Peer Reviewed Publications and Pre-Prints:



Komluski, J., Stukenbrock, E.H., Habig, M. (2022). Non-Mendelian transmission of accessory chromosomes in fungi. Chromosome Research, 1-13.

Yuan, Z., Wu, Q.I.,  Xu, L., Druzhinina, I.S., Stukenbrock, E.H. et. al. (2022). Genomic landscape of a relict fir-associated fungus reveals rapid convergent adaptation towards endophytism. The ISME journal, 16, 5.


Spanner, R., Taliadoros D., Richards J., Rivera-Varas, V., Neubauer, J., Natwick, M., Hamilton, O., Vaghefi, N., Pethybridge, S., Secor G., A., Friesen, T.L., Stukenbrock, E.H.,  Bolton, M.D. (2021). Genome-Wide Association and Selective Sweep Studies Reveal the Complex Genetic Architecture of DMI Fungicide Resistance in Cercospora beticola. Genome Biology and Evolution, 13, 9.

Habig, M., Lorrain, C. Feurtey, A. Komluski, J. and Stukenbrock, E.H. (2021) Epigenetic modifications affect the rate of spontaneous mutations in a pathogenic fungus. Nature communications, 12, 1–13.

Habig, M., Schotanus, K. Hufnagel, K. Happel, P. and Stukenbrock, E.H. (2021) Ago1 Affects the Virulence of the Fungal Plant Pathogen Zymoseptoria tritici. Genes, 12, 1011.

Soyer JL, Clairet C,  Gay EJ, Lapalu N, Rouxel T, Stukenbrock EH, Fudal, I. 2021. Genome-wide mapping of histone modifications during axenic growth in two species of Leptosphaeria maculans showing contrasting genomic organization. Chromosome Research, In Press 

Boynton PJ, Wloch-Salamon D, Landermann D. and Stukenbrock EH. 2021. Forest Saccharomyces paradoxus are robust to seasonal biotic and abiotic changes. Ecology and Evolution doi: 10.1002/ece3.7515

Soluch, R., Hülter, N.F., Romero Picazo, D., Özkurt, E., Stukenbrock, E.H. and Dagan, T., 2021. Colonization dynamics of Pantoea agglomerans in the wheat root habitat. Environmental Microbiology.

Möller M, Habig M, Lorrain C, Feurtey A, Haueisen J, Fagundes W, Alizadeh A, Freitag M, Stukenbrock EH. 2021. Recent loss of the Dim2 DNA methyltransferase decreases mutation rate in repeats and changes evolutionary trajectory in a fungal pathogen. PLoS Genet 17(3): e1009448.

Lorrain C, Feurtey A, Möller M, Haueisen J and Stukenbrock EH. Dynamics of transposable elements in recently diverged fungal pathogens: lineage-specific transposable element content and efficiency of genome defences. G3, 11(4), jkab068.

Ebert, M.K., Rangel, L.I., Spanner, R.E., Taliadoros, D., Wang, X., Friesen, T.L., de Jonge, R., Neubauer, J.D., Secor, G.A., Thomma, B.P. and Stukenbrock, E.H., Bolton, M. 2021. Identification and characterization of Cercospora beticola necrosis‐inducing effector CbNip1. Molecular Plant Pathology, 22(3), pp.301-316.

Miller, M.E., Nazareno, E.S., Rottschaefer, S.M., Riddle, J., Dos Santos Pereira, D., Li, F., Nguyen-Phuc, H., Henningsen, E., Persoons, A., Saunders, D.G. Stukenbrock, E., Dodds P, Kianian, S, Figueroa, M 2021. Increased virulence of Puccinia coronata f. sp.avenae populations through allele frequency changes at multiple putative Avr loc. PLoS Genet 16(12): e1009291.


Vasighzadeh, A, Sharifnabi, B, Javan‐Nikkhah, M, Seifollahi E, Landermann‐Habetha D, Feurtey A, Stukenbrock EH. Population genetic structure of four regional populations of the barley pathogen Pyrenophora teres f. maculata in Iran is characterized by high genetic diversity and sexual recombination. Plant Pathol. 2020; 00: 1– 10.

Fagundes, W.C., Haueisen, J. and Stukenbrock, E.H., 2020. Dissecting the Biology of the Fungal Wheat Pathogen Zymoseptoria tritici: A Laboratory Workflow. Current Protocols in Microbiology, 59(1), p.e128.

Dutheil, J.Y., Münch, K., Schotanus, K., Stukenbrock, E.H. and Kahmann, R., 2020. The insertion of a mitochondrial selfish element into the nuclear genome and its consequences. Ecology and evolution, 10(20), pp.11117-11132.

Özkurt E, Hassani MA, Uğur Sesiz, Künzel S, Dagan T, Özkan H, Stukenbrock EH. 2020. Higher stochasticity of microbiota composition in seedlings of domesticated wheat compared to wild wheat. Mbio 11 (6) 

Petters-Vandresen DAL, Rossi BJ, Groenewald JZ, Crous PW, Machado MA, Stukenbrock EH, Glienke C. 2020. Mating-type locus rearrangement leads to shift from homothallism to heterothallism in Citrus-associated Phyllosticta species. Fungal Genetics and Biology, 144, p.103444.

Feurtey A, Lorrain C, Croll D, Eschenbrenner C, Freitag M, Habig M, Haueisen J, Möller M, Schotanus K, Stukenbrock EH. 2020. Genome compartmentalization predates species divergence in the plant pathogen genus Zymoseptoria. BMC Genomics, In Press

Rangel LI, Spanner RE, Ebert MK, Pethybridge SJ, Stukenbrock EH, de Jonge R, Secor GA, Bolton MD. 2020. Cercospora beticola: The intoxicating lifestyle of the leaf spot pathogen of sugar beet. Mol. Plant Pathol. 21:1020–1041

Hassani, M.A., Özkurt, E., Franzenburg, S. and Stukenbrock, E.H., 2020. Ecological assembly processes of the bacterial and fungal microbiota of wild and domesticated wheat species. Phytobiome, 01-20-0001-SC

Gruner, K., Esser, T., Acevedo-Garcia, J., Freh, M., Habig, M., Strugala, R., Stukenbrock, E., Schaffrath, U. and Panstruga, R., 2020. Wheat mlo Mutants Show Allele-Specific Levels of Enhanced Susceptibility to the Hemibiotrophic Fungal Pathogen Magnaporthe oryzae pv. Triticum. Genes, In Press

Petre B, Lorrain C, Stukenbrock EH and Duplessis S. 2020. Host-specialized transcriptome of plant-associated organisms. Current Opinion in Plant Biology56, pp.81-88.

Fisher, MC, Gurr, SJ, Cuomo, CA, Blehert, DS, Jin, H, Stukenbrock, EH, Stajich, JE, Kahmann, R, Boone, C, Denning, DW and Gow, NA, 2020. Threats Posed by the Fungal Kingdom to Humans, Wildlife, and Agriculture. mBio11(3).

Dutheil J Y, Münch K, Schotanus K, Stukenbrock, EH, and Kahmann R. 2020. The insertion of a mitochondrial selfish element into the nuclear genome and its consequences. Ecology and Evolution. In Press

Potgieter L, Feurtey A, Dutheil JY, Stukenbrock EH. 2020. On Variant Discovery in Genomes of Fungal Plant Pathogens. Frontiers in Microbiology. 2020. p. 626.

de Vries, S., Stukenbrock, E.H. and Rose, L.E., 2020. Rapid evolution in plant–microbe interactions–an evolutionary genomics perspective. New Phytologist , 226: 1256-1262.

Seybold, H., Demetrowitsch, T., Hassani, M.A., Szymczak, S., Reim, E., Haueisen, J., Rühlemann, M., Franke, A., Schwarz, K. and Stukenbrock, E.H., 2020. Hemibiotrophic fungal pathogen induces systemic susceptibility and systemic shifts in wheat metabolome and microbiome composition.  Nature Communications, 11(1), pp.1-12.


P. Rausch, M. Rühlemann, B. Hermes, S. Doms, T. Dagan, K. Dierking, H. Domin, S. Fraune, J. von Frieling, U. H. Humeida, F.-A. Heinsen, M. Höppner, M. Jahn, C. Jaspers, K. A. B. Kissoyan, D. Langfeldt, A. Rehman, T. B. H. Reusch, T. Röder, R. A. Schmitz, H. Schulenburg, R. Soluch, F. Sommer, E. Stukenbrock, N. Weiland-Bräuer, P. Rosenstiel, A. Franke, T. Bosch, and J. F. Baines. 2019. Comparative analysis of amplicon and metagenomic sequencing methods reveals key features in the evolution of animal metaorganisms. Microbiome, 7(1), pp.1-19.

Habig, M. , Bahena‐Garrido, S. M., Barkmann, F. , Haueisen, J. and Stukenbrock, E. H. 2019. The transcription factor Zt107320 affects the dimorphic switch, growth and virulence of the fungal wheat pathogen Zymoseptoria tritici. Molecular Plant Pathology 21(1), pp.124-138.

Hassani MA, Özkurt E, Seybold H, Dagan T, Stukenbrock EH. 2019. Interactions and Coadaptation in Plant Metaorganisms. Annu Rev Phytopathol. 57, pp.483-503.

Richards JK, Stukenbrock EH, Carpenter J, Liu Z, Cowger C, Faris JD, Friesen TD. 2019. Local adaptation drives the diversification of effectors in the fungal wheat pathogen Parastagonospora nodorum in the United States. PLoS Genetics, 15(10).

Boynton PJ, Kowallik V, Landermann D, Stukenbrock EH. 2019. Quantifying the efficiency and biases of forest Saccharomyces sampling strategies. Yeast, 36(11), pp.657-668.

Soyer JL, Grandaubert J, Haueisen J, Schotanus K, Stukenbrock EH. 2019. In planta chromatin immunoprecipitation in Zymoseptoria tritici reveals chromatin-based regulation of putative effector gene expression. BioRxiv,

Möller M, Schotanus K, Soyer J, Haueisen J, Happ K, Stralucke M, Happel P, Smith KM, Connolly LR, Freitag M, Stukenbrock EH. 2019. Destabilization of chromosome structure by histone H3 lysine 27 methylation. PLoS genetics, 15(4), p.e1008093.

Grandaubert J, Dutheil JY, Stukenbrock EH. 2019. The genomic rate of adaptation in the fungal wheat pathogen Zymoseptoria tritici. Evolution Letters , 3(3), pp.299-312.


Miller, M., Rottschaefer, S., Persoons, A., Hirsch, C., Saunders, D., Stukenbrock, E. H., Kianian, S., & Figueroa, M. (2018). Genome architecture and virulence gene dynamics in oat crown rust populations . In: Phytopathology, 104–105. doi: 10.1094/PHYTO-108-10-S1.1.

Habig M, Kema G, Stukenbrock E. 2018. Meiotic drive of female-inherited supernumerary chromosomes in a pathogenic fungus. Elife 7:e40251 

Haueisen J, Moeller M, Eschenbrenner CJ, Grandaubert J, Seybold H, Adamiak H, Stukenbrock EH. 2018. Highly flexible infection programs in a fungal plant pathogen. Evolution and Ecology, 9(1): 275-294

Möller, M, Habig M, Freitag M and Stukenbrock EH. 2018. Extraordinary genome instability and widespread chromosome rearrangements during vegetative growth. Genetics, (2):517-529

Feurtey A and Stukenbrock EH. 2018. Interspecific Gene Exchange as a Driver of Adaptive Evolution in Fungi. 2018. Ann. Rev. Microbiol. 72, 377-398

Schirrmann MK, Zoller S, Croll D, Stukenbrock EH, Leuchtmann A and Fior S. 2018. Genome-wide signatures of selection in Epichloë reveal candidate genes for host specialization. Molecular Ecology (15):3070-3086

Stukenbrock EH and Dutheil JY. 2018. Comparison of fine-scale recombination maps in fungal plant pathogens reveals dynamic recombination landscapes and intragenic hotspots. Genetics 208.3: 1209-1229


Habig M, Quade J, Stukenbrock EH. 2017. Forward genetics approach reveals host-genotype dependent importance of accessory chromosomes in the fungal wheat pathogen Zymoseptoria tritici. mBio, 8(6), e01919-17

Möller, M and Stukenbrock EH. 2017. Evolution and genome architecture in fungal plant pathogens. Nature Reviews Microbiology: 15.12 (2017): 756


McDonald, BA and Stukenbrock, EH. 2016. Rapid emergence of pathogens in agro-ecosystems - global threats to agricultural sustainability and food security. Phil Trans R Soc B 371:20160026

Haueisen, J and Stukenbrock, EH. 2016. Life cycle specialization of filamentous pathogens—colonization and reproduction in plant tissues. Current opinion in microbiology, 32, pp.31-37.

Stukenbrock EH. The role of hybridization in the evolution and emergence of new fungal plant pathogens. 2016. Phytopathology 106.2: 104-112.


Alizadeh A, Javan-Nikkhah M, Zare R, Fotouhifar KB, Damm U, Stukenbrock EH. 2015 New records of Colletotrichum species for the mycobiota of Iran. Mycol Iran; 94–108.

Atghia O, Alizadeh A, Fotouhifar KB, Damm U, Stukenbrock EH, Javan-Nikkhah M. 2015. First Report of Colletotrichum fructicola as the causal agent of Anthracnose on Common Bean and Cowpea. Mycol Iran; 135–136.

Schotanus K, Soyer J, Connolly L, Grandabuert J, Happel P, Smith K, Freitag M, Stukenbrock EH. 2015. Histone modifications rather than the novel regional centromeres of Zymoseptoria tritici distinguish core and accessory chromosomes. Epigenetics and Chromatin, 8:41

Poppe S, Dorsheimer L, Happel P and Stukenbrock EH. 2015. Rapidly Evolving Genes are Key Players in Host Specialization and Virulence of the Fungal Wheat Pathogen Zymoseptoria tritici (Mycosphaerella graminicola). PLoS Pathog 11(7): e1005055.

Grandaubert J, Bhattacharyya A. and Stukenbrock EH. 2015. RNA-seq based gene annotation and comparative genomics of four fungal grass pathogens in the genus Zymoseptoria identify novel orphan genes and species-specific invasions of transposable elements. G3: g3.115.017731

Soyer J, Möller M, Schotanus K, Connolly LR, Galazka JM, Freitag M and Stukenbrock EH. 2015. Chromatin analyses of Zymoseptoria tritici: methods for chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq). Fungal Genet Biol p1087-1845(15)00042-0.


Kellner R, Bhattacharyya A, Poppe S, Hsu TY, Brem RB, Stukenbrock EH. 2014. Transcriptome sequencing at early stage infection of the wheat pathogen Z. tritici reveals chromosomal differences in transcription patterns and host specific gene expression. Genome Biol and Evol. 6 (6), S. 1353–1365

BrunnerPC, Torriani SFF, Croll D, Stukenbrock EH, McDonald BA. 2014. Hitchhiking selection is driving intron gain in the fungal plant pathogen Zymoseptoria tritici. Mol Biol Evol.31 (7), S. 1741–1749. DOI: 10.1093/molbev/msu123

Dutheil JY, Gaillard S, Stukenbrock, EH. 2014. MafFilter: a highly flexible and extensible multiple genome alignment processor. BMC Genomics 15.1: 53

Stukenbrock EH, Croll D. 2014. The evolving fungal genome. Fungal Biol. Rev. (invited review) Fungal Biology Reviews 28 (1), S. 1–12.


Stukenbrock EH 2013. Evolution, Selection and isolation: A genomic view of speciation in fungal plant pathogens. New Phytologist 199(4): 895–907. (invited Tansley review)

Brunner PC, Torriani SFF, Croll D, Stukenbrock EH, McDonald BA. 2013. Coevolution and life cycle specialization of plant cell wall degrading enzymes in a hemibiotrophic pathogen. Mol Biol Evol 30(6), 1337-1347 


Hjortshøj RL, Ravnshøj AR,  Nyman M, Orabi J, Backes G, Pinnschmidt H, Havis N, Stougaard J, Stukenbrock EH. 2012. High levels of genetic diversity and evidence of clonal reproduction in the barley pathogen Ramularia collo-cygni. Eur J Plant Pathol. doi:10.1007/s10658-012-0137-8

Stukenbrock EH and Bataillon T. 2012. A population genomics perspective on the emergence and adaptation of  new plant pathogens in agro-ecosystems. PLoS Pathog 8(9): e1002893. doi:10.1371/journal.ppat.1002893

Stukenbrock EH, Christiansen FB, Hansen TH, Dutheil JY, Schierup MH. 2012. Fusion of two divergent fungal individuals led to the recent emergence of a new widespread pathogen species. Proc. Natl. Acad. Sci. USA. doi: 10.1073/pnas.1201403109

Stukenbrock EH, Quaedvlieg W, Javan-Nikah M, Zala M, Crous P, McDonald P. 2012. Zymoseptoria ardabilia and Z. pseudotritici, two progenitor species of the septoria tritici leaf blotch fungus Z. tritici (synonym: Mycosphaerella graminicola). Mycologia doi:10.3852/11-374

Rybak K, Ferguson-Hunt M, Waters ODC, Stanley W, Bond C, Stukenbrock EH, Friesen T, Faris J, McDonald B and Oliver. RP. Quantitative variation in effector activity of ToxA isoforms from Stagonospora nodorum and Pyrenophora tritici-repentis. 2012. Mol Plant Microb Interact. 25(4):515-22.


Torriani SFF, Stukenbrock EH, Brunner PC, McDonald BA, Croll D (2011) Evidence for extensive recent intron transposition in closely related fungi. Current Biology, vol. 21(6) 2017–2022

Stukenbrock EH, Bataillon T, Duthei JY, Hansen TT, Li R, Zala M, McDonald BA, Wang J, Schierup MH (2011). The making of a new pathogen: Insights from comparative population genomics of the domesticated wheat pathogen Mycosphaerella graminicola andits wild sister species. Genome Research doi: 10.1101/gr.118851.110 (featured in Nature Reviews Microbiology Reid AJ (2012) Adapting to domesticity. Nat Rev Micro 10: 163-163).

Schirawski J, Mannhaupt G, Karin M, Brefort T, Schipper K, Doehlemann G, Di Stasio M, Rössel NM-M, Artemio , Pester D, Müller O, Winterberg B, Meyer E, Münsterkötter M, Wong P, Walter M, Stukenbrock EH, Güldener U,  Kahmann R. (2011). Pathogenicity determinants in smut fungi revealed by genome comparison. Science Vol. 330 no. 6010 pp. 1546-1548


Stukenbrock EH, Jørgensen FG, Zala M, Hansen TT, McDonald BA,  Schierup MH. (2010). Whole genome and chromosome evolution associated with host adaptation and speciation of the wheat pathogen Mycosphaerella graminicola. PLoS Genet. 6(12): e1001189. doi:10.1371/journal.pgen.1001189


Stukenbrock EH, McDonald BA. 2009. Population genetics of fungal elicitors involved in gene-for-gene interactions. Molecular Plant Microbe Interactions. 22:371-380


Stukenbrock EH, McDonald BA. 2008. The evolutionary emergence of plant pathogens in Agroecosystems. Annual Review of Phytopathology . 46:75-100


Stukenbrock EH, McDonald BA. 2007. Geographic variation and positive diversifying selection in the host specific toxin SnToxA. Molecular Plant Pathology 8: 321-332

Stukenbrock EH, Banke S, Javan-Nikkhah M, McDonald BA. 2007. Origin and domestication of the fungal wheat pathogen Mycosphaerella graminicola via sympatric speciation. Molecular Biology and Evolution 24: 398-411


Friesen TL, Stukenbrock EH, Liu Z, Meinhardt S, Ling H, Faris JF, Rasmussen JB, Solomon PS, McDonald BA, Oliver RP. 2006. Emergence of a new disease as a result of interspecific virulence gene transfer. Nature Genetics 38: 953-956

Stukenbrock EH, Banke S, McDonald BA. 2006. Global migration patterns in the fungal wheat pathogen Phaeosphaeria nodorumMolecular Ecology . 14: 743-752


Stukenbrock EH, Banke S, Zala M, McDonald BA, Oliver RP. 2005. Isolation and characterization of EST-derived microsatellite loci from the fungal wheat pathogen Phaeosphaeria nodorum. Molecular Ecology Notes 5: 931-933

Stukenbrock EH, Rosendahl S. 2005. Lack of host preferences among the dominant arbuscular mycorrhizal fungi in undisturbed vegetation. Mycorrhiza 15: 497-503


Stukenbrock EH, Rosendahl S. 2004. Clonal diversity and population genetic structure of arbuscular mycorrhizal fungi (Glomus spp.) studied by multilocus genotyping of single spores. Molecular Ecology 14: 743-752

Stukenbrock EH, Rosendahl S. 2004. Development of multiple co-dominant genetic markes from single spores of arbuscular mycorrhizal fungi by nested multiplex PCR. Fungal Genetics and Biology 42:73-80

Rosendahl S, Stukenbrock EH. 2004. Community structure of arbuscular mycorrhizal fungi in undisturbed vegetation revealed by analyses of LSU rDNA sequences. Molecular Ecology 13: 3179-3186

Books, Book Chapters and Commentaries:

Haueisen, J., Lorrain, C. and Stukenbrock, E.H., 2020. Molecular interactions of microbes and the plant phyllosphere: The phyllosphere-microbiome is shaped by the interpay of secreted microbial molecules and the plant immune system. In Cellular Dialogues in the Holobiont (pp. 267-285). CRC Press

Seybold H, Haueisen J, Stukenbrock EH (2019). Können wir unsere Nutzpflanzen nachhaltig von Krankheiten schützen? BioSpektrum. BIOspektrum 25:254–257

Habig M, Stukenbrock EH (2019). Origin, function and transmission of accessory chromosomes, Ed. L. Glass and K. Schippert, in The Mycota. Springer. In Press

Heitman J, Howlett BJ, Crous PW, Stukenbrock EH, James TY, Gow NAR  (ed). 2018. The Fungal Kingdom. ASM Press, Washington, DC.

Stukenbrock EH. 2016. Hybridization speeds up the emergence and evolution of a new pathogen species. Nature genetics 48.2: 113.

Stukenbrock EH. (2014). Advances in Botanical Research: Genomics of Plant-Related Fungi, Speciation genomics of fungal plant pathogens. Ed. Martin, F. Elsevier, pp 397-423.

Stukenbrock EH and Dutheil JY (2012). Methods in Molecular Biology, Comparing fungal genomes: Insight into functional and evolutionary processes. Human Press, Springer. 835:531-48.

© Stukenbrock Lab 2018-2020