BioRxiv pre-print
Sato Y, Bex R, van den Berg G.C.M, Höfte M, Seidl M.F., Thomma B.P.H.J (2025). Starship giant transposons dominate plastic genomic regions in a fungal plant pathogen and drive virulence evolution. BioRxiv
Mesny F, Thomma BPHJ (2024). AMAPEC: accurate antimicrobial activity prediction for fungal effector proteins. BioRxiv
Li J, Faino L, Lorencini G, Bashyal S, Schaveling A, van den Berg GCM, Seidl MF, Thomma BPHJ (2022). A single Verticillium dahliae effector determines pathogenicity on tomato by targeting auxin response factors. BioRxiv
2025
Kanda Y, Shinya T, Wari D, Hojo Y, Fujiwara Y, Tsuchiya W, Fujimoto Z, Thomma BPHJ, Nishizawa Y, Kamakura T, Galis I, Mori M. (2025). Chitin-signaling-dependent responses to insect oral secretions in rice cells propose the involvement of chitooligosaccharides in plant defense against herbivores. Plant Journal: 121(1):e17157.
2024
Kraege A, Chavarro-Carrero E, Guiglielmoni N, Schnell E, Kirangawa J, Heilmann-Heimbach S, Becker K, Köhrer K, Schiffer P, Thomma BPHJ, Rovenich H. (2024). High quality genome assembly and annotation (v1) of the terrestrial microalga Coccomyxa viridis SAG 216-4. Peer Community Journal 4: e72
Kraege A, Chavarro-Carrero E, Schnell E, Heilmann-Heimbach S, Becker K, Köhrer K, Hüettel B, Sargheini N, Schiffer P, Waldvogel AM, Thomma BPHJ, Rovenich H. (2024). High quality genome assembly and annotation (v1) of the eukaryotic freshwater microalga Coccomyxa elongata SAG 216-3b. G3 13:jkae294.
Mesny F, Bauer M, Zhu J, Thomma BPHJ. (2024). Meddling with the microbiota: Fungal tricks to infect plant hosts. Current Opinion in Plant Biology 2:102622.
Pradeu T, Thomma BPHJ, Girardin SE, Lemaitre B. (2024). The conceptual foundations of innate immunity: Taking stock 30 years later. Immunity: 57(4):613-631.
David E. Torres, H. Martin Kramer, Vittorio Tracanna, Gabriel L. Fiorin, David E. Cook, Michael F. Seidl, Bart P.H.J. Thomma (2024). Implications of the three-dimensional chromatin organization for genome evolution in a fungal plant pathogen. Nature Communications 15: 1701.
Chavarro-Carrero AE, Snelders NC, Torres DE, Kraege A, López-Moral A, Petti GC, Punt W, Wieneke J, García-Velasco R, López-Herrera CJ, Seidl MF, Thomma BPHJ (2024). The soil-borne white root rot pathogen Rosellinia necatrix expresses antimicrobial proteins during host colonization. PLoS Pathogens 20: e1011866.
2023
Kramer HM, Cook DE, Seidl MF, Thomma BPHJ (2023). Epigenetic regulation of nuclear processes in fungal plant pathogens. PLoS Pathogens 19: e1011525.
Mesny F, Hacquard S, Thomma BPHJ (2023). Co-evolution within the plant holobiont drives host performance. EMBO Reports 24: e57455.
Rovenich H, Thomma BPHJ (2023). Battle of the bugs: how an oomycete pathogen shapes the microbiota of its host. New Phytologist 239: 2064-2066.
Weiland P, Dempwolff F, Steinchen W, Freibert SA, Tian H, Glatter T, Martin R, Thomma BPHJ, Bange G, Altegoer F (2023). Structural and functional analysis of the cerato-platanin-like protein Cpl1 suggests diverging functions in smut fungi. Molecular Plant Pathology 24: 768-787.
Snelders NC, Boshoven JC, Song Y, Schmitz N, Fiorin GL, Rovenich H, van den Berg GCM, Torres DE, Petti GC, Prockl Z, Faino L, Seidl MF, Thomma BPHJ (2023). A highly polymorphic effector protein promotes fungal virulence through suppression of plant-associated Actinobacteria. New Phytologist 237: 944-958.
2022
Tian H, Fiorin GL, Kombrink A, Mesters JR, Thomma BPHJ (2022). Fungal dual-domain LysM effectors undergo chitin-induced intermolecular, and not intramolecular, dimerization. Plant Physiology 190: 2033-2044.
Snelders NC, Rovenich H, Thomma BPHJ (2022). Microbiota manipulation through the secretion of effector proteins is fundamental to the wealth of lifestyles in the fungal kingdom. FEMS Microbiology Reviews 46: fuac022.
Kramer HM, Seidl MF, Thomma BPHJ*, Cook DE* (2022). Local rather than global H3K27me3 dynamics associates with differential gene expression in Verticillium dahliae. mBio 13: e03566-21
2021
Snelders N, Petti GC, van den Berg GCM, Seidl MF, Thomma BPHJ (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 USA 118: e2110968118.
Pruitt RN, Locci F, Wanke F, Zhang L, Saile SC, Joe A, Karelina D, Hua C, Fröhlich K, Wan W-L, Rao S, Stolze SC, Harzen A, Gust AA, Harter K, Joosten MHAJ, Thomma BPHJ, Zhou J-M, Dangl JL, Weigel D, Nakagami H, Oecking C, El Kasmi F, Parker JE, Nürnberger F (2021). The EDS1-PAD4-ADR1 node mediates Arabidopsis pattern-triggered immunity. Nature 598: 495-499.
Torres DE, Thomma BPHJ*, Seidl MF* (2021). Transposable elements contribute to genome dynamics and gene expression variation in the fungal plant pathogen Verticillium dahliae. Genome Biology & Evolution 13: evab135.
Depotter JRL, van Beveren F#, Rodriguez-Moreno L#, Kramer HM#, Chavarro Carrero EA#, Fiorin GL, van den Berg GCM, Wood TA*, Thomma BPHJ*, Seidl MF* (2021). The interspecific fungal hybrid Verticillium longisporum displays subgenome-specific gene expression. mBio 12: e01496-21.
Harting R#, Starke J#, Kusch H, Pöggeler S, Maurus I, Schlüter R, Landesfeind M, Bulla I, Nowrousian M, de Jonge R, Stahlhut G, Hoff KJ, Aßhauer KP, Thürmer A, Stanke M, Daniel R, Morgenstern B, Thomma BPHJ, Kronstad JW, Braus-Stromeyer SA, Braus GH (2021). A 20-kb lineage-specific genomic region tames virulence in pathogenic amphidiploid Verticillium longisporum. Molecular Plant Pathology 22:939-953.
Chavarro-Carrero EA#, Vermeulen JP#, Torres D, Usami T, Schouten HJ, Bai Y, Seidl MF*, Thomma BPHJ* (2020). 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: 1941-1958.
Ebert MK#, Rangel LI#, Spanner RE, Taliadoros D, Wang X, Friesen TL, de Jonge R, Neubauer JD, Secor GA, Thomma BPHJ, Stukenbrock EH, Bolton MD (2021). Identification and characterization of Cercospora beticola necrosis-inducing effector CbNip1. Molecular Plant Pathology 22: 301-316.
Tian H, MacKenzie CI#, Rodriguez-Moreno L#, van den Berg GCM, Chen H, Rudd JJ, Mesters JR, Thomma BPHJ (2021). Three LysM effectors of Zymoseptoria tritici collectively disarm chitin-triggered plant immunity. Molecular Plant Pathology 22: 683-693.
Kramer HM#, Cook DE#, van den Berg GCM, Seidl MF, Thomma BPHJ (2021). Three putative DNA methyltransferases of Verticillium dahliae differentially contribute to DNA methylation that is dispensable for growth, development and virulence. Epigenetics & Chromatin 14: 21.
2020
Snelders N, Rovenich H#, Petti GC#, Rocafort M, van den Berg GCM, Vorholt JA, Mesters JR, Seidl MF, Nijland R, Thomma BPHJ (2020). Microbiome manipulation by a soilborne fungal plant pathogen using effector proteins. Nature Plants 6: 1365-1374.
Seidl MF, Kramer HM, Cook DE, Fiorin GL, van den Berg GCM, Faino L, Thomma BPHJ (2020). Repetitive elements contribute to the diversity and evolution of centromeres in the fungal genus Verticillium. mBio 11: e01714-20.
Sánchez-Vallet A#, Tian H#, Rodriguez-Moreno L, Valkenburg DJ, Saleem-Batcha R, Wawra S, Kombrink A, Verhage L, de Jonge R, van Esse HP, Zuccaro A, Croll D, Mesters JR*, Thomma BPHJ* (2020). A secreted LysM effector protects fungal hyphae through chitin-dependent homodimer polymerization. PLoS Pathogens 16: e1008652.
Cook DE, Kramer HM, Torres DE, Seidl MF, Thomma BPHJ (2020). A unique chromatin profile defines adaptive genomic regions in a fungal plant pathogen. eLife 9: e62208.
(superscript symbols (#,*) indicate equal contributions).
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