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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    Detecting signatures of pathogen-mediated selection using population genomics
    Buckley, James ; Holub, Eric B. ; Koch, Marcus A. ; Vergeer, P. ; Mable, Barbara K. - \ 2018
    University of Glasgow
    SRP148549 - PRJNA472246 - Arabidopsis lyrata
    This study used RAD-sequencing of Arabidopsis lyrata individuals sampled from across the range of two subspecies, A.l. lyrata (N.American) and A.l .petraea (European), to determine genome-wide patterns of polymorphism and genetic structure in this species. Using these data we also investigated whether genomic smoothing approaches across RAD loci could detect genomic regions showing signatures of balancing selection, specifically significantly elevated diversity and either elevated differentiation among geographic regions or shifts towards intermediate allele frequencies within regions. We then identified annotated disease resistance loci within these genomic regions of interest. Together this project shows that genome scans based on a small number of individuals sampled from a wide range of populations confirmed the relative scarcity of signatures of balancing selection across the genome, but also identified new potential disease resistance candidates within genomic regions showing signatures of balancing selection that would be strong candidates for further sequencing efforts.
    Restriction associated DNA-genotyping at multiple spatial scales in Arabidopsis lyrata reveals signatures of pathogen-mediated selection
    Buckley, James ; Holub, Eric B. ; Koch, Marcus A. ; Vergeer, Philippine ; Mable, Barbara K. - \ 2018
    BMC Genomics 19 (2018)1. - ISSN 1471-2164
    Arabidopsis lyrata - Balancing selection - Disease resistance - Genome scan - Mating system - Pathogens - Polymorphism - R-genes - RAD-seq

    Background: Genome scans based on outlier analyses have revolutionized detection of genes involved in adaptive processes, but reports of some forms of selection, such as balancing selection, are still limited. It is unclear whether high throughput genotyping approaches for identification of single nucleotide polymorphisms have sufficient power to detect modes of selection expected to result in reduced genetic differentiation among populations. In this study, we used Arabidopsis lyrata to investigate whether signatures of balancing selection can be detected based on genomic smoothing of Restriction Associated DNA sequencing (RAD-seq) data. We compared how different sampling approaches (both within and between subspecies) and different background levels of polymorphism (inbreeding or outcrossing populations) affected the ability to detect genomic regions showing key signatures of balancing selection, specifically elevated polymorphism, reduced differentiation and shifts towards intermediate allele frequencies. We then tested whether candidate genes associated with disease resistance (R-gene analogs) were detected more frequently in these regions compared to other regions of the genome. Results: We found that genomic regions showing elevated polymorphism contained a significantly higher density of R-gene analogs predicted to be under pathogen-mediated selection than regions of non-elevated polymorphism, and that many of these also showed evidence for an intermediate site-frequency spectrum based on Tajima's D. However, we found few genomic regions that showed both elevated polymorphism and reduced FST among populations, despite strong background levels of genetic differentiation among populations. This suggests either insufficient power to detect the reduced population structure predicted for genes under balancing selection using sparsely distributed RAD markers, or that other forms of diversifying selection are more common for the R-gene analogs tested. Conclusions: Genome scans based on a small number of individuals sampled from a wide range of populations were sufficient to confirm the relative scarcity of signatures of balancing selection across the genome, but also identified new potential disease resistance candidates within genomic regions showing signatures of balancing selection that would be strong candidates for further sequencing efforts.

    Evolutionary dynamics of DNA-binding sites and direct target genes of a floral master regulatory transcription factor [ChIP-Seq]
    Muiño, J.M. ; Bruijn, S.A. de; Vingron, Martin ; Angenent, G.C. ; Kaufmann, K. - \ 2015
    Wageningen University & Research
    Arabidopsis lyrata - Arabidopsis thaliana - GSE63463 - PRJNA267854 - Arabidopsis thaliana - Arabidopsis lyrata
    Plant development is controlled by transcription factors (TFs) which form complex gene-regulatory networks. Genome-wide TF DNA-binding studies revealed that these TFs have several thousands of binding sites in the Arabidopsis genome, and may regulate the expression of many genes directly. Given the importance of natural variation in plant developmental programs, there is a need to understand the molecular basis of this variation at the level of developmental gene regulation. However, until now, the evolutionary turnover and dynamics of TF binding sites among plant species has not yet experimentally determined. Here, we performed comparative ChIP-seq studies of the MADS-box TF SEPALLATA3 (SEP3) in inflorescences of two Arabidopsis species: A. thaliana and A. lyrata. Comparative RNA-seq analysis shows that the loss/gain of BSs is often followed by a change in gene expression. Chromatin was crosslinked and isolated from wildtype A. lyrata inflorescences up to floral stage 10/11. The immunoprecipitation of protein-DNA complexes was performed using a peptide SEP3 antibody that was raised against A. thaliana SEP3, and is also able to recognize the homolog from A. lyrata due to protein similarity. As a control, de-crosslinked 'input-DNA' was used. SEP3 ChIP-seq on Arabidopsis thaliana can be found in the accessions GSM364939 and GSM364941. Re-analyzed peak positions for these samples are included as a supplementary file on the series level (SEP3Ratiobg5@TAIR10-win.csv).
    Evolutionary dynamics of DNA-binding sites and direct target genes of a floral master regulatory transcription factor [RNA-Seq]
    Muiño, J.M. ; Bruijn, S.A. de; Vingron, Martin ; Angenent, G.C. ; Kaufmann, Kerstin - \ 2015
    Wageningen University & Research
    Arabidopsis thaliana - Arabidopsis lyrata - GSE63462 - PRJNA267853
    Plant development is controlled by transcription factors (TFs) which form complex gene-regulatory networks. Genome-wide TF DNA-binding studies revealed that these TFs have several thousands of binding sites in the Arabidopsis genome, and may regulate the expression of many genes directly. Given the importance of natural variation in plant developmental programs, there is a need to understand the molecular basis of this variation at the level of developmental gene regulation. However, until now, the evolutionary turnover and dynamics of TF binding sites among plant species has not yet experimentally determined. Here, we performed comparative ChIP-seq studies of the MADS-box TF SEPALLATA3 (SEP3) in inflorescences of two Arabidopsis species: A. thaliana and A. lyrata. Comparative RNA-seq analysis shows that the loss/gain of BSs is often followed by a change in gene expression. RNA-seq libraries were generated from 3 tissues: A. lyrata leaves, A. lyrata inflorescences, and A.thaliana inflorescences. 3 biological replicates were sequenced.
    Evolutionary dynamics of DNA-binding sites and direct target genes of a floral master regulatory transcription factor
    Muino, J.M. ; Bruijn, S.A. de; Pajoro, A. ; Geuten, K. - \ 2015
    Humboldt University
    Arabidopsis thaliana - Arabidopsis lyrata - GSE63464 - PRJNA267851
    Expression profiling by high throughput sequencing Genome binding/occupancy profiling by high throughput sequencing This SuperSeries is composed of the SubSeries listed below.
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