Evaluation and optimization of a high-throughput sequencing based strategy to detect viruses and bacteria in view of certification and in vitro therapy to create virus free mother plants

Search results

• 2025

  Gezonde Planten beginnen met virusvrij uitgangsmateriaal

  Dewitte, I., De Jonghe, K., Werbrouck, S. & Van Haecke, D., 30-Sept-2025, In: Sierteelt & Groenvoorziening. 69, 9, p. 34-35 2 p.

  Research output: Contribution to journal › A4: Article in journal not included in A1, A2 or A3

• HTS: The key to virus-free starting material

  Dewitte, I., De Jonghe, K., Heyneman, M., Werbrouck, S. & Guldentops, E., 2025.

  Research output: Contribution to conference › Poster

  4 Downloads (Pure)

• HTS: The key to virus-free starting material

  Dewitte, I., De Jonghe, K., Heyneman, M., Werbrouck, S. & Guldentops, E., 2025.

  Research output: Contribution to conference › Poster

  3 Downloads (Pure)

• 2024

  Correction: Haegeman et al. Looking beyond Virus Detection in RNA Sequencing Data: Lessons Learned from a Community-Based Effort to Detect Cellular Plant Pathogens and Pests. Plants 2023, 12, 2139

  Haegeman, A., Foucart, Y., De Jonghe, K., Goedefroit, T., Al Rwahnih, M., Boonham, N., Candresse, T., Gaafar, Y. Z. A., Hurtado-Gonzales, O. P., Kogej Zwitter, Z., Kutnjak, D., Lamovšek, J., Lefebvre, M., Malapi, M., Mavrič Pleško, I., Önder, S., Reynard, J.-S., Salavert Pamblanco, F., Schumpp, O. & Stevens, K. & 8 others, Pal, C., Tamisier, L., Ulubaş Serçe, Ç., van Duivenbode, I., Waite, D. W., Hu, X., Ziebell, H. & Massart, S., 24-Feb-2024, In: Plants. 13, 5

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Plant Pathogen 100%
  • Community-based 100%
  • Lessons Learned 100%
  • Virus Detection 100%
  • Plant Pest 100%

• Werken aan virusvrij uitgangsmateriaal

  Dielemans, P., De Jonghe, K., Dewitte, I. & Werbrouck, S., 31-Oct-2024, In: Sierteelt & Groenvoorziening. 68, 10, p. 44-45

  Research output: Contribution to journal › A4: Article in journal not included in A1, A2 or A3

• 2023

  Assessment of ONT sequencing (MinION) for plant virus detection and comparison with Illumina-based sequencing

  Guldentops, E., Heyneman, M., Werbrouck, S. & De Jonghe, K., 9-Jul-2023.

  Research output: Contribution to conference › Poster

• Assessment of ONT sequencing (MinIon) for plant virus detection and comparison with Illumina-based sequencing.

  Guldentops, E., Heyneman, M., Werbrouck, S. & De Jonghe, K., 23-Aug-2023.

  Research output: Contribution to conference › Poster

• Assessment of ONT sequencing (MinIon) for plant virus detection and comparison with Illumina-based sequencing.

  Guldentops, E., De Jonghe, K., Heyneman, M. & Werbrouck, S., 17-Apr-2023, In: Abstract book, First conference of Cost Action CA21157 European Network for Innovative Plant Cloning.

  Research output: Contribution to journal › Conference abstract in journal

• Detection of single nucleotide polymorphisms in virus genomes assembled from high-throughput sequencing data: large-scale performance testing of sequence analysis strategies

  Rollin, J., Bester, R., Brosteaux, Y., Caglayan, K., De Jonghe, K., Eichmeier, A., Foucart, Y., Haegeman, A., Koloniuk, I., Kominek, P., Maree, H., Onder, S., Posada Cespedes, S., Roumi, V., Safarova, D., Schumpp, O., Ulubas Serce, C., Somera, M., Tamisier, L. & Vainio, E. & 2 others, van der Vlugt, R. & Massart, S., 16-Aug-2023, In: PeerJ. 11, p. 1-25 25 p., 15816.

  Research output: Contribution to journal › A1: Web of Science-article › peer-review

  Open Access

  • Sequence Analysis 100%
  • Single nucleotide Polymorphism 100%
  • Performance Test 100%
  • High-throughput Sequencing Data 100%
  • Virus Genome 100%

• Efficiënte tool voor de productie van virusvrij uitgangsmateriaal

  De Jonghe, K., Guldentops, E., Werbrouck, S. & Vanhaecke, D., 30-Nov-2023, In: Sierteelt & Groenvoorziening. 10, 11, p. 38-39 2 p.

  Research output: Contribution to journal › A4: Article in journal not included in A1, A2 or A3

• Looking beyond Virus Detection in RNA Sequencing Data: Lessons Learned from a Community-Based Effort to Detect Cellular Plant Pathogens and Pests

  Haegeman, A., Foucart, Y., De Jonghe, K., Goedefroit, T., Al Rwahnih, M., Boonham, N., Candresse, T., Gaafar, Y., Hurtado-Gonzales, O., Kogej, Z., Kutnjak, D., Lamovsek, J., Lefebvre, M., Malapi-Wight, M., Mavric-Plesko, I., Onder, S., Reynard, J.-S., Pamblanco Salavert, F., Schumpp, O. & Stevens, K. & 8 others, Pal, C., Tamisier, L., Ulubas Serce, C., Van Duivenbode, I., Waite, D., Xiaojun, H., Ziebell, H. & Massart, S., 29-May-2023, In: Plants. 12, 11, p. 1-20 20 p., 2139.

  Research output: Contribution to journal › A1: Web of Science-article › peer-review

  Open Access

  • Plant Pathogen 100%
  • Community-based 100%
  • Lessons Learned 100%
  • Virus Detection 100%
  • Plant Pest 100%

• Revisiting high throughput sequencing data used for plant virus detection in order to find evidence of non-viral plant pathogens and pests

  Haegeman, A., Foucart, Y., Goedefroit, T., De Jonghe, K., Al Rwahnih, M., Candresse, T., Gaafar, Y., Hurtado-Gonzales, O., Kogej, Z., Kutnjak, D., Lamovsek, J., Lefebvre, M., Malapi-Wight, M., Mavric-Plesko, I., Onder, S., Reynard, J.-S., Pamblanco Salavert, F., Schumpp, O., Stevens, K. & Pal, C. & 7 others, Tamisier, L., Ulubas Serce, C., Van Duivenbode, I., Waite, D., Xiaojun, H., Ziebell, H. & Massart, S., 20-Aug-2023.

  Research output: Contribution to conference › C3: Conference - meeting abstract

• Revisiting high throughput sequencing data used for plant virus detection in order to find evidence of non-viral plant pathogens and pests

  Haegeman, A., Foucart, Y., Goedefroit, T., De Jonghe, K., Al Rwahnih, M., Candresse, T., Gaafar, Y., Hurtado-Gonzales, O., Kogej, Z., Kutnjak, D., Lamovsek, J., Lefebvre, M., Malapi-Wight, M., Mavric-Plesko, I., Onder, S., Reynard, J.-S., Pamblanco Salavert, F., Schumpp, O., Stevens, K. & Pal, C. & 7 others, Tamisier, L., Ulubas Serce, C., Van Duivenbode, I., Waite, D., Xiaojun, H., Ziebell, H. & Massart, S., 21-Aug-2023.

  Research output: Contribution to conference › Poster

• 2022

  Detection of plant viruses with high-throughput sequencing and in vitro elimination of detected viruses in Dioscorea spp.

  Guldentops, E., Mihaylova , A., De Vos, C., Foucart, Y., Ben Ghozlen, H., Pupo, J. S., De Jonghe, K. & Werbrouck, S., Aug-2022.

  Research output: Contribution to conference › Poster

• Facilitating the adoption of high-throughput sequencing technologies as a plant pest diagnostic test in laboratories: A step-by- step description

  Lebas, B. S. M., Adams, I., Al Rwahnih, M., Baeyen, S., Bilodeau, G. J., Blouin, A. G., Boonham, N., Candresse, T., Chandelier, A., De Jonghe, K., Fox, A., Gaafar, Y., Gentit, P., Haegeman, A., Ho, W., Hurtado-Gonzales, O., Jonkers, W., Kreuze, J., Kutnjak, D. & Landa, B. B. & 34 others, Liu, M., Maclot, F., Malapi-Wight, M., Maree, H., MArtoni, F., Mehle, N., Minafra, A., Mollov, D., Moreira, A., Nakhla, M., Petter, F., Piper, A. M., Ponchart, J. P., Rae, R., Remenant, B., Rivera, Y., Rodoni, B., Roenhorst, J. W., Rollin, J., Saldarelli, P., Santala, J., Souza-Richards, R., Spadaro, D., Studholme, D. J., Sultmanis, S., van der Vlugt, R., Tamisier, L., Trontin, C., Vazquez-Iglesias, I., Vicente, C. S. L., van de Vossenberg, B. T. L. H., Wetzel, T., Ziebell, H. & Massart, S., 1-Aug-2022, In: EPPO Bulletin. 52, 2, p. 394-418 25 p.

  Research output: Contribution to journal › A2: International peer reviewed article (not A1-type) › peer-review

  Open Access

  • High-throughput Sequencing 100%
  • Diagnostic Test 100%
  • Plant Pest 100%
  • Nematode 100%
  • Protozoon 100%

• Guidelines for the reliable use of high throughput sequencing technologies to detect plant pathogens and pests

  Massart, S., Adams, I., Al Rwahnih, M., Baeyen, S., Bilodeau, G. J., Blouin, A. G., Boonham, N., Candresse, T., Chandelier, A., De Jonghe, K., Fox, A., Gaafar, Y., Gentit, P., Haegeman, A., Ho, W., Hurtado-Gonzales, O., Jonkers, W., Kreuze, J., Kutnjak, D. & Landa, B. B. & 35 others, Liu, M., Maclot, F., Malapi-Wight, M., Maree, H., MArtoni, F., Mehle, N., Minafra, A., Mollov, D., Moreira, A., Nakhla, M., Petter, F., Piper, A. M., Ponchart, J. P., Rae, R., Remenant, B., Rivera, Y., Rodoni, B., Botermans, M., Roenhorst, J. W., Rollin, J., Saldarelli, P., Santala, J., Sousa-Richards, R., Spadaro, D., Studholme, D. J., Sultmanis, S., van der Vlugt, R., Tamisier, L., Trontin, C., Vicente, C. S. L., van de Vossenberg, B. T. L. H., Westenberg, M., Wetzel, T., Ziebell, H. & Lebas, B. S. M., 25-Oct-2022, In: Peer Community Journal. 2, p. 1-34 34 p., e62.

  Research output: Contribution to journal › A2: International peer reviewed article (not A1-type) › peer-review

  Open Access

  • Plant Pathogen 100%
  • High-throughput Sequencing 100%
  • Plant Pest 100%
  • Plant Pathogens 100%
  • Plant Pests 100%

• 2021

  A Primer on the Analysis of High‐Throughput Sequencing Data for Detection of Plant Viruses

  Kutnjak, D., Tamisier, L., Adams, I., Boonham, N., Candresse, T., Chiumenti, M., De Jonghe, K., Kreuze, J., Lefebvre, M., Silva, G., Malapi-Wight, M., Margaria, P., Mavric-Plesko, I., McGreig, S., Miozzi, L., Remenant, B., Reynard, J.-S., Rollin, J., Rott, M. & Schumpp, O. & 1 others, Haegeman, A., 14-Apr-2021, In: Microorganisms. 9, 841, p. 1-31 31 p., 841.

  Research output: Contribution to journal › A1: Web of Science-article › peer-review

  Open Access

• Interlaboratory comparison study on ribodepleted total RNA high-throughput sequencing for plant virus diagnostics and bioinformatic competence

  Gaafar, Y., Westenberg, M., Botermans, M., Laszlo, K., De Jonghe, K., Foucart, Y., Ferretti, L., Kutnjak, D., Pecman, A., Mehle, N., Kreuze, J., Muller, G., Vakirlis, N., Beris, D., Varveri, C. & Ziebell, H., 12-Sept-2021, In: Pathogens. 2021/10, p. 1-17 17 p.

  Research output: Contribution to journal › A1: Web of Science-article › peer-review

  Open Access

• Raising awareness among plant virologists on the richness of their high-throughput sequencing data

  Haegeman, A., Foucart, Y., Goedefroit, T., De Jonghe, K., Al Rwahnih, M., Candresse, T., Gaafar, Y., Hurtado-Gonzales, O., Kogej, Z., Kutnjak, D., Lamovsek, J., Lefebvre, M., Malapi-Wight, M., Mavric-Plesko, I., Onder, S., Reynard, J.-S., Pamblanco Salavert, F., Schumpp, O., Stevens, K. & Pal, C. & 7 others, Tamisier, L., Ulubas Serce, C., Van Duivenbode, I., Waite, D., Xiaojun, H., Ziebell, H. & Massart, S., 20-Apr-2021.

  Research output: Contribution to conference › Poster

  File

  48 Downloads (Pure)

• Semi-artificial datasets as a resource for validation of bioinformatics pipelines for plant virus detection

  Tamisier, L., Foucart, Y., Haegeman, A., Fouillien, N., Al Rwahnih, M., Candresse, T., Chiumenti, M., De Jonghe, K., Lefebre, M., Margaria, P., Reynard, J.-S., Stevens, K., Kutnjak, D. & Massart, S., 21-Apr-2021.

  Research output: Contribution to conference › Poster

• Semi-artificial datasets as a resource for validation of bioinformatics pipelines for plant virus detection

  Tamisier, L., Haegeman, A., Foucart, Y., Fouillien, N., Al Rwahnih, M., Buzkan, N., Candresse, T., Chiumenti, M., De Jonghe, K., Lefebvre, M., Margaria, P., Reynard, J.-S., Stevens, K., Kutnjak, D. & Massart, S., 2-Dec-2021, In: Peer community Journal. 1, 1, p. 1-15 15 p., e53.

  Research output: Contribution to journal › A2: International peer reviewed article (not A1-type) › peer-review

  Open Access