Publications

Commentaries and Book Chapters

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.

 

Peer Reviewed Publications:

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. New records of Colletotrichum species for the mycobiota of Iran. Mycol Iran. 2015; 94–108.

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

Brunner PC, 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 and its 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 nodorum. Molecular 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