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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    How diverse is the genus Wolbachia? Multiple-gene sequencing reveals a putatively new Wolbachia supergroup recovered from spider mites (Acari: Tetranychidae)
    Ros, V.I.D. ; Fleming, V. ; Feil, E.J. ; Breeuwer, J.A.J. - \ 2009
    Applied and Environmental Microbiology 75 (2009)4. - ISSN 0099-2240 - p. 1036 - 1043.
    phylogenetic analysis - cytoplasmic incompatibility - reproductive incompatibility - bacterium wolbachia - filarial nematodes - dna amplification - genome sequence - f-supergroup - pipientis - arthropods
    At least 20% of all arthropods and some nematode species are infected with intracellular bacteria of the genus Wolbachia. This highly diverse genus has been subdivided into eight “supergroups” (A to H) on the basis of nucleotide sequence data. Here, we report the discovery of a new Wolbachia supergroup recovered from the spider mite species Bryobia species V (Acari: Tetranychidae), based on the sequences of three protein-coding genes (ftsZ, gltA, and groEL) and the 16S rRNA gene. Other tetranychid mites possess supergroup B Wolbachia strains. The discovery of another Wolbachia supergroup expands the known diversity of Wolbachia and emphasizes the high variability of the genus. Our data also clarify the existing supergroup structure and highlight the use of multiple gene sequences for robust phylogenetic analysis. In addition to previous reports of recombination between the arthropod-infecting supergroups A and B, we provide evidence for recombination between the nematode-infecting supergroups C and D. Robust delineation of supergroups is essential for understanding the origin and spread of this common reproductive parasite and for unraveling mechanisms of host adaptation and manipulation across a wide range of hosts
    The effects of, and interactions between, Cardinium and Wolbachia in the doubly infected spider mite Bryobia sarothamni (Acari: Tetranychidae)
    Ros, V.I.D. ; Breeuwer, J.A.J. - \ 2009
    Heredity 102 (2009)4. - ISSN 0018-067X - p. 413 - 422.
    induced cytoplasmic incompatibility - tetranychus-urticae - drosophila-simulans - host genotype - nasonia-vitripennis - bacterial symbiont - haplodiploid mite - dna amplification - genome sequence - fecundity
    Many arthropods are infected with vertically transmitted, intracellular bacteria manipulating their host's reproduction. Cytoplasmic incompatibility (CI) is commonly observed and is expressed as a reduction in the number of offspring in crosses between infected males and uninfected females (or females infected with a different bacterial strain). CI is often related to the presence of Wolbachia, but recent findings indicate that a second reproductive parasite, Cardinium, is also capable of inducing CI. Although both Wolbachia and Cardinium occur in arthropods and may infect the same host species, little is known about their interactions. We observed Wolbachia and Cardinium in the sexual spider mite Bryobia sarothamni (Acari: Tetranychidae) and investigated the effects of both bacteria on reproduction. We performed all possible crossing combinations using naturally infected strains, and show that Cardinium induces strong CI, expressed as an almost complete female mortality. B. sarothamni is the third host species in which Cardinium-induced CI is observed, and this study reveals the strongest CI effect found so far. Wolbachia, however, did not induce CI. Even so, CI was not induced by doubly infected males, and neither singly Wolbachia-infected nor doubly infected females could rescue CI induced by Cardinium-infected males. Possibly, this is related to the differences between Cardinium strains infecting singly and doubly infected individuals. We found a cost of infection in single infected individuals, but not in doubly infected individuals. We show that infection frequencies in field populations ranged from completely uninfected to a polymorphic state. In none of the populations infections were fixed
    Genetic diversity analysis using lowly polymorphic dominant markers: The example of AFLP in pigs.
    Foulley, J.L. ; Schriek, M. van; Groenen, M.A.M. ; Heuven, H.C.M. - \ 2006
    Journal of Heredity 97 (2006)3. - ISSN 0022-1503 - p. 244 - 252.
    dierveredeling - varkens - varkensrassen - rasverschillen - genetische diversiteit - genetische afstand - genetische analyse - genetische merkers - dna-fingerprinting - genfrequentie - dna-vermenigvuldiging - genetische polymorfie - genetische bronnen van diersoorten - aflp - animal breeding - pigs - pig breeds - breed differences - genetic diversity - genetic distance - genetic analysis - genetic markers - dna fingerprinting - gene frequency - dna amplification - genetic polymorphism - animal genetic resources - amplified fragment length polymorphism - population diversity - selective neutrality - distance - frequency
    DNA markers are commonly used for large-scale evaluation of genetic diversity in farm animals, as a component of the management of animal genetic resources. AFLP markers are useful for such studies as they can be generated relatively simply; however, challenges in analysis arise from their dominant scoring and the low level of polymorphism of some markers. This paper describes the results obtained with a set of AFLP markers in a study of 59 pig breeds. AFLP fingerprints were generated using four primer combinations (PC), yielding a total of 148 marker loci, and average harmonic mean of breed sample size was 37.3. The average proportion of monomorphic populations was 63% (range across loci: 3%-98%). The moment-based method of Hill and Weir (2004, Mol Ecol 13:895-908) was applied to estimate gene frequencies, gene diversity (F ST), and Reynolds genetic distances. A highly significant average FST of 0.11 was estimated, together with highly significant PC effects on gene diversity. The variance of FST across loci also significantly exceeded the variance expected under the hypothesis of AFLP neutrality, strongly suggesting the sensitivity of AFLP to selection or other forces. Moment estimates were compared to estimates derived from the square root estimation of gene frequency, as currently applied for dominant markers, and the biases incurred in the latter method were evaluated. The paper discusses the hypotheses underlying the moment estimations and various issues relating to the biallelic, dominant, and lowly polymorphic nature of this set of AFLP markers and to their use as compared to microsatellites for measuring genetic diversity
    Microvariation Artifacts Introduced by PCR and Cloning of Closely Related 16S rRNA Gene Sequences
    Speksnijder, A.G.C.L. ; Kowalchuk, G.A. ; Jong, S. de; Kline, E. ; Stephen, J.R. ; Laanbroek, H.J. - \ 2001
    Applied and Environmental Microbiology 67 (2001)1. - ISSN 0099-2240 - p. 469 - 472.
    ribosomal-rna genes - polymerase chain-reaction - chimeric molecules - dna amplification - escherichia-coli - heteroduplexes - populations - coamplification - consequence - diversity
    A defined template mixture of seven closely related 16S-rDNA clones was used in a PCR-cloning experiment to assess and track sources of artifactual sequence variation in 16S rDNA clone libraries. At least 14% of the recovered clones contained aberrations. Artifact sources were polymerase errors, a mutational hot spot, and cloning of heteroduplexes and chimeras. These data may partially explain the high degree of microheterogeneity typical of sequence clusters detected in environmental clone libraries
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