeria ribis could be distinguished from B. parva based on ß-tubulin and EF1- sequence data. A combined phylogeny of the three gene regions used in this study also showed that the genus Botryosphaeria represents two distinct phylogenetic assemblages that correspond to species with Diplodia and Fusicoccum anamorphs
    Morphology, phylogeny and evolution of the superfamily Plectoidea Örley, 1880 (Nematoda: Plectida
    Holovachov, O.V. - \ 2004
    Annales zoologici 54 (2004)4. - ISSN 0003-4541 - p. 631 - 672.
    n-sp nematoda - revised taxonomy - phylum nematoda - genus - ultrastructure - classification - araeolaimida - leptolaimidae - rhabditidae - sequences
    The phylogeny and classification of the superfamily Plectoidea Örley, 1880 is revised on the basis of published and updated morphological data for 35 ingroup and 2 outgroup species. The following features are here considered to support the monophyletic origin of the superfamily: 1) stegostom developed and differentiated into two sections; 2) dorsal gland orifice opening into the second stegostom section; 3) pharynx cylindrical, with distinct subdivision into corpus and postcorpus by the orifices of the subventral pharyngeal glands and a discontinuity in the muscular pharyngeal tissue; 4) corpus cylindrical, with subdivision into procorpus and metacorpus homologues; 5) pharyngeal radii of the corpus with prominent pharyngeal tubes along the procorpus; 6) cuticular lumen of the basal part of postcorpus (within basal bulb if latter is present) is modified to form a valvular apparatus. In addition the inner labial sensilla open inside the cheilostom. New data on postembryonic development of Anaplectus grandepapillatus (Ditlevsen, 1928), Plectus parietinus Bastian, 1865, P. decens Andrássy, 1985 and P. communis Bütschli, 1873 are given and supplemented with a discussion of the phylogenetic significance of the ontogeny in Plectoidea. Following the proposal of a phylogeny, some key events in the evolution of Plectidae Örley, 1880 are discussed. It is suggested that the superfamily Plectoidea includes four families: Pakiridae Inglis, 1983, Chronogastridae Gagarin, 1975, Metateratocephalidae Eroshenko, 1973 and Plectidae. Plectolaimus supplementatus Keppner, 1988 is transferred to the genus Caribplectus Andrássy, 1973. The genus Keralanema Siddiqi, 2003 is considered a junior synonim of Chronogaster Cobb, 1913. The genus Chiloplectus Andrássy, 1984 is considered a junior synonim of Plectus Bastian, 1865. The family Anaplectidae Zell, 1993 is downgraded to the subfamily level
    The relationship between global and regional distribution diminishes among phylogenetically basal species
    Prinzing, A. ; Ozinga, W.A. ; Durka, W. - \ 2004
    Evolution 58 (2004)12. - ISSN 0014-3820 - p. 2622 - 2633.
    range size - diversification rates - geographical range - flowering plants - body-size - macroecological patterns - chloroplast ndhf - gene rbcl - phylogeny - sequences
    Phylogenetic legacy and phylogenetic trends affect the ecology of species—except, apparently, for the width of their distribution. As a result, “macroecological” patterns of species distributions emerge constantly in phylogenetically very distinct species assemblages. The width of the global distribution of species, for instance, constantly correlates positively to the width of their regional distribution. However, such patterns primarily reflect the phylogenetically derived species that dominate most assemblages. Basal species, in contrast, might show different macroecological patterns. We tested the hypothesis that the correlation between global and regional distributions of species diminishes among the phylogenetically basal species. We considered central European higher plants and defined global distribution as the occupancy of global floristic zones, regional distribution as the grid occupancy in Eastern Germany, and phylogenetic position as the rank distance to tree base. We also took into account a number of confounding variables. We found that, across all lineages, the global/regional correlation diminished among basal species. We then reanalyzed 19 lineages separately and always found the same pattern. The pattern reflected both increases in global distributions and decreases in regional distributions among basal species. The results indicate that many basal species face a risk of global or at least regional extinction, but have escaped the downward spiral of mutually reinforcing extinction risks at multiple scales. We suggest that many basal species had much time to expand their global ranges but are presently displaced locally by more derived species. Overall, the study shows that macroecological patterns may not be static and universal, but may undergo macroevolutionary trends. Analyses of macroecological patterns across a phylogeny may thus provide insights into macroevolutionary processes.
    A high-resolution radiation hybrid map of chicken chromosome 5 and comparison with human chromosomes
    Pitel, F. ; Abasht, B. ; Morrison, M. ; Crooijmans, R.P.M.A. ; Vignoles, F. ; Leroux, S. ; Feve, K. ; Bardes, S. ; Milan, D. ; Lagarrigue, S. ; Groenen, M.A.M. ; Douaire, M. ; Vignal, A. - \ 2004
    BMC Genomics 5 (2004). - ISSN 1471-2164 - 9 p.
    in-situ hybridization - human genome - genes - assignment - sequences - synteny - panel - pig
    Background - The resolution of radiation hybrid (RH) maps is intermediate between that of the genetic and BAC (Bacterial Artificial Chromosome) contig maps. Moreover, once framework RH maps of a genome have been constructed, a quick location of markers by simple PCR on the RH panel is possible. The chicken ChickRH6 panel recently produced was used here to construct a high resolution RH map of chicken GGA5. To confirm the validity of the map and to provide valuable comparative mapping information, both markers from the genetic map and a high number of ESTs (Expressed Sequence Tags) were used. Finally, this RH map was used for testing the accuracy of the chicken genome assembly for chromosome 5. Results - A total of 169 markers (21 microsatellites and 148 ESTs) were typed on the ChickRH6 RH panel, of which 134 were assigned to GGA5. The final map is composed of 73 framework markers extending over a 1315.6 cR distance. The remaining 61 markers were placed alongside the framework markers within confidence intervals. Conclusion - The high resolution framework map obtained in this study has markers covering the entire chicken chromosome 5 and reveals the existence of a high number of rearrangements when compared to the human genome. Only two discrepancies were observed in relation to the sequence assembly recently reported for this chromosome.
    Downstream targets of the Phytophthora infestans G alpha subunit PiGPA1 revealed by cDNA-AFLP
    Dong, W. ; Latijnhouwers, M. ; Jiang, R.H.Y. ; Meijer, H.J.G. ; Govers, F. - \ 2004
    Molecular Plant Pathology 5 (2004)5. - ISSN 1464-6722 - p. 483 - 494.
    gene-expression profiles - gtp-binding proteins - beta-subunit - sequences - mutations - infection - database
    In many plant pathogens heterotrimeric G-proteins are essential signalling components involved in development and pathogenicity. In the late blight oomycete pathogen Phytophthora infestans the G-protein (x subunit PiGPA1 controls zoospore motility and is required for virulence. To identify G-protein targets and signalling pathways downstream of PiGPA1, we used an optimized cDNA-AFLP protocol for analysing gene expression profiles in hypovirulent P. infestans strains that were previously generated by silencing the Pigpa1 gene. First, expression profiles in sporangia and mycelium of the wild-type strain were compared, and this revealed a substantial number of mycelium- or sporangia-specific transcript derived fragments (TDFs). Subsequently, profiles in sporangia of wild-type, Pigpa1-silenced mutants and of a strain expressing a constitutively active form of PiGPA1 were compared. From a total of 2860 TDFs, 92 were down- and 19 upregulated in the Pigpa1-silenced mutants. A subset of the differential TDFs was cloned and sequenced, and homology searches were carried out against Phytophthora EST and genomic databases and the NCBI database. cDNA-AFLP expression profiles were verified by Northern blot analysis or RT-PCR. The power of cDNA-AFLP for the identification of target genes in knock-down or gain-of-function mutants is discussed.
    Isolation and biodiversity of hitherto undescribed soil bacteria related to Bacillus niacini
    Felske, A. ; Tzeneva, V.A. ; Heyrman, J. ; Langeveld, M.A. ; Akkermans, A.D.L. ; Vos, P. - \ 2004
    Microbial Ecology 48 (2004)1. - ISSN 0095-3628 - p. 111 - 119.
    16s ribosomal-rna - genus bacillus - culturable bacteria - agricultural soil - paddy soil - sp-nov - diversity - sequences - dna - identification
    The hitherto largely not described phylogenetic neighborhood of Bacillus niacini has been explored by a comprehensive cultivation experiment and genomic variety studies. Previous culture-independent studies demonstrated that similar to15% of all Bacillus 16S rDNA directly extracted from soils worldwide was affiliated to B. niacini. Seven different media were inoculated with soil suspensions in serial dilutions and incubated at different temperatures. Then, bacterial colonies were picked and analyzed by sequencing. A mineral medium with acetate as carbon source yielded a B. niacini rate of >3% of all picked colonies. Other media were less efficient but also successful. Applying this culturing approach, we succeeded in obtaining 64 isolates from different Dutch soils. The isolates turned out to be diverse, although closely related to B. niacini as revealed by 16S rDNA sequencing. Close matches with environmental clones were also found, thus demonstrating much more diversity beyond previously known 16S rDNA sequences. The rep-PCR fingerprinting method revealed a high genomic variety, redundancy could not be observed among our isolates. Hence, the hitherto neglected B. niacini lineage, apparently among the most abundant soil Bacillus, was accessible to our cultivation approach.
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