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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    We will mail you new results for this query: keywords==Genome sequence
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Genome sequence of two members of the chloroaromatic-degrading MT community : Pseudomonas reinekei MT1 and Achromobacter xylosoxidans MT3
Gutierrez-Urrutia, Izabook ; Miossec, Matthieu J. ; Valenzuela, Sandro L. ; Meneses, Claudio ; Martins dos Santos, Vitor A.P. ; Castro-Nallar, Eduardo ; Poblete-Castro, Ignacio - \ 2018
Journal of Biotechnology 275 (2018). - ISSN 0168-1656 - p. 13 - 16.
Biodegradation - Chloro- and nitro-aromatic compounds - Genome sequence - MT bacterial community
We describe the genome sequence of Pseudomonas reinekei MT1 and Achromobacter xylosoxidans MT3, the most abundant members of a bacterial community capable of degrading chloroaromatic compounds. The MT1 genome contains open reading frames encoding enzymes responsible for the catabolism of chlorosalicylate, methylsalicylate, chlorophenols, phenol, benzoate, p-coumarate, phenylalanine, and phenylacetate. On the other hand, the MT3 strain genome possesses no ORFs to metabolize chlorosalicylates; instead the bacterium is capable of metabolizing nitro-phenolic and phenolic compounds, which can be used as the only carbon and energy source by MT3. We also confirmed that MT3 displays the genetic machinery for the metabolism of chlorocathecols and chloromuconates, where the latter are toxic compounds secreted by MT1 when degrading chlorosalicylates. Altogether, this work will advance our fundamental understanding of bacterial interactions.
Data from: The genome of the yellow potato cyst nematode Globodera rostochiensis reveals insights into the basis of parasitism and virulence
Eves-van den Akker, Sebastian ; Laetsch, Dominik R. ; Thorpe, Peter ; Lilley, Catherine J. ; Danchin, Etienne G.J. ; Rocha, Martine Da; Rancurel, Corinne ; Holroyd, Nancy E. ; Cotton, James A. ; Szitenberg, Amir ; Grenier, Eric ; Montarry, Josselin ; Mimee, Benjamin ; Duceppe, Marc Olivier ; Boyes, Ian ; Marvin, Jessica M.C. ; Jones, Laura M. ; Yusup, Hazijah B. ; Lafond-Lapalme, Joël ; Esquibet, Magali ; Sabeh, Michael ; Rott, Michael ; Overmars, H.A. ; Finkers-Tomczak, A.M. ; Smant, G. - \ 2016
Plant-parasitic nematode - Genome sequence - Virulence - Effectors - Horizontal gene transfer
For each gene, lists the normalized expression data for each life stage, and (if significantly differentially expressed) which expression super cluster it is grouped into.
Complete genome sequence of thermophilic Bacillus smithii type strain DSM 4216T
Bosma, Elleke F. ; Koehorst, Jasper J. ; Hijum, Sacha A.F.T. van; Renckens, Bernadet ; Vriesendorp, Bastienne ; Weijer, Tom van de; Schaap, Peter J. ; Vos, Willem M. de; Oost, John van der; Kranenburg, Richard van - \ 2016
Standards in Genomic Sciences 11 (2016). - ISSN 1944-3277 - 11 p.
Bacillus smithii - Biotechnology - Genome sequence - Lactic acid - Thermophile - Thermophilic bacillus

Bacillus smithii is a facultatively anaerobic, thermophilic bacterium able to use a variety of sugars that can be derived from lignocellulosic feedstocks. Being genetically accessible, it is a potential new host for biotechnological production of green chemicals from renewable resources. We determined the complete genomic sequence of the B. smithii type strain DSM 4216T, which consists of a 3,368,778 bp chromosome (GenBank accession number CP012024.1) and a 12,514 bp plasmid (GenBank accession number CP012025.1), together encoding 3880 genes. Genome annotation via RAST was complemented by a protein domain analysis. Some unique features of B. smithii central metabolism in comparison to related organisms included the lack of a standard acetate production pathway with no apparent pyruvate formate lyase, phosphotransacetylase, and acetate kinase genes, while acetate was the second fermentation product.

The genome of the yellow potato cyst nematode, Globodera rostochiensis, reveals insights into the basis of parasitism and virulence
Eves-van den Akker, Sebastian ; Laetsch, Dominik R. ; Thorpe, Peter ; Lilley, Catherine J. ; Danchin, Etienne G.J. ; Rocha, Martine Da; Rancurel, Corinne ; Holroyd, Nancy E. ; Cotton, James A. ; Szitenberg, Amir ; Grenier, Eric ; Montarry, Josselin ; Mimee, Benjamin ; Duceppe, Marc Olivier ; Boyes, Ian ; Marvin, Jessica M.C. ; Jones, Laura M. ; Yusup, Hazijah B. ; Lafond-Lapalme, Joël ; Esquibet, Magali ; Sabeh, Michael ; Rott, Michael ; Overmars, Hein ; Finkers-Tomczak, Anna ; Smant, Geert ; Koutsovoulos, Georgios ; Blok, Vivian ; Mantelin, Sophie ; Cock, Peter J.A. ; Phillips, Wendy ; Henrissat, Bernard ; Urwin, Peter E. ; Blaxter, Mark ; Jones, John T. - \ 2016
Genome Biology 17 (2016)1. - ISSN 1474-7596
Effectors - Genome sequence - Horizontal gene transfer - Plant-parasitic nematode - Virulence

Background: The yellow potato cyst nematode, Globodera rostochiensis, is a devastating plant pathogen of global economic importance. This biotrophic parasite secretes effectors from pharyngeal glands, some of which were acquired by horizontal gene transfer, to manipulate host processes and promote parasitism. G. rostochiensis is classified into pathotypes with different plant resistance-breaking phenotypes. Results: We generate a high quality genome assembly for G. rostochiensis pathotype Ro1, identify putative effectors and horizontal gene transfer events, map gene expression through the life cycle focusing on key parasitic transitions and sequence the genomes of eight populations including four additional pathotypes to identify variation. Horizontal gene transfer contributes 3.5 % of the predicted genes, of which approximately 8.5 % are deployed as effectors. Over one-third of all effector genes are clustered in 21 putative 'effector islands' in the genome. We identify a dorsal gland promoter element motif (termed DOG Box) present upstream in representatives from 26 out of 28 dorsal gland effector families, and predict a putative effector superset associated with this motif. We validate gland cell expression in two novel genes by in situ hybridisation and catalogue dorsal gland promoter element-containing effectors from available cyst nematode genomes. Comparison of effector diversity between pathotypes highlights correlation with plant resistance-breaking. Conclusions: These G. rostochiensis genome resources will facilitate major advances in understanding nematode plant-parasitism. Dorsal gland promoter element-containing effectors are at the front line of the evolutionary arms race between plant and parasite and the ability to predict gland cell expression a priori promises rapid advances in understanding their roles and mechanisms of action.

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