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Author Correction: Rapid de novo assembly of the European eel genome from nanopore sequencing reads : Rapid de novo assembly of the European eel genome from nanopore sequencing reads (Scientific Reports, (2017), 7, 1, (7213), 10.1038/s41598-017-07650-6)
Jansen, Hans J. ; Liem, Michael ; Jong-Raadsen, Susanne A. ; Dufour, Sylvie ; Weltzien, Finn Arne ; Swinkels, William ; Koelewijn, Alex ; Palstra, Arjan P. ; Pelster, Bernd ; Spaink, Herman P. ; Thillart, Guido E. van den; Dirks, Ron P. ; Henkel, Christiaan V. - \ 2019
Scientific Reports 9 (2019). - ISSN 2045-2322
This Article contains errors. Since the publication of this Article, the website hosting the assembly data has become inactive. The data has now been re-deposited in the DataverseNO repository. As such, the corrected Data Availability section should be as follows. Data Availability The nanopore sequencing data are available in the European Nucleotide Archive (accession number PRJEB20018). The Racon- and Pilon-corrected candidate assembly is available at https://doi.org/10.18710/NMTGUN. The TULIP-scripts are available at https://github.com/Generade-nl.
|Een duurzaam agrarisch ecosysteem op Mars
Wamelink, G.W.W. ; Frissel, J.Y. ; Schug, Line ; Pilon, Steven - \ 2019
Zenit 2019 (2019)maart. - p. 37 - 39.
Plant Selenium Hyperaccumulation Affects Rhizosphere: Enhanced Species Richness and Altered Species Composition
Cochran, Alyssa T. ; Bauer, Jemma ; Metcalf, Jessica L. ; Lovecka, Petra ; Jong, Martina S. de; Warris, S. ; Mooijman, P.J.W. ; Meer, I.M. van der; Knight, Rob ; Pilon-Smits, E.A.H. - \ 2018
Phytobiomes Journal 2 (2018)2. - ISSN 2471-2906 - p. 82 - 91.
Little is known about the microbiomes associated with plants with unusual properties, including plants that hyperaccumulate toxic elements such as selenium (Se). Se hyperaccumulators contain up to 1.5% of their dry weight in Se, concentrations shown to affect ecological interactions with herbivores, fungal pathogens and neighboring plants. Hyperaccumulators also enrich their surrounding soil with Se, which may alter the rhizobiome. To investigate whether plant Se affects rhizobacterial diversity and composition, we used a combination of culture-independent and culture-based approaches. Sequencing of 16S rRNA gene amplicons using the Illumina platform revealed that the rhizosphere microbiomes of Se hyperaccumulators were significantly different from nonaccumulators from the same site, with a higher average relative abundance of Pedobacter and Deviosa. Additionally, hyperaccumulators harbored a higher rhizobacterial species richness when compared with nonaccumulators from the same family on the same site. Independent from Se present at the site or in the host plant, the bacterial isolates were extremely resistant to selenate and selenite (up to 200 mM) and could reduce selenite to elemental Se. In conclusion, Se hyperaccumulation does not appear to negatively affect rhizobacterial diversity, and may select for certain taxa in the rhizosphere microbiome. Additionally, Se resistance in hyperaccumulator-associated bacteria and archaea may be widespread and not under selection by the host plant.
Fennel pondweed: a world citizen : geographic variation in life-cycle characteristics of the clonal water plant Potamogeton pectinatus L.
Pilon, J. - \ 2002
Wageningen University. Promotor(en): W. van Vierssen; L. Santamaria. - S.l. : S.n. - ISBN 9789058086822 - 136
potamogeton pectinatus - onkruiden - plassen - ruimtelijke variatie - levenscyclus - klonale variatie - potamogeton pectinatus - weeds - ponds - spatial variation - life cycle - clonal variation
The performance of broadly distributed plants is potentially constrained by geographic variation in climatic factors. Several patterns of response have been proposed that can be considered of adaptive value if variation in abiotic conditions is pronounced. Firstly, species may possess a high capacity for phenotypic plasticity that results in increased tolerance to variation in abiotic factors. Secondly, locally adapted genotypes may evolve that show phenotypic characteristics that are only suited for a restricted set of environmental conditions. Thirdly, populations may avoid unfavourable conditions by showing changes in phenology that result in a compression of the life cycle.
As compared to terrestrial species, many aquatic plants are widespread and have the ability to thrive in different climatic regions. To evaluate to what extent phenotypic plasticity, local adaptation and differences in phenology might contribute to the globally wide distribution of the aquatic macrophyte fennel pondweed ( Potamogeton pectinatus L.), a series of experiments were performed that focused on geographic variation in life-history traits. For this purpose we used up to 15 clones obtained from a gradient in latitude (24-68°N) and studied their performance in dependence of variation in abiotic factors that relate to climate. We thereby focussed at various stages of the life cycle, such as tuber sprouting, vegetative growth and asexual reproduction.
At northern localities, where the length of the growth season is restricted, genetically fixed changes in phenology result for P. pectinatus in a compression of the life cycle. To prevent young plants to be damaged from low spring temperatures, tubers of higher-latitude clones possess a higher thermal threshold for sprouting. In addition, northern clones show early reproduction, which constrains the size of the tubers. Furthermore, adaptive phenotypic plasticity allows P. pectinatus to grow at contrasting environmental conditions ) . Although thermal acclimation in gas-exchange is constrained, plastic changes in morphology are of special importance to attain a comparable biomass between 15/20 and 30°C. P. pectinatus can also cope with considerable differences in the light climate. Increased light capture through canopy formation and acclimative changes in photosynthesis result in a relatively high biomass yield at low irradiance (i.e. 2.5% of full sunlight in temperate regions). Similarly, photoperiods varying between 13 and 22 h did result in plastic changes in morphology and physiology that limited the loss of biomass productivity at shorter days. Despite the fact that changes in phenology and high phenotypic plasticity allowed P. pectinatus to grow and reproduce in different climatic regions, the Mediterranean clones showed local adaptation resulting from increased perenniality and the absence of asexual reproduction.
In conclusion, this thesis has shown that not a single evolutionary mechanism is responsible for the ability of P. pectinatus to thrive in different climatic regions, but that at different stages of the plant's life cycle phenotypic plasticity, local adaptation and changes in phenology play an important role in maintaining the observed distributional pattern.
|Climate and Water - A 1998 perspective
Dooge, J.C.I. ; Kuusisto, E. ; Askew, A. ; Bergström, A. ; Bonnell, M. ; Burn, D. ; Edmunds, W.M. ; Feddes, R.A. ; Hall, A. ; Kundzewicz, Z. ; Liebscher, H.J. ; Lins, H. ; Llasat, M.C. ; Lucero, O. ; Pilon, P. ; Roald, L. ; Saelthun, N.R. ; Schädler, B. ; Shiklomanov, I. ; Strupczevski, W.G. ; Vaikmäe, R. ; Varis, O. ; Vorosmarty, C. - \ 1998
In: The Second International Conference on Climate and Water, Finland, August 1998 / J.C.I. Dooge, E. Kuusisto, A. Askew, S. Bergström, M. Bonnell, D. Burn, W.M. Edmunds, R.A. Feddes, A. Hall, Z. Kundzewicz, H.J. Liebscher, H. Lins, M-C. Llasat, O. Lucero, P. Pilon, L. Roald, N.R. Saelthun, B. Schädler, I. Shiklomanov, W.G. Strupczevski, R. Vaikmäe, O. Varis, C. Vorosmarty. - [S.l.] : [s.n.], 1998 - p. 1670 - 1670.
|Transgenic fructanaccumulating tobacco and potato
Smeekens, S. ; Pilon-Smits, E.A.H. ; Ebskamp, M.J.M. ; Turk, S. ; Visser, R.G.F. ; Weisbeek, P.J. - \ 1997
In: Fuchs, A. (Ed.). Proceedings 5th Seminar on Inulin, European Fructan Association, The Hague - p. 53 - 58.
|Transgenic fructan-accumulating tobacco and potato plants.
Smeekens, S. ; Pilon-Smits, E.A.H. ; Ebskamp, M.J.M. ; Turk, S. ; Visser, R.G.F. ; Weisbeek, P.J. - \ 1996
In: Proc. 5th seminar on inulin, A. Fuchs (ed.). Wageningen - p. 53 - 58.
Microbial fructan production in transgenic potato plants and tubers.
Pilon-Smits, E.A.H. ; Ebskamp, M.J.M. ; Jeuken, M.J.W. ; Meer, I.M. van der; Visser, R.G.F. ; Weisbeek, P.J. ; Smeekens, S.C.M. - \ 1996
Industrial Crops and Products 5 (1996). - ISSN 0926-6690 - p. 35 - 46.
Fructans (fructose polymers) derived from plants usually have a very low degree of polymerisation (DP) and this limits the technical application of this versatile carbohydrate polymer. Previously we showed that the expression of bacterial fructosyltransferase genes in transgenic plants results in the accumulation of high molecular weight fructans with a DP of over 25,000. Here we report on our progress in accumulating such high DP fructans in potato plants and tubers. In these plants growth, tuber formation and carbohydrate partitioning were analyzed. Young plants showed no difference in growth between wildtype and fructan-producing (KP) plants. However, at a certain timepoint growth in KP plants is reduced and photosynthate starts to accumulate in source leaves. In these plants no diurnal turnover of starch and sucrose is observed. At harvest, the sink organs (roots, tubers) are reduced in weight. Depending on fructan content the KP tubers display a brown phenotype and yield was reduced. The starch content in the KP tubers is inversely correlated with the fructan level, whereas the sucrose, glucose, fructose and protein levels increase substantially, concomitant with fructan concentration. The cellular location of the fructans was investigated via immunofluorescence using monoclonal antibodies against levan and this showed the presence of fructan located along the cell rim instead of in the expected vacuolar location. It is concluded that fructan accumulation in these plants dramatically affects growth and carbohydrate partitioning and possible solutions for these problems are discussed.
Precursor-mediated opening of translocation pores in chloroplast envelopes.
Bulychev, A.A. ; Pilon, M. ; Dassen, H. ; Hof, R. van 't; Vredenberg, W.J. ; Kruijff, B. de - \ 1994
FEBS Letters 356 (1994). - ISSN 0014-5793 - p. 204 - 206.