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Dr. M.F. (Michael) Seidl

Associate Professor 
Science
Biology
Biodynamics and Biocomplexity
Bioinformatics
Bioinformatics
Hugo R. Kruytgebouw
Padualaan 8
Kamer N611
3584 CH Utrecht

Dr. M.F. (Michael) Seidl

Associate Professor
Bioinformatics
+31 30 253 3694
m.f.seidl@uu.nl
Profile CV Publications Teaching Ancillary activities Contact
Profile CV Publications Teaching Ancillary activities Contact
Areas of expertise
Research areas

Publications

2025

Scholarly publications

van Westerhoven, A. C., Fokkens, L., Wissink, K., Kema, G. H. J., Rep, M., & Seidl, M. F. (2025). Reference-free identification and pangenome analysis of accessory chromosomes in a major fungal plant pathogen. NAR Genomics and Bioinformatics, 7(2), Article lqaf034. https://doi.org/10.1093/nargab/lqaf034
https://research-portal.uu.nl/ws/files/261302872/lqaf034.pdf
Brasier, C. M., Grünwald, N. J., Bourret, T. B., Govers, F., Scanu, B., Cooke, D. E. L., Bose, T., Hawksworth, D. L., Abad, Z. G., Albarracin, M. V., Alsultan, W., Altamirano-Junqueria, A. E., Arifin, A. R., Arnet, M. J., Aumentado, H. D. R., Bakonyi, J., Belisle, W. H., Benigno, A., Bienapfl, J. C., ... Jung, T. (2025). Preserving the Biologically Coherent Generic Concept of Phytophthora, 'Plant Destroyer'. Phytopathology. Advance online publication. https://doi.org/10.1094/PHYTO-11-24-0372-LE
Oberti, H., Sessa, L., Oliveira-Rizzo, C., Di Paolo, A., Sanchez-Vallet, A., Seidl, M. F., & Abreo, E. (2025). Novel genomic features in entomopathogenic fungus Beauveria bassiana ILB308: accessory genomic regions and putative virulence genes involved in the infection process of soybean pest Piezodorus guildinii. Pest Management Science, 81(4), 2323-2336. https://doi.org/10.1002/ps.8631

2024

Scholarly publications

van Westerhoven, A. C., Dijkstra, J., Aznar Palop, J. L., Wissink, K., Bell, J., Kema, G. H. J., & Seidl, M. F. (2024). Frequent genetic exchanges revealed by a pan-mitogenome graph of a fungal plant pathogen. mBio, 15(12), Article e0275824. https://doi.org/10.1128/mbio.02758-24
https://research-portal.uu.nl/ws/files/248498167/van-westerhoven-et-al-2024-frequent-genetic-exchanges-revealed-by-a-pan-mitogenome-graph-of-a-fungal-plant-pathogen.pdf
Zhang, X., Leahy, I., Collemare, J., & Seidl, M. F. (2024). Genomic Localization Bias of Secondary Metabolite Gene Clusters and Association with Histone Modifications in Aspergillus. Genome Biology and Evolution, 16(11), Article evae228. https://doi.org/10.1093/gbe/evae228
https://research-portal.uu.nl/ws/files/245797004/evae228.pdf
Skiadas, P., Vidal, S. R., Dommisse, J., Mendel, M. N., Elberse, J., Van den Ackerveken, G., de Jonge, R., & Seidl, M. F. (2024). Pangenome graph analysis reveals extensive effector copy-number variation in spinach downy mildew. PLoS Genetics, 20(10 October), Article e1011452. https://doi.org/10.1371/journal.pgen.1011452
https://research-portal.uu.nl/ws/files/243754393/journal.pgen.1011452.pdf
Mendel, M., Zuijdgeest, X. C. L., van den Berg, F., van der Meer, L., Elberse, J., Skiadas, P., Seidl, M. F., den Ackerveken, G. V., & de Jonge, R. (2024). Exploiting Pseudomonas syringae Type 3 secretion to study effector contribution to disease in spinach. bioRxiv. https://doi.org/10.1101/2024.06.14.599008
https://research-portal.uu.nl/ws/files/243030134/2024.06.14.599008v2.full.pdf
Huang, W. R. H., Braam, C., Kretschmer, C., Villanueva, S. L., Liu, H., Ferik, F., van der Burgh, A. M., Boeren, S., Wu, J., Zhang, L., Nürnberger, T., Wang, Y., Seidl, M. F., Evangelisti, E., Stuttmann, J., & Joosten, M. H. A. J. (2024). Correction to: Receptor-like cytoplasmic kinases of different subfamilies differentially regulate SOBIR1/BAK1-mediated immune responses in Nicotiana benthamiana (Nature Communications, (2024), 15, 1, (4339), 10.1038/s41467-024-48313-1). Nature Communications, 15(1), Article 7910. https://doi.org/10.1038/s41467-024-52322-5
https://research-portal.uu.nl/ws/files/239621076/s41467-024-52322-5.pdf
van Ingen-Buijs, V. A., van Westerhoven, A. C., Skiadas, P., Zuijdgeest, X. C. L., Haridas, S., Daum, C., Duffy, K., Guo, J., Hundley, H., LaButti, K., Lipzen, A., Pangilinan, J., Riley, R., Wang, J., Yan, M., Martin, F., Barry, K., Grigoriev, I. V., Groenewald, J. Z., ... Seidl, M. F. (2024). Phyllosticta paracitricarpa is synonymous with the EU quarantine fungus P. Citricarpa based on phylogenomic analyses. Fungal Genetics and Biology, 175, Article 103925. https://doi.org/10.1016/j.fgb.2024.103925
https://research-portal.uu.nl/ws/files/239602097/1-s2.0-S1087184524000628-main.pdf
Martínez-de la Parte, E., Pérez-Vicente, L., Torres, D. E., van Westerhoven, A., Meijer, H. J. G., Seidl, M. F., & Kema, G. H. J. (2024). Genetic diversity of the banana Fusarium wilt pathogen in Cuba and across Latin America and the Caribbean. Environmental Microbiology, 26(5), Article e16636. https://doi.org/10.1111/1462-2920.16636
https://dspace.library.uu.nl/bitstream/handle/1874/452575/Environmental_Microbiology_-_2024_-_Mart_nez_de_la_Parte_-_Genetic_diversity_of_the_banana_Fusarium_wilt_pathogen_in_Cuba.pdf?sequence=1
Huang, W. R. H., Braam, C., Kretschmer, C., Villanueva, S. L., Liu, H., Ferik, F., van der Burgh, A. M., Wu, J., Zhang, L., Nürnberger, T., Wang, Y., Seidl, M. F., Evangelisti, E., Stuttmann, J., & Joosten, M. H. A. J. (2024). Receptor-like cytoplasmic kinases of different subfamilies differentially regulate SOBIR1/BAK1-mediated immune responses in Nicotiana benthamiana. Nature Communications, 15(1), 1-18. Article 4339. https://doi.org/10.1038/s41467-024-48313-1
https://dspace.library.uu.nl/bitstream/handle/1874/452502/s41467-024-48313-1.pdf?sequence=1
Rodenburg, S. Y. A., de Ridder, D., Govers, F., & Seidl, M. F. (2024). Oomycete metabolism is highly dynamic and reflects lifestyle adaptations. Molecular Plant-Microbe Interactions, 37(7), 571-582. https://doi.org/10.1094/MPMI-12-23-0200-R
https://research-portal.uu.nl/ws/files/233893575/mpmi-12-23-0200-r.pdf
Nakasato tagami, G., Van westerhoven, A. C., Seidl, M., Van der sluis, J., Cozzarelli, M., Balarezo, D., Pflücker, R., Marquez rosillo, C., Clercx, L., & Kema, G. H. J. (2024). Aerial mapping of the Peruvian Chira Valley banana production system to monitor the expansion of Fusarium wilt caused by Tropical Race 4. PhytoFrontiers™, 4(2), 196-204. https://doi.org/10.1094/PHYTOFR-07-23-0097-R
https://dspace.library.uu.nl/bitstream/handle/1874/452021/phytofr-07-23-0097-r.pdf?sequence=1
van Westerhoven, A. C., Aguilera-Galvez, C., Nakasato-Tagami, G., Shi-Kunne, X., Martinez de la Parte, E., Chavarro-Carrero, E., Meijer, H. J. G., Feurtey, A., Maryani, N., Ordóñez, N., Schneiders, H., Nijbroek, K., Wittenberg, A. H. J., Hofstede, R., García-Bastidas, F., Sørensen, A., Swennen, R., Drenth, A., Stukenbrock, E. H., ... Seidl, M. F. (2024). Segmental duplications drive the evolution of accessory regions in a major crop pathogen. The New phytologist, 242(2), 610-625. https://doi.org/10.1111/nph.19604
https://dspace.library.uu.nl/bitstream/handle/1874/437279/New_Phytologist_-_2024_-_Westerhoven_-_Segmental_duplications_drive_the_evolution_of_accessory_regions_in_a_major_crop.pdf?sequence=1
Torres, D. E., Kramer, H. M., Tracanna, V., Fiorin, G. L., Cook, D. E., Seidl, M. F., & Thomma, B. P. H. J. (2024). Implications of the three-dimensional chromatin organization for genome evolution in a fungal plant pathogen. Nature Communications, 15(1), Article 1701. https://doi.org/10.1038/s41467-024-45884-x
https://dspace.library.uu.nl/bitstream/handle/1874/436640/s41467-024-45884-x.pdf?sequence=1
Chavarro-Carrero, E. A., Snelders, N. C., Torres, D. E., Kraege, A., López-Moral, A., Petti, G. C., Punt, W., Wieneke, J., García-Velasco, R., López-Herrera, C. J., Seidl, M. F., & Thomma, B. P. H. J. (2024). The soil-borne white root rot pathogen Rosellinia necatrix expresses antimicrobial proteins during host colonization. PLoS Pathogens, 20(1), 1-32. Article e1011866. https://doi.org/10.1371/journal.ppat.1011866
https://dspace.library.uu.nl/bitstream/handle/1874/435737/journal.ppat.1011866.pdf?sequence=1
van Westerhoven, A. C., Mehrabi, R., Talebi, R., Steentjes, M. B. F., Corcolon, B., Chong, P. A., Kema, G. H. J., & Seidl, M. F. (2024). A chromosome-level genome assembly of Zasmidium syzygii isolated from banana leaves. G3: Genes, Genomes, Genetics, 14(3), Article jkad262. https://doi.org/10.1093/g3journal/jkad262
https://dspace.library.uu.nl/bitstream/handle/1874/437678/jkad262.pdf?sequence=1

2023

Scholarly publications

de Potter, B., Raas, M. W. D., Seidl, M. F., Verrijzer, C. P., & Snel, B. (2023). Uncoupled evolution of the Polycomb system and deep origin of non-canonical PRC1. Communications Biology, 6(1), Article 1144. https://doi.org/10.1038/s42003-023-05501-x
https://dspace.library.uu.nl/bitstream/handle/1874/433327/s42003-023-05501-x.pdf?sequence=1
Kramer, H. M., Cook, D. E., Seidl, M. F., & Thomma, B. P. H. J. (2023). Epigenetic regulation of nuclear processes in fungal plant pathogens. PLoS Pathogens, 19(8), Article e1011525. https://doi.org/10.1371/journal.ppat.1011525
https://dspace.library.uu.nl/bitstream/handle/1874/430193/journal.ppat.1011525.pdf?sequence=1
Yang, Y., Steidele, C. E., Rössner, C., Löffelhardt, B., Kolb, D., Leisen, T., Zhang, W., Ludwig, C., Felix, G., Seidl, M. F., Becker, A., Nürnberger, T., Hahn, M., Gust, B., Gross, H., Hückelhoven, R., & Gust, A. A. (2023). Convergent evolution of plant pattern recognition receptors sensing cysteine-rich patterns from three microbial kingdoms. Nature Communications, 14(1), 1-12. Article 3621. https://doi.org/10.1038/s41467-023-39208-8
https://dspace.library.uu.nl/bitstream/handle/1874/429056/s41467-023-39208-8.pdf?sequence=1
Torres, D. E., Reckard, A. T., Klocko, A. D., & Seidl, M. F. (2023). Nuclear genome organization in fungi: From gene folding to Rabl chromosomes. FEMS Microbiology Reviews, 47(3), Article fuad021. https://doi.org/10.1093/femsre/fuad021
https://dspace.library.uu.nl/bitstream/handle/1874/429354/fuad021.pdf?sequence=1
Zhang, X., Noberini, R., Vai, A., Bonaldi, T., Seidl, M. F., & Collemare, J. (2023). Detection and quantification of the histone code in the fungal genus Aspergillus. Fungal Genetics and Biology, 167, Article 103800. https://doi.org/10.1016/j.fgb.2023.103800
https://dspace.library.uu.nl/bitstream/handle/1874/428658/1_s2.0_S1087184523000312_main.pdf?sequence=1
Feurtey, A., Lorrain, C., McDonald, M. C., Milgate, A., Solomon, P. S., Warren, R., Puccetti, G., Scalliet, G., Torriani, S. F. F., Gout, L., Marcel, T. C., Suffert, F., Alassimone, J., Lipzen, A., Yoshinaga, Y., Daum, C., Barry, K., Grigoriev, I. V., Goodwin, S. B., ... Croll, D. (2023). A thousand-genome panel retraces the global spread and adaptation of a major fungal crop pathogen. Nature Communications, 14(1), Article 1059. https://doi.org/10.1038/s41467-023-36674-y
https://dspace.library.uu.nl/bitstream/handle/1874/427722/s41467_023_36674_y.pdf?sequence=1
Van westerhoven, A. C., Meijer, H., Houdijk, J., Martínez de la parte, E., Matabuana, E. L., Seidl, M., & Kema, G. H. J. (2023). Dissemination of Fusarium wilt of banana in Mozambique caused by Fusarium odoratissimum Tropical Race 4. Plant Disease, 107(3), 628-632. https://doi.org/10.1094/PDIS-07-22-1576-SC
https://dspace.library.uu.nl/bitstream/handle/1874/429475/pdis-07-22-1576-sc.pdf?sequence=1
Snelders, N. C., Boshoven, J. C., Song, Y., Schmitz, N., Fiorin, G. L., Rovenich, H., van den Berg, G. C. M., Torres, D. E., Petti, G. C., Prockl, Z., Faino, L., Seidl, M. F., & Thomma, B. P. H. J. (2023). A highly polymorphic effector protein promotes fungal virulence through suppression of plant-associated Actinobacteria. New Phytologist, 237(3), 944-958. https://doi.org/10.1111/nph.18576
https://dspace.library.uu.nl/bitstream/handle/1874/426082/New_Phytologist_2022_Snelders_A_highly_polymorphic_effector_protein_promotes_fungal_virulence_through_suppression_of.pdf?sequence=1

2022

Scholarly publications

van Westerhoven, A. C., Meijer, H. J. G., Seidl, M. F., & Kema, G. H. J. (2022). Uncontained spread of Fusarium wilt of banana threatens African food security. PLoS Pathogens, 18(9), 1-7. Article e1010769. https://doi.org/10.1371/journal.ppat.1010769
https://dspace.library.uu.nl/bitstream/handle/1874/423476/journal.ppat.1010769.pdf?sequence=1
Zhang, X., Noberini, R., Bonaldi, T., Collemare, J., & Seidl, M. F. (2022). The histone code of the fungal genus Aspergillus uncovered by evolutionary and proteomic analyses. Microbial genomics, 8(9), 1-19. Article 000856. https://doi.org/10.1099/mgen.0.000856
https://dspace.library.uu.nl/bitstream/handle/1874/423475/mgen000856.pdf?sequence=1
García-Bastidas, F. A., Arango-Isaza, R., Rodriguez-Cabal, H. A., Seidl, M. F., Cappadona, G., Segura, R., Salacinas, M., & Kema, G. H. J. (2022). Induced resistance to Fusarium wilt of banana caused by Tropical Race 4 in Cavendish cv Grand Naine bananas after challenging with avirulent Fusarium spp. PLoS One, 17(9), 1-19. Article e0273335. https://doi.org/10.1371/journal.pone.0273335
https://dspace.library.uu.nl/bitstream/handle/1874/423474/journal.pone.0273335.pdf?sequence=1
Snel, B., van den Heuvel, S., & Seidl, M. F. (2022). Caenorhabditis elegans MES-3 is a highly divergent ortholog of the canonical PRC2 component SUZ12. iScience, 25(7), 1-10. Article 104633. https://doi.org/10.1016/j.isci.2022.104633
https://dspace.library.uu.nl/bitstream/handle/1874/422459/PIIS2589004222009051.pdf?sequence=1
Melkonian, C., Seidl, M. F., van der Hooft, J. J. J., & de Vos, M. G. J. (2022). Metabolic interactions shape a community's phenotype. Trends in Microbiology, 30(7), 609-611. https://doi.org/10.1016/j.tim.2022.05.001
https://dspace.library.uu.nl/bitstream/handle/1874/421100/1_s2.0_S0966842X22001135.pdf?sequence=1
Buijs, V. A., Groenewald, J. Z., Haridas, S., LaButti, K. M., Lipzen, A., Martin, F. M., Barry, K., Grigoriev, I. V., Crous, P. W., & Seidl, M. F. (2022). Enemy or ally: a genomic approach to elucidate the lifestyle of Phyllosticta citrichinaensis. G3: Genes, Genomes, Genetics, 12(5), 1-13. https://doi.org/10.1093/g3journal/jkac061
https://dspace.library.uu.nl/bitstream/handle/1874/421158/jkac061.pdf?sequence=1
Skiadas, P., Klein, J., Quiroz Monnens, T., Elberse, J., de Jonge, R., Van den Ackerveken, G., & Seidl, M. F. (2022). Sexual reproduction contributes to the evolution of resistance breaking isolates of the spinach pathogen Peronospora effusa. Environmental Microbiology, 24(3), 1622-1637. https://doi.org/10.1111/1462-2920.15944
https://dspace.library.uu.nl/bitstream/handle/1874/419719/Environmental_Microbiology_2022_Skiadas_Sexual_reproduction_contributes_to_the_evolution_of_resistance_breaking.pdf?sequence=1
Kramer, H. M., Seidl, M. F., Thomma, B. P. H. J., & Cook, D. E. (2022). Local Rather than Global H3K27me3 Dynamics Are Associated with Differential Gene Expression in Verticillium dahliae. mBio, 13(1), 1-16. Article e0356621. https://doi.org/10.1128/mbio.03566-21
https://dspace.library.uu.nl/bitstream/handle/1874/419533/mbio.03566_21.pdf?sequence=1

2021

Scholarly publications

Snelders, N. C., Petti, G. C., van den Berg, G. C. M., Seidl, M. F., & Thomma, B. P. H. J. (2021). An ancient antimicrobial protein co-opted by a fungal plant pathogen for in planta mycobiome manipulation. Proceedings of the National Academy of Sciences of the United States of America, 118(49), 1-11. Article e2110968118. https://doi.org/10.1073/pnas.2110968118
https://dspace.library.uu.nl/bitstream/handle/1874/414119/e2110968118.full.pdf?sequence=1
Rodenburg, S. Y. A., Seidl, M. F., de Ridder, D., & Govers, F. (2021). Uncovering the Role of Metabolism in Oomycete-Host Interactions Using Genome-Scale Metabolic Models. Frontiers in Microbiology, 12, 1-17. Article 748178. https://doi.org/10.3389/fmicb.2021.748178
https://dspace.library.uu.nl/bitstream/handle/1874/413380/fmicb_12_748178.pdf?sequence=1
Kramer, H. M., Cook, D. E., van den Berg, G. C. M., Seidl, M. F., & Thomma, B. P. H. J. (2021). Three putative DNA methyltransferases of Verticillium dahliae differentially contribute to DNA methylation that is dispensable for growth, development and virulence. Epigenetics and Chromatin, 14(1), 1-15. Article 21. https://doi.org/10.1186/s13072-021-00396-6
https://dspace.library.uu.nl/bitstream/handle/1874/412993/s13072_021_00396_6.pdf?sequence=1
Torres, D. E., Thomma, B. P. H. J., & Seidl, M. F. (2021). Transposable elements contribute to genome dynamics and gene expression variation in the fungal plant pathogen Verticillium dahliae. Genome Biology and Evolution, 13(7), 1-19. Article evab135. https://doi.org/10.1093/gbe/evab135
https://dspace.library.uu.nl/bitstream/handle/1874/412992/evab135.pdf?sequence=1
Depotter, J. R. L., van Beveren, F., Rodriguez-Moreno, L., Kramer, H. M., Chavarro Carrero, E. A., Fiorin, G. L., van den Berg, G. C. M., Wood, T. A., Thomma, B. P. H. J., & Seidl, M. F. (2021). The interspecific fungal hybrid Verticillium longisporum displays subgenome-specific gene expression. mBio, 12(4), 1-20. Article e0149621. https://doi.org/10.1128/mBio.01496-21
https://dspace.library.uu.nl/bitstream/handle/1874/412991/mBio.01496_21.pdf?sequence=1
Chong, P., Essoh, J. N., Arango Isaza, R. E., Keizer, P., Stergiopoulos, I., Seidl, M. F., Guzman, M., Sandoval, J., Verweij, P. E., Scalliet, G., Sierotzski, H., de Lapeyre de Bellaire, L., Crous, P. W., Carlier, J., Cros, S., Meijer, H. J. G., Peralta, E. L., & Kema, G. H. J. (2021). A world-wide analysis of reduced sensitivity to DMI fungicides in the banana pathogen Pseudocercospora fijiensis. Pest Management Science, 77(7), 3273-3288. https://doi.org/10.1002/ps.6372
https://dspace.library.uu.nl/bitstream/handle/1874/418789/Pest_Management_Science_2021_Chong_A_world_wide_analysis_of_reduced_sensitivity_to_DMI_fungicides_in_the_banana.pdf?sequence=1
Schoina, C., Rodenburg, S. Y. A., Meijer, H. J. G., Seidl, M. F., Lacambra, L. T., Bouwmeester, K., & Govers, F. (2021). Mining oomycete proteomes for metalloproteases leads to identification of candidate virulence factors in Phytophthora infestans. Molecular Plant Pathology, 22(5), 551-563. https://doi.org/10.1111/mpp.13043
https://dspace.library.uu.nl/bitstream/handle/1874/411848/mpp.13043.pdf?sequence=1
Chavarro-Carrero, E. A., Vermeulen, J. P., E Torres, D., Usami, T., Schouten, H. J., Bai, Y., Seidl, M. F., & Thomma, B. P. H. J. (2021). Comparative genomics reveals the in planta-secreted Verticillium dahliae Av2 effector protein recognized in tomato plants that carry the V2 resistance locus. Environmental Microbiology, 23(4), 1941-1958. https://doi.org/10.1111/1462-2920.15288
https://dspace.library.uu.nl/bitstream/handle/1874/409798/1462_2920.15288.pdf?sequence=1

2020

Scholarly publications

Cook, D. E., Kramer, H. M., Torres, D. E., Seidl, M. F., & Thomma, B. P. H. J. (2020). A unique chromatin profile defines adaptive genomic regions in a fungal plant pathogen. eLife, 9, Article e62208. https://doi.org/10.7554/eLife.62208
https://dspace.library.uu.nl/bitstream/handle/1874/410519/elife_62208_v2.pdf?sequence=1
Seidl, M. F., Kramer, H. M., Cook, D. E., Fiorin, G. L., van den Berg, G. C. M., Faino, L., & Thomma, B. P. H. J. (2020). Repetitive Elements Contribute to the Diversity and Evolution of Centromeres in the Fungal Genus Verticillium. mBio, 11(5), 1-22. Article e01714-20. https://doi.org/10.1128/mBio.01714-20
https://dspace.library.uu.nl/bitstream/handle/1874/409799/mBio_2020_Seidl_e01714_20.full.pdf?sequence=1
Snelders, N. C., Rovenich, H., Petti, G. C., Rocafort, M., van den Berg, G. C. M., Vorholt, J. A., Mesters, J. R., Seidl, M. F., Nijland, R., & Thomma, B. P. H. J. (2020). Microbiome manipulation by a soil-borne fungal plant pathogen using effector proteins. Nature Plants, 6(11), 1365-1374. https://doi.org/10.1038/s41477-020-00799-5
https://dspace.library.uu.nl/bitstream/handle/1874/409797/s41477_020_00799_5.pdf?sequence=1
García-Bastidas, F. A., Quintero-Vargas, J. C., Ayala-Vasquez, M., Schermer, T., Seidl, M. F., Santos-Paiva, M., Noguera, A. M., Aguilera-Galvez, C., Wittenberg, A., Hofstede, R., Sørensen, A., & Kema, G. H. J. (2020). First report of Fusarium Wilt Tropical race 4 in Cavendish Bananas Caused by Fusarium odoratissimum in Colombia. Plant Disease, 104(3). https://doi.org/10.1094/PDIS-09-19-1922-PDN
Torres, D. E., Oggenfuss, U., Croll, D., & Seidl, M. F. (2020). Genome evolution in fungal plant pathogens: looking beyond the two-speed genome model. Fungal Biology Reviews, 34(3), 136-143. https://doi.org/10.1016/j.fbr.2020.07.001
https://dspace.library.uu.nl/bitstream/handle/1874/408841/1_s2.0_S1749461320300257_main.pdf?sequence=1
Thines, M., Sharma, R., Rodenburg, S. Y. A., Gogleva, A., Judelson, H. S., Xia, X., van den Hoogen, J., Kitner, M., Klein, J., Neilen, M., de Ridder, D., Seidl, M. F., van den Ackerveken, G., Govers, F., Schornack, S., & Studholme, D. J. (2020). The Genome of Peronospora belbahrii Reveals High Heterozygosity, a Low Number of Canonical Effectors, and TC-Rich Promoters. Molecular Plant-Microbe Interactions, 33(5), 742-753. https://doi.org/10.1094/MPMI-07-19-0211-R
https://dspace.library.uu.nl/bitstream/handle/1874/408286/mpmi_07_19_0211_r.pdf?sequence=1

2019

Scholarly publications

Ordóñez, N., Salacinas, M., Mendes, O., Seidl, M. F., Meijer, H. J. G., Schoen, C. D., & Kema, G. H. J. (2019). A loop-mediated isothermal amplification (LAMP) assay based on unique markers derived from genotyping by sequencing data for rapid in planta diagnosis of Panama disease caused by Tropical Race 4 in banana. Plant Pathology, 68(9), 1682-1693. https://doi.org/10.1111/ppa.13093
Shi-Kunne, X., Jové, R. D. P., Depotter, J. R. L., Ebert, M. K., Seidl, M. F., & Thomma, B. P. H. J. (2019). In silico prediction and characterisation of secondary metabolite clusters in the plant pathogenic fungus Verticillium dahliae. FEMS Microbiology Letters, 366(7), Article fnz081. https://doi.org/10.1093/femsle/fnz081
https://dspace.library.uu.nl/bitstream/handle/1874/388360/fnz081.pdf?sequence=1
Depotter, J. R. L., Shi-Kunne, X., Missonnier, H., Liu, T., Faino, L., van den Berg, G. C. M., Wood, T. A., Zhang, B., Jacques, A., Seidl, M. F., & Thomma, B. P. H. J. (2019). Dynamic virulence-related regions of the plant pathogenic fungus Verticillium dahliae display enhanced sequence conservation. Molecular Ecology, 28(15), 3482-3495. https://doi.org/10.1111/mec.15168
https://dspace.library.uu.nl/bitstream/handle/1874/388359/Depotter_et_al_2019_Molecular_Ecology.pdf?sequence=1
Seidl, M. F., & Van den Ackerveken, G. (2019). Activity and Phylogenetics of the Broadly Occurring Family of Microbial Nep1-Like Proteins. Annual Review of Phytopathology, 57, 367-386. https://doi.org/10.1146/annurev-phyto-082718-100054
https://research-portal.uu.nl/ws/files/236324973/annurev-phyto-082718-100054.pdf
Rodenburg, S. Y. A., Seidl, M. F., Judelson, H. S., Vu, A. L., Govers, F., & de Ridder, D. (2019). Metabolic model of the Phytophthora infestans-tomato interaction reveals metabolic switches during host colonization. mBio, 10(4), Article 454-19. https://doi.org/10.1128/mBio.00454-19
https://dspace.library.uu.nl/bitstream/handle/1874/388358/mBio_2019_Rodenburg_e00454_19.full.pdf?sequence=1
Collemare, J., & Seidl, M. F. (2019). Chromatin-dependent regulation of secondary metabolite biosynthesis in fungi: is the picture complete? FEMS Microbiology Reviews, 43(6), 591–607. https://doi.org/10.1093/femsre/fuz018
https://dspace.library.uu.nl/bitstream/handle/1874/391654/fuz018.pdf?sequence=1
Shi-Kunne, X., van Kooten, M., Depotter, J. R. L., Thomma, B. P. H. J., & Seidl, M. F. (2019). The genome of the fungal pathogen Verticillium dahliae reveals extensive bacterial to fungal gene transfer. Genome Biology and Evolution, 11(3), 855-868. https://doi.org/10.1093/gbe/evz040
https://dspace.library.uu.nl/bitstream/handle/1874/379569/shi_kunne.pdf?sequence=1

2018

Scholarly publications

Rodenburg, S. Y. A., Seidl, M. F., de Ridder, D., & Govers, F. (2018). Genome-wide characterization of Phytophthora infestans metabolism: a systems biology approach. Molecular Plant Pathology, 19(6), 1403-1413. https://doi.org/10.1111/mpp.12623
https://dspace.library.uu.nl/bitstream/handle/1874/381261/Rodenburg_et_al_2018_Molecular_Plant_Pathology.pdf?sequence=1
Shi-Kunne, X., Faino, L., van den Berg, G. C. M., Thomma, B. P. H. J., & Seidl, M. F. (2018). Evolution within the fungal genus Verticillium is characterized by chromosomal rearrangement and gene loss. Environmental Microbiology, 20(4), 1362-1373. https://doi.org/10.1111/1462-2920.14037
https://dspace.library.uu.nl/bitstream/handle/1874/381003/Shi_Kunne_et_al_2018_Environmental_Microbiology.pdf?sequence=1
van den Hoogen, D. J., Meijer, H. J. G., Seidl, M. F., & Govers, F. (2018). The Ancient Link between G-Protein-Coupled Receptors and C-Terminal Phospholipid Kinase Domains. mBio, 9(1). https://doi.org/10.1128/mBio.02119-17
https://dspace.library.uu.nl/bitstream/handle/1874/381002/mBio_2018_van_den_Hoogen_e02119_17.full.pdf?sequence=1
Wolters, P. J., Faino, L., van den Bosch, T. B. M., Evenhuis, B., Visser, R. G. F., Seidl, M. F., & Vleeshouwers, V. G. A. A. (2018). Gapless Genome Assembly of the Potato and Tomato Early Blight Pathogen Alternaria solani. Molecular Plant-Microbe Interactions, 31(7), 692-694. https://doi.org/10.1094/MPMI-12-17-0309-A
https://dspace.library.uu.nl/bitstream/handle/1874/381572/mpmi_12_17_0309_a.pdf?sequence=1
Kema, G. H. J., Mirzadi Gohari, A., Aouini, L., Gibriel, H. A. Y., Ware, S. B., van den Bosch, F., Manning-Smith, R., Alonso-Chavez, V., Helps, J., Ben M'Barek, S., Mehrabi, R., Diaz-Trujillo, C., Zamani, E., Schouten, H. J., van der Lee, T. A. J., Waalwijk, C., de Waard, M. A., de Wit, P. J. G. M., Verstappen, E. C. P., ... Seidl, M. F. (2018). Stress and sexual reproduction affect the dynamics of the wheat pathogen effector AvrStb6 and strobilurin resistance. Nature Genetics, 50(3), 375-380. https://doi.org/10.1038/s41588-018-0052-9
Zheng, S.-J., García-Bastidas, F. A., Li, X., Zeng, L., Bai, T., Xu, S., Yin, K., Li, H., Fu, G., Yu, Y., Yang, L., Nguyen, H. C., Douangboupha, B., Khaing, A. A., Drenth, A., Seidl, M. F., Meijer, H. J. G., & Kema, G. H. J. (2018). New Geographical Insights of the Latest Expansion of Fusarium oxysporum f.sp. cubense Tropical Race 4 Into the Greater Mekong Subregion. Frontiers in Plant Science, 9, Article 457. https://doi.org/10.3389/fpls.2018.00457
https://dspace.library.uu.nl/bitstream/handle/1874/381001/fpls_09_00457.pdf?sequence=1

2017

Scholarly publications

Song, Y., Zhang, Z., Seidl, M. F., Majer, A., Jakse, J., Javornik, B., & Thomma, B. P. H. J. (2017). Broad taxonomic characterization of Verticillium wilt resistance genes reveals an ancient origin of the tomato Ve1 immune receptor. Molecular Plant Pathology, 18(2), 195-209. https://doi.org/10.1111/mpp.12390
https://dspace.library.uu.nl/bitstream/handle/1874/382191/Song_et_al_2017_Molecular_Plant_Pathology.pdf?sequence=1
Derbyshire, M., Denton-Giles, M., Hegedus, D., Seifbarghy, S., Rollins, J., van Kan, J., Seidl, M. F., Faino, L., Mbengue, M., Navaud, O., Raffaele, S., Hammond-Kosack, K., Heard, S., & Oliver, R. (2017). The complete genome sequence of the phytopathogenic fungus Sclerotinia sclerotiorum reveals insights into the genome architecture of broad host range pathogens. Genome Biology and Evolution, 9(3), 593–618. https://doi.org/10.1093/gbe/evx030
Depotter, J. R. L., Seidl, M. F., van den Berg, G. C. M., Thomma, B. P. H. J., & Wood, T. A. (2017). A distinct and genetically diverse lineage of the hybrid fungal pathogen Verticillium longisporum population causes stem striping in British oilseed rape. Environmental Microbiology, 19(10), 3997-4009. https://doi.org/10.1111/1462-2920.13801
Seidl, M. F. (2017). Adenine N6-methylation in diverse fungi. Nature Genetics, 49(6), 823-824. https://doi.org/10.1038/ng.3873
Seidl, M. F., & Thomma, B. P. H. J. (2017). Transposable Elements Direct The Coevolution between Plants and Microbes. Trends in Genetics, 33(11), 842-851. https://doi.org/10.1016/j.tig.2017.07.003
Van Kan, J. A. L., Stassen, J. H. M., Mosbach, A., Van Der Lee, T. A. J., Faino, L., Farmer, A. D., Papasotiriou, D. G., Zhou, S., Seidl, M. F., Cottam, E., Edel, D., Hahn, M., Schwartz, D. C., Dietrich, R. A., Widdison, S., & Scalliet, G. (2017). A gapless genome sequence of the fungus Botrytis cinerea. Molecular Plant Pathology, 18(1), 75-89. https://doi.org/10.1111/mpp.12384
Kombrink, A., Rovenich, H., Shi-Kunne, X., Rojas-Padilla, E., van den Berg, G. C. M., Domazakis, E., de Jonge, R., Valkenburg, D.-J., Sanchez-Vallet, A., Seidl, M. F., & Thomma, B. P. H. J. (2017). Verticillium dahliae LysM effectors differentially contribute to virulence on plant hosts. Molecular Plant Pathology, 18(4), 596-608. https://doi.org/10.1111/mpp.12520
https://dspace.library.uu.nl/bitstream/handle/1874/359421/Kombrink_et_al_2017_Molecular_Plant_Pathology.pdf?sequence=1

2016

Scholarly publications

Gibriel, H. A. Y., Thomma, B. P. H. J., & Seidl, M. F. (2016). The Age of Effectors: Genome-Based Discovery and Applications. Phytopathology, 106(10), 1206-1212. https://doi.org/10.1094/PHYTO-02-16-0110-FI
Depotter, J. R., Seidl, M. F., Wood, T. A., & Thomma, B. P. (2016). Interspecific hybridization impacts host range and pathogenicity of filamentous microbes. Current Opinion in Microbiology, 32, 7-13. https://doi.org/10.1016/j.mib.2016.04.005
Faino, L., Seidl, M. F., Shi-Kunne, X., Pauper, M., van den Berg, G. C. M., Wittenberg, A. H. J., & Thomma, B. P. H. J. (2016). Transposons passively and actively contribute to evolution of the two-speed genome of a fungal pathogen. Genome Research, 26(8), 1091-100. https://doi.org/10.1101/gr.204974.116
Seidl, M. F., Cook, D. E., & Thomma, B. P. H. J. (2016). Chromatin Biology Impacts Adaptive Evolution of Filamentous Plant Pathogens. PLoS Pathogens, 12(11), e1005920. https://doi.org/10.1371/journal.ppat.1005920
Abd-El-Haliem, A. M., Vossen, J. H., van Zeijl, A., Dezhsetan, S., Testerink, C., Seidl, M. F., Beck, M., Strutt, J., Robatzek, S., & Joosten, M. H. A. J. (2016). Biochemical characterization of the tomato phosphatidylinositol-specific phospholipase C (PI-PLC) family and its role in plant immunity. Biochimica et Biophysica Acta, 1861(9 Pt B), 1365-1378. https://doi.org/10.1016/j.bbalip.2016.01.017
Thomma, B. P. H. J., Seidl, M. F., Shi-Kunne, X., Cook, D. E., Bolton, M. D., van Kan, J. A. L., & Faino, L. (2016). Mind the gap; seven reasons to close fragmented genome assemblies. Fungal Genetics and Biology, 90, 24-30. https://doi.org/10.1016/j.fgb.2015.08.010

2015

Scholarly publications

Seidl, M. F., Faino, L., Shi-Kunne, X., Van Den Berg, G. C. M., Bolton, M. D., & Thomma, B. P. H. J. (2015). The genome of the saprophytic fungus Verticillium tricorpus reveals a complex effector repertoire resembling that of its pathogenic relatives. Molecular Plant-Microbe Interactions, 28(3), 362-373. https://doi.org/10.1094/MPMI-06-14-0173-R
Woudenberg, J. H. C., Seidl, M. F., Groenewald, J. Z., de Vries, M., Stielow, J. B., Thomma, B. P. H. J., & Crous, P. W. (2015). Alternaria section Alternaria: Species, formae speciales or pathotypes? Studies in Mycology, 82, 1-21. https://doi.org/10.1016/j.simyco.2015.07.001
Faino, L., Seidl, M. F., Datema, E., van den Berg, G. C. M., Janssen, A., Wittenberg, A. H. J., & Thomma, B. P. H. J. (2015). Single-Molecule Real-Time Sequencing Combined with Optical Mapping Yields Completely Finished Fungal Genome. mBio, 6(4). https://doi.org/10.1128/mBio.00936-15
Ordonez, N., Seidl, M. F., Waalwijk, C., Drenth, A., Kilian, A., Thomma, B. P. H. J., Ploetz, R. C., & Kema, G. H. J. (2015). Worse Comes to Worst: Bananas and Panama Disease--When Plant and Pathogen Clones Meet. PLoS Pathogens, 11(11), e1005197. https://doi.org/10.1371/journal.ppat.1005197
Frébortová, J., Greplová, M., Seidl, M. F., Heyl, A., & Frébort, I. (2015). Biochemical Characterization of Putative Adenylate Dimethylallyltransferase and Cytokinin Dehydrogenase from Nostoc sp. PCC 7120. PLoS One, 10(9), e0138468. https://doi.org/10.1371/journal.pone.0138468
Shi-Kunne, X., Seidl, M. F., Faino, L., & Thomma, B. P. H. J. (2015). Draft Genome Sequence of a Strain of Cosmopolitan Fungus Trichoderma atroviride. Genome Announcements, 3(3). https://doi.org/10.1128/genomeA.00287-15
Gruhn, N., Seidl, M. F., Halawa, M., & Heyl, A. (2015). Members of a recently discovered subfamily of cytokinin receptors display differences and similarities to their classical counterparts. Plant Signaling & Behavior, 10(2), e984512. https://doi.org/10.4161/21659087.2014.984512
Zeilmaker, T., Ludwig, N. R., Elberse, J., Seidl, M. F., Berke, L., Van Doorn, A., Schuurink, R. C., Snel, B., & Van den Ackerveken, G. (2015). DOWNY MILDEW RESISTANT 6 and DMR6-LIKE OXYGENASE 1 are partially redundant but distinct suppressors of immunity in Arabidopsis. Plant Journal, 81(2), 210-222. https://doi.org/10.1111/tpj.12719
https://dspace.library.uu.nl/bitstream/handle/1874/320978/Zeilmaker_et_al_2015_The_Plant_Journal.pdf?sequence=1

2014

Scholarly publications

Meijer, H. J. G., Mancuso, F. M., Espadas, G., Seidl, M. F., Chiva, C., Govers, F., & Sabidó, E. (2014). Profiling the secretome and extracellular proteome of the potato late blight pathogen Phytophthora infestans. Molecular and Cellular Proteomics, 13(8), 2101-2113. https://doi.org/10.1074/mcp.M113.035873
Seidl, M. F., & Thomma, B. P. H. J. (2014). Sex or no sex: evolutionary adaptation occurs regardless. BioEssays, 36(4), 335-45. https://doi.org/10.1002/bies.201300155
Resjö, S., Ali, A., Meijer, H. J. G., Seidl, M. F., Snel, B., Sandin, M., Levander, F., Govers, F., & Andreasson, E. (2014). Quantitative label-free phosphoproteomics of six different life stages of the late blight pathogen phytophthora infestans reveals abundant phosphorylation of members of the CRN effector family. Journal of Proteome Research, 13(4), 1848-1859. https://doi.org/10.1021/pr4009095
Gruhn, N., Halawa, M., Snel, B., Seidl, M. F., & Heyl, A. (2014). A subfamily of putative cytokinin receptors is revealed by an analysis of the evolution of the two-component signaling system of plants. Plant Physiology, 165(1), 227-37. https://doi.org/10.1104/pp.113.228080
https://dspace.library.uu.nl/bitstream/handle/1874/307313/227.full.pdf?sequence=1
Van Hooff, J. J. E., Snel, B., & Seidl, M. F. (2014). Small homologous blocks in phytophthora genomes do not oint to an ancient whole-genome duplication. Genome Biology and Evolution, 6(5), 1079-1085. https://doi.org/10.1093/gbe/evu081
https://dspace.library.uu.nl/bitstream/handle/1874/307249/Genome_Biol_Evol_2014_van_Hooff_1079_85.pdf?sequence=1
Pel, M. J. C., van Dijken, A. J. H., Bardoel, B. W., Seidl, M. F., van der Ent, S., van Strijp, J. A. G., & Pieterse, C. M. J. (2014). Pseudomonas syringae evades host immunity by degrading flagellin monomers with alkaline protease AprA. Molecular Plant-Microbe Interactions, 27(7), 603-610. https://doi.org/10.1094/MPMI-02-14-0032-R
https://dspace.library.uu.nl/bitstream/handle/1874/307489/MPMI_Pel_2014.pdf?sequence=1
Pel, M. J. C., Wintermans, P. C. A., Cabral, A., Robroek, B. J. M., Seidl, M. F., Bautor, J., Parker, J. E., Van den Ackerveken, G., & Pieterse, C. M. J. (2014). Functional Analysis of Hyaloperonospora arabidopsidis RXLR Effectors. PLoS One, 9(11), Article e110624. https://doi.org/10.1371/journal.pone.0110624
https://dspace.library.uu.nl/bitstream/handle/1874/307440/PLoSONE_Pel_2014.pdf?sequence=1

2013

Scholarly publications

Jiang, R. H. I., de Bruijn, I., Haas, B. J., Belmonte, R., Löbach, L., Christie, J., van den Ackerveken, A. F. J. M., Bottin, A., Bulone, V., Diaz-Moreno, S. M., Dumas, B., Fan, L., Gaulin, E., Govers, F., Grenville-Briggs, L. J., Horner, N. R., Levin, J. Z., Mammella, M., Meijer, H. J., ... West, P. (2013). Distinctive expansions of the potential virulence genes in the genome of the oomycete fish pathogen. PLoS Genetics, 9(6), Article e1003272. https://doi.org/10.1371/journal.pgen.1003272
https://dspace.library.uu.nl/bitstream/handle/1874/429112/Jiang2013.pdf?sequence=1
Seidl, M. F., Schneider, A., Govers, F., & Snel, B. (2013). A predicted functional gene network for the plant pathogen Phytophthora infestans as a framwork for genomic biology. BMC Genomics, 14, 483. https://doi.org/10.1186/1471-2164-14-483
Schneider, A., Seidl, M. F., & Snel, B. (2013). Shared protein complex subunits contribute to explaining disrupted co-occurrence. PLoS Computational Biology, 9(7), e1003124. https://doi.org/10.1371/journal.pcbi.1003124
Seidl, M. F. (2013). Exploring Evolution and Biology of Oomycetes: Integrative and Comparative Genomics. [Doctoral thesis 1 (Research UU / Graduation UU), Utrecht University]. Utrecht University.
https://dspace.library.uu.nl/bitstream/handle/1874/273869/seidl.pdf?sequence=2

2012

Scholarly publications

Seidl, M. F., Wang, R.-P., Van den Ackerveken, G., Govers, F., & Snel, B. (2012). Bioinformatic Inference of Specific and General Transcription Factor Binding Sites in the Plant Pathogen Phytophthora infestans. PLoS One, 7(12). https://doi.org/10.1371/journal.pone.0051295
Stassen, J. H. M., Seidl, M. F., Vergeer, P. W. J., Nijman, I. J., Snel, B., Cuppen, E., & van den Ackerveken, A. F. J. M. (2012). Effector identification in the lettuce downy mildew Bremia lactucae by massively parallel transcriptome sequencing. Molecular Plant Pathology, 13(7), 719-731. https://doi.org/10.1111/j.1364-3703.2011.00780.x
https://dspace.library.uu.nl/bitstream/handle/1874/268271/Effector%2520identification%2520in%2520the%2520lettuce%2520downy%2520mildew%2520Bremia%2520lactucae%2520by%2520massively%2520parallel.pdf?sequence=1
Seidl, M. F., van den Ackerveken, A. F. J. M., Govers, F., & Snel, B. (2012). Reconstruction of oomycete genome evolution identifies differences in evolutionary trajectories leading to present-day larte gene families. Genome Biology and Evolution, 4, 199-211.
Seidl, M. F., Wang, R. P., van den Ackerveken, A. F. J. M., Govers, F., & Snel, B. (2012). Bioinformatic inference of specific and general transcription factor binding sites in the plant pathogen phytophtora infestans. PLoS One, 7, e51295.
Seidl, M. F., van den Ackerveken, A. F. J. M., Govers, F., & Snel, B. (2012). Reconstruction of oomycete genome evolution identifies differences in evolutionary trajectories leading to present-day largegene families. Genome Biology and Evolution, 4(3), 199–211. https://doi.org/10.1093/gbe/evs003
https://dspace.library.uu.nl/bitstream/handle/1874/257246/Reconstruction%2520of%2520oomycete%2520genome%2520evolution%2520identifies%2520differences%2520in.pdf?sequence=1

Other output

Zeilmaker, T., Elberse, J. H. M., Seidl, M. F., Berke, L., Snel, B., & van den Ackerveken, A. F. J. M. (2012). DMR6 and DM6-like lxygenase 1 have overlapping but distinct activities as negative regulators of immunity in Arabidopsis. Paper presented at 23rd International Conference on Arabidopsis Research, Vienna, Austria.
Zeilmaker, T., Elberse, J. H. M., Cabral, A., Yatusevich, R., Parker, J., Seidl, M. F., Berke, L., Snel, B., & van den Ackerveken, A. F. J. M. (2012). Suppression of plant immunity. Paper presented at Plant Biology Congress, Freiburg, Germany.

2011

Scholarly publications

da Cruz Cabral, A., Stassen, J. H. M., Seidl, M. F., Bautor, J., Parker, J. E., & Van den Ackerveken, G. (2011). Identification of Hyaloperonospora arabidopsidis Transcript Sequences Expressed during Infection Reveals Isolate-Specific Effectors. PLoS One, 6(5). https://doi.org/10.1371/journal.pone.0019328
Cabral, A., Stassen, J. H. M., Seidl, M. F., Bautor, J., Parker, J. E., & van den Ackerveken, A. F. J. M. (2011). Identification of Hyaloperonospora arabidopsis transcript sequences expressed during infection reveals isolate-specific effectors. PLoS One, 6, e19328.
Seidl, M. F., van den Ackerveken, A. F. J. M., Govers, F., & Snel, B. (2011). A domain-centric analysis of oomycete plant pathogen genomes reveals unique protein organization. Plant Physiology, 155, 628-644. https://doi.org/10.1104/pp.110.167841

2009

Scholarly publications

Seidl, M. F., & Schultz, J. (2009). Evolutionary flexibility of protein complexes. BMC Evolutionary Biology, 9, 155. https://doi.org/10.1186/1471-2148-9-155
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