Staff Publications

Staff Publications

  • external user (warningwarning)
  • Log in as
  • language uk
  • About

    '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.

    We have a manual that explains all the features 

    Current refinement(s):

    Records 1 - 5 / 5

    • help
    • print

      Print search results

    • export

      Export search results

    • alert
      We will mail you new results for this query: keywords==genome assembly
    Check title to add to marked list
    The Nesidiocoris tenuis genome manuscript supporting data
    Pannebakker, Bart ; Ferguson, Kimberley - \ 2019
    Wageningen University & Research
    genome - biocontrol - biological control - insect - mirid - Nesidiocoris tenuis - genomics - genome assembly
    In presenting the first mirid genome, Nesidiocoris tenuis, several supporting information is made available. Following the main supplemetary material document (link), the contents are in this database: S1.2. Flow cytometry data for N. tenuis S1.3. Decontamination and potential LGT indentification S1.4. Gene list (UniProtKB list) and DAVID Reports S1.5. Full protein set S1.7. Poolseq results in full
    The Trichogramma brassicae genome, supporting data
    Pannebakker, Bart ; Ferguson, Kimberley - \ 2019
    Wageningen University & Research
    genome - biocontrol - biological control - insect - parasitoid - Trichogramma - Trichogramma brassicae - genome assembly
    In presenting the Trichogramma brassicae genome, supporting information is made available. Following the main supplemetary material document, the contents in this database entry are as follows: S1.2. Contaminated Wolbachia scaffolds from assembly v3.0 (Backbone_1176.fa and Backbone_1392.fa) S1.3. DAVID input gene list S1.5. Full Trichogramma brassicae protein set from annotation.
    The Bracon brevicornis genome, supporting data
    Pannebakker, Bart ; Ferguson, Kimberley - \ 2019
    Wageningen University & Research
    genome - biocontrol - biological control - insect - parasitoid - Trichogramma - Trichogramma brassicae - genome assembly
    In presenting the Bracon brevicornis genome, supporting information is made available. The material available in this database entry are as follows: 1. Contamination scaffolds from decontamination process (note, identified as being neither the carrier DNA of tomato, nor belonging to the group Arthropoda in a BlobTools analysis. For more details, refer to source manuscript. 2. Two sets of pseudohaplotype FASTA files, generated from decontaminated B. brevicornis reads and output from Supernova assembler.
    Hybrid de novo genome assembly of Chinese chestnut (Castanea mollissima)
    Xing, Yu ; Liu, Yang ; Zhang, Qing ; Nie, Xinghua ; Sun, Yamin ; Zhang, Zhiyong ; Li, Huchen ; Fang, Kefeng ; Wang, Guangpeng ; Huang, Hongwen ; Bisseling, Ton ; Cao, Qingqin ; Qin, Ling - \ 2019
    GigaScience 8 (2019)9. - ISSN 2047-217X
    Castanea mollissima - annotation - evolution - genome assembly

    BACKGROUND: The Chinese chestnut (Castanea mollissima) is widely cultivated in China for nut production. This plant also plays an important ecological role in afforestation and ecosystem services. To facilitate and expand the use of C. mollissima for breeding and its genetic improvement, we report here the whole-genome sequence of C. mollissima. FINDINGS: We produced a high-quality assembly of the C. mollissima genome using Pacific Biosciences single-molecule sequencing. The final draft genome is ∼785.53 Mb long, with a contig N50 size of 944 kb, and we further annotated 36,479 protein-coding genes in the genome. Phylogenetic analysis showed that C. mollissima diverged from Quercus robur, a member of the Fagaceae family, ∼13.62 million years ago. CONCLUSIONS: The high-quality whole-genome assembly of C. mollissima will be a valuable resource for further genetic improvement and breeding for disease resistance and nut quality.

    Data from: Remarkably divergent regions punctuate the genome assembly of the Caenorhabditis elegans Hawaiian strain CB4856
    Thompson, O.A. ; Snoek, Basten ; Nijveen, Harm ; Sterken, Mark ; Volkers, Rita ; Brenchley, R. ; Hof, A. van 't; Bevers, Roel ; Cossins, A.R. ; Yanai, I. ; Hajnal, A. ; Schmid, T. ; Perkins, J.D. ; Spencer, D. ; Kruglyak, L. ; Andersen, E.C. ; Moerman, D.G. ; Hillier, L.W. ; Kammenga, Jan ; Waterston, R.H. - \ 2016
    University of Washington
    Caenorhabditis elegans - evolution - genome assembly - variation
    The Hawaiian strain (CB4856) of Caenorhabditis elegans is one of the most divergent from the canonical laboratory strain N2 and has been widely used in developmental, population and evolutionary studies. To enhance the utility of the strain, we have generated a draft sequence of the CB4856 genome, exploiting a variety of resources and strategies. The CB4856 genome when compared against the N2 reference has 327,050 single nucleotide variants (SNVs) and 79,529 insertion-deletion events (indels) that result in a total of 3.3 megabasepairs (Mb) of N2 sequence missing from CB4856 and 1.4 Mb of sequence present in CB4856 not present in N2. As previously reported, the density of SNVs varies along the chromosomes, with the arms of chromosomes showing greater average variation than the centers. In addition, we find 61 regions totaling 2.8 Mb, distributed across all six chromosomes, that have a greatly elevated SNV density, ranging from 2% to 16% SNVs. A survey of other wild isolates show that the two alternative haplotypes for each region are widely distributed, suggesting they have been maintained by balancing selection over long evolutionary times. These divergent regions contain an abundance of genes from large rapidly evolving families encoding F-box, MATH, BATH, seven-transmembrane G-coupled receptors, and nuclear hormone receptors suggesting that they provide selective advantages in natural environments. The draft sequence makes available a comprehensive catalog of sequence differences between the CB4856 and N2 strains that will facilitate the molecular dissection of their phenotypic differences. Our work also emphasizes the importance of going beyond simple alignment of reads to a reference genome when assessing differences between genomes.
    Check title to add to marked list

    Show 20 50 100 records per page

     
    Please log in to use this service. Login as Wageningen University & Research user or guest user in upper right hand corner of this page.