Bakkeren Molecular Plant Pathology Lab



Cuomo, C, Bakkeren, G., Khalil, H.B., Panwar, V.,.Joly, D., Linning, R., Sakthikumar, S., Song, X., Adiconis, X., Fan, L., Goldberg, J. M., Levin, J.Z., Young, S., Zeng, Q., Anikster, Y., Bruce, M., Wang, M., Yin, C., McCallum, B., Szabo, L.J., Hulbert, S., Chen, X. and Fellers, J.P. 2017. Comparative analysis highlights variable genome content of wheat rusts and divergence of the mating loci. G3: Genes|Genomes|Genetics. 7(2): 361-376. DOI:10.1534/g3.116.032797. [Abstract] [PDF]


Panwar, V., McCallum, B., Jordan, M., Loewen, M., Fobert, P., McCartney, C. and Bakkeren, G. 2016. RNA silencing approaches for identifying pathogenicity and virulence elements towards engineering crop resistance to plant pathogenic fungi. In: CABI Reviews. Perspectives in Agriculture, Veterinary Science, Nutrition and Natural Resources. 11(027). DOI:10.1079/PAVSNNR201611027. [Abstract] [PDF]


Bakkeren, G., Joly, D. L. and Duplessis, S. 2016. Genomics research on non-model plant pathogens: delivering novel insights into rust fungus biology. Front. Plant Sci. 5: 216. Editorial to Frontiers E-book (, covering 14 published papers for which these 3 authors were co-editors. DOI:10.3389/fpls.2016.00216.


Cervantes-Chávez, J. A., Valdés-Santiago, L., Bakkeren, G., Hurtado-Santiago, E., León-Ramírez, C. G., Esquivel-Naranjo, E. U., Landeros-Jaime, F., Rodríguez-Aza, Y., Ruiz-Herrera, J. 2016. Trehalose is required for stress resistance and virulence of the Basidiomycota plant pathogen Ustilago maydis. Microbiology. 162(6): 1009-1022. DOI:10.1099/mic.0.000287. [Abstract]


McCallum, B. D., Hiebert, C. W., Cloutier, S., Bakkeren, G., Rosa, S. B., Humphreys, G., Marais, G. F., McCartney, C. A., Panwar, V., Rampitch, C., Saville, B. J., Wang, X. 2016. A review of wheat leaf rust research and the development of resistant cultivars in Canada. Can. J. Plant Pathol. 38(1), 1-18. DOI:10.1080/07060661.2016.1145598. [Abstract] [PDF]


Ali, S. and Bakkeren, G. 2015. Conversion of BAC clones into binary BAC (BIBAC) vectors and their delivery into basidiomycete fungal cells using Agrobacterium tumefaciens. Bacterial Artificial Chromosomes. Ed. K. Narayanan. Clifton, N.J., Springer New York. Chapter 9: 199-215. [Abstract] [PDF]


Panwar, V., McCallum, B. and Bakkeren, G. 2015. A functional genomics method for assaying gene function in phytopathogenic fungi through host-induced gene silencing mediated by Agroinfiltration. In: Plant Gene Silencing: Methods and Protocols. Eds. Mysore, K. S. and Muthappa, S-K. Springer New York. Chapter 13: 179-189. DOI:10.1007/978-1-4939-2453-0. [Abstract] [PDF]


Ali, S. and Bakkeren, G. 2015. Conversion of BAC clones into binary BAC (BIBAC) vectors and their delivery into basidiomycete fungal cells using Agrobacterium tumefaciens. Bacterial Artificial Chromosomes. Ed. K. Narayanan. Clifton, N.J., Springer New York. 1227: 199-215. DOI:10.1007/978-1-4939-1652-8_9


Segovia, V., Bruce, M., Shoup Rupp, J. L., Huang, L., Bakkeren, G., Trick, H. N. and Fellers, J. P. 2016. Two small secreted proteins from Puccinia triticina induce reduction of ß-glucoronidase transient expression in wheat isolines containing Lr9, Lr24, and Lr26. Can. J. Plant Pathol. 38(1): 91-102. DOI:10.1080/07060661.2016.1150884. [Abstract] [PDF]


Wang, X.,  McCallum, B. D., Fetch, T., Bakkeren, G. and Saville, B. 2015. Sr36- and Sr5-mediated resistance response to Puccinia graminis f. sp. tritici is associated with callose deposition in wheat guard cells, Phytopathology, 105(6): 728-737. DOI:10.1094/PHYTO-08-14-0213-R. [Abstract] [PDF]


Bakkeren, G. and B. Valent. 2014. Do pathogen effectors play peek-a-boo? Front. Plant Sci. 5:638. DOI:10.3389/fpls.2014.00638


Ali, S., Laurie, J.D., Linning, R., Cervantes-Chávez, J.A., Gaudet, D. and Bakkeren, G. 2014. An immunity-triggering effector from the barley smut fungus Ustilago hordei resides in an Ustilaginaceae-specific cluster bearing signs of transposable element-assisted evolution. PLoS Pathog 10: e1004223 [Abstract] [PDF] [Supplemental]


Bruce, M., K. A. Neugebauer, D. L. Joly, P. Migeon, C. A. Cuomo, S. Wang, E. Akhunov, G. Bakkeren, J. A. Kolmer and J. P. Fellers 2014. Using transcription of six Puccinia triticina races to identify the effective secretome during infection of wheat. Front. Plant Sci. 4, 520. doi: 10.3389/fpls.2013.00520 [Abstract] [PDF]


Panwar, V., McCallum, B. and Bakkeren, G. 2014. A functional genomics method for assaying gene function in phytopathogenic fungi through host-induced gene silencing mediated by Agroinfiltration. In: Plant Gene Silencing: Methods in Molecular Biology. Eds. Mysore, K. S. and Muthappa, S-K. Springer New York. Pp.179-189. DOI:10.1007/978-1-4939-2453-0_13 [PDF]


Duplessis, S., Bakkeren, G. and Hamelin, R. Advancing knowledge on biology of rust fungi through genomics. 2014. Chapter 6. In: Advances in Botanical research. Vol. 70. Ed. Francis Martin. Elsevier. Pp. 173-209. DOI:org/10.1016/B978-0-12-397940-7.00006-9 [PDF]


Lefebvre, F., Joly, D.L., Labbé, C., Teichmann, B., Linning, R., Belzile, F., Bakkeren, G. and Bélanger, R.R. 2013. The transition from a phytopathogenic smut ancestor to an anamorphic biocontrol agent deciphered by comparative whole genome analysis. Plant Cell 25, 1946-1959. Open Access. [Abstract] [PDF]


Panwar, V., McCallum, B. and Bakkeren, G. 2013. Host-generated trans-specific RNAi of wheat leaf rust fungus Puccinia triticina pathogenicity genes induced by the Barley stripe mosaic virus. Plant Mol Biol 81, 595-608 [Abstract] [PDF]


Panwar, V., McCallum, B. and Bakkeren, G. 2013. Endogenous silencing of Puccinia triticina pathogenicity genes through in planta-expressed sequences leads to suppression of rust diseases on wheat. Plant J 73, 521-532 [Abstract] [PDF]


Fellers, J. P., Soltani, B. M., Bruce, M., Linning, R., Cuomo, C. A., Szabo, L. and Bakkeren, G. 2013. Conserved loci of leaf and stem rust share synteny interrupted by lineage-specific influx of repeat elements. BMC Genomics 14:60 [Abstract] [PDF]


Wang, X., McCallum, B.D., Fetch, T., Bakkeren, G. Marais, G.F. and Saville, B.J. 2013. Comparative microscopic and molecular analysis of Thatcher near-isogenic lines with wheat leaf rust resistance genes Lr2a, Lr3, LrB or Lr9 upon challenge with different Puccinia triticina races. Plant Pathology 62, 698-707 [Abstract] [PDF]


Laurie, J. D., Linning, R., Wong, P. and Bakkeren G. 2013. Do TE activity and counteracting genome defenses, RNAi and methylation, shape the sex lives of smut fungi? Plant Signal. Behavior 8, e23853 [Abstract] [PDF]


Laurie, J. D., Ali, S. Linning, R., Mannhaupt, G., Wong, P., Güldener, U., Münsterkötter, M., Moore, R., Kahmann, R., Bakkeren, G., and Schirawski, J. 2012. Genome comparison of barley and maize smut fungi reveals targeted loss of RNA silencing components and species-specific presence of TEs. Plant Cell 24, 1733-1745 [Abstract] [PDF] [PDF Supplemental]


Bakkeren, G. Kruzel, E.K., and Hull, C.M. 2012. Sex and virulence in basidiomycete pathogens. In: Evolution of virulence in eukaryotic microbes. Eds. L. David Sibley, Barbara J. Howlett, and Joseph Heitman. Wiley-Blackwell, Hoboken, New Jersey. ISBN 978-1-118-03818-5. Pp. 437-460 [Abstract] [PDF]


Ali, S., and Bakkeren, G. 2012. Fungal and oomycete effectors; strategies to subdue a host. Can. J. Plant Pathol. 33, 425-446 [Abstract] [PDF]


Xu, J., Linning, R., Fellers, J., Dickinson, M., Zhu, W., Antonov, I., Joly, D.L., Donaldson, M.E., Eilam, T., Anikster, Y., Banks, T., Munro, S., Mayo, M., Wynhoven, B., Ali, J., Moore, R., McCallum, B., Borodovsky, M., Saville, B. and Bakkeren, G. 2011. Gene discovery in EST sequences from the wheat leaf rust fungus Puccinia triticina sexual spores, asexual spores and haustoria, compared to other rust and corn smut fungi. BMC Genomics 12:161 [Abstract] [PDF]


Song, X., Rampitsch, C., Soltani, B., Mauthe, W., Linning, R., Banks, T., McCallum, B. and Bakkeren, G. 2011. Proteome analysis of wheat leaf rust fungus, Puccinia triticina, infection structures enriched for haustoria. Proteomics 11, 944-963 [Abstract] [PDF]

Cervantes-Chávez, J. A., Ali, S. and Bakkeren, G. 2011. Response to environmental stresses, cell wall integrity and virulence are orchestrated through the calcineurin pathway in Ustilago hordei. Mol Plant-Microbe Interact 24, 219-232 [Abstract] [PDF]


Ali, S. and Bakkeren, G. 2011. Introduction of large DNA inserts into the barley pathogenic fungus, Ustilago hordei, via recombined binary BAC vectors and Agrobacterium-mediated transformation. Curr Genet 57(1), 63-73 [Abstract] [PDF]


Gaudet, D. A., Wang, Y., Penniket, C., Frick, M., Lu, Z-X., Bakkeren, G. and Laroche, A. 2010. Morphological and molecular analyses of host and nonhost interactions involving barley and wheat and the covered smut pathogen Ustilago hordei. Mol Plant-Microbe Interact 23, 1619-1634 [Abstract] [PDF]


Wang, X., Bakkeren, G. And McCallum, B. 2010. Virulence and molecular polymorphisms of the wheat leaf rust fungus Puccinia triticina in Canada from 1997 to 2007. Botany 88, 575-589 [Abstract] [PDF]


Wang, X., Mulock, B., Bakkeren, G. and McCallum, B. 2010. Development of EST-derived simple sequence repeat markers for the wheat leaf rust fungus, Puccinia triticina Eriks. Can J Plant Pathol 32, 98-107 [Abstract] [PDF]


Laurie, J. D., Linning, R. and Bakkeren, G. 2008. Hallmarks of RNA silencing are found in the smut fungus Ustilago hordei but not in its close relative Ustilago maydis. Curr Genetics 53, 49-58. DOI:10.1007/s00294-007-0165-7 [Abstract] [PDF]


Bakkeren, G., Kämper, J. and Schirawski, J. 2008. Sex in smut fungi: structure, function and evolution of mating type complexes. Review; special Fungal Genome issue. Fungal Genetics & Biology 45, S15-S21. [Abstract] [PDF]


Grewal, T. S., Rossnagel, B. G., Bakkeren, G. and Scoles, G. J. 2008. Identification of barley covered smut resistance genes and mapping of Ruh1 using Ustilago hordei strains with defined avirulence genes. Can J Plant Pathol. 30(2), 277-284. [Abstract] [PDF]


Hu, G. G., Linning, R., McCallum, B., Banks, T., Cloutier, S., Butterfield, Y., Liu, J., Kirkpatrick, R., Stott, J., Yang, G., Smailus, D., Jones, S., Marra, M., Schein, J. and Bakkeren, G. (2007). Generation of a wheat leaf rust, Puccinia triticina, EST database from stage-specific cDNA libraries. Mol Plant Pathol, 8 (4), 451-467. [Abstract] [PDF] [Supplemental]


Hu, G., Kamp, A., Linning, R., Naik, S. and Bakkeren, G. (2007) Complementation of Ustilago maydis MAPK mutants by a Wheat Leaf Rust, Puccinia triticin, homolog: potential for functional analyses of rust genes. Mol. Plant-Microbe Interact. 20, 637-647. [Abstract] [PDF]


Bakkeren, G. and Kronstad, J. W. (2007) Bipolar and tetrapolar mating systems in the Ustilaginales. In: Sex in fungi:  molecular determination and evolutionary Implications, Eds. J. Heitman, J. W. Kronstad, J. Taylor, L. Casselton. American Society for Microbiology (ASM), pp. 389-404. [Abstract] [PDF]


Bakkeren, G., Jiang, G., Warren, R., Butterfield, Y., Shin, H., Chiu, R., Schein, J., Lee, N., Kupfer, D., Roe, B., Jones, S., Marra, M., Kronstad, J. W. (2006) Physical mapping of the genome of the fungal pathogen Ustilago hordei and annotation of the 500 kb MAT-1 sequence. Fungal Genet Biol, 43, 655-666. [Abstract] [PDF] [Supplemental]


Naik, S., Hampson, C., Gasic, K., Bakkeren, G. and Korban, S. S. (2006) Development and linkage mapping of E-STS and RGA markers for functional gene homologues in apple. Genome, 49, 959-968. [Abstract] [PDF]


Webb, C. A., Szabo, L. J., Bakkeren, G., Garry, C., Staples, R. C., Eversmeyer, M. and Fellers, J. P. (2006) Transient Expression and insertional mutagenesis of Puccinia triticina using biolistics. Funct Int Genomics, 6, 250-260. [Abstract] [PDF]


Horton, J. S., Bakkeren, G., Klosterman, S. J., Garcia-Pedrajas, M. and Gold, S. E. (2005) Genetics of morphogenesis in Basidiomycetes. In: Applied Mycology and Biotechnology. Vol. 5 & 6. ‘Genetics, Genomics and Bioinformatics’. (Ed. D. K. Arora) Elsevier, Dordrecht. pp 353-422. [Abstract] [PDF]


Zhou, L., Kappel, F., Wiersma, P.A., Hampson, C.R., and Bakkeren, G. (2005), "Genetic analysis and DNA fingerprinting of sweet cherry cultivars and selections using amplified fragment length polymorphisms (AFLP).", Acta Horticulturae (ISHS), 667, pp. 37-44.


Linning, R., Lin, D., Lee, N., Abdennadher, M., Gaudet, D., Thomas, P., Mills, D., Kronstad, J. W. and Bakkeren, G. (2004) Marker-based cloning of the region containing the UhAvr1 avirulence gene from the basidiomycete barley pathogen Ustilago hordei. Genetics 166, 99 - 111. [Abstract] [PDF]


Bakkeren, G. and Gold, S. (2004) The path in fungal plant pathogenicity; many opportunities to outwit the intruders? Review. In: Genetic Engineering, Principles & Methods, Vol. 26. (Ed. J. K. Setlow), Plenum Press, New York., pp. 175 - 223. [Abstract] [PDF]


Braithwaite, K. S., Bakkeren, G., Croft, B. J., and Brumbley, S. M. (2004) Genetic variation in a worldwide collection of the sugarcane smut fungus Ustilago scitaminea. Proc Aust Soc Sugar Cane Technol, Vol. 26, 48-56. [Abstract] [PDF]


Hu, G.G., Linning, R., and Bakkeren, G. (2003) Ultrastructural comparison of a compatible and incompatible interaction triggered by the presence of an avirulence gene during early infection of the smut fungus, Ustilago hordei, in barley. Physiological Mol Plant Pathol, 62, 155-166. [Abstract] [PDF]


Menzies, J.G., Bakkeren, G., Matheson, F., Procunier, J. D. and Wood, S. (2003) The use of inter-simple sequence repeats (ISSRs) and amplified fragment length polymorphisms (AFLPs) to analyze genetic relationships among species of Ustilago. Phytopathology 93, 167-175. [Abstract] [PDF]


Hu, G.G., Linning, R., and Bakkeren, G. (2002) Sporidial mating and infection process of the smut fungus, Ustilago hordei, in susceptible barley. Can J Bot, 80, 1103-1114. [Abstract] [PDF]


Zhou, L., Kappel, F., Hampson, C., Wiersma, P. A. and Bakkeren, G. (2002) Genetic analysis and discrimination of sweet cherry cultivars using amplified fragment length polymorphism fingerprints. J Amer Soc Hort Sci, 127, 786-792. [Abstract] [PDF]


Zhou, L., Kappel, F., MacDonald, R., Bakkeren, G., Hampson C. and Wiersma, P. (2002) Determination of S-genotype and self-fertility of sweet cherry in Summerland advanced selections. J Amer Pom Soc 56(3), 173-179. [PDF]


Bakkeren, G., Kronstad, J. W. and Lévesque, C. A. (2000) Comparison of AFLP fingerprints and ITS sequences as phylogenetic markers in Ustilaginomycetes. Mycologia, 92, 510-521. [Abstract] [PDF]


Lee, N., Bakkeren, G., Wong, K., Sherwood, J. E. and Kronstad, J. W. (1999) The mating type and pathogenicity locus of the fungus Ustilago hordei spans a 500-kb region. Proc Natl Acad Sci USA, 96, 15026-15031. [Abstract] [PDF]


Bakkeren, G. and Kronstad, J. W. (1996) The pheromone cell signalling components of the Ustilago a mating-type loci determine intercompatibility between species. Genetics, 143, 1601-1613. [Abstract] [PDF]


Bakkeren, G. and Kronstad, J. W. (1994) Linkage of Mating-Type Loci Distinguishes Bipolar from Tetrapolar Mating in Basidiomycetous Smut Fungi. Proc Natl Acad Sci USA, 91, 7085-7089. [Abstract] [PDF]


Gold, S. E., Bakkeren, G., Davies, J. E. and Kronstad, J. W. (1994) Three selectable markers for transformation of Ustilago maydis. Gene, 142, 225-230. [Abstract] [PDF]


Bakkeren, G. and Kronstad, J.W. (1993) Conservation of the b Mating-Type Gene Complex among Bipolar and Tetrapolar Smut Fungi. Plant Cell, 5, 123-136. [Abstract] [PDF]


Bakkeren, G., Gibbard, B., Yee, A., Froeliger, E., Leong, S. and Kronstad, J. (1992) The a and b loci of Ustilago maydis hybridize with DNA sequences from other smut fungi. Mol Plant-Microbe Interact , 5, 347-355. [Abstract] [PDF]


Mayerhofer, R., Koncz-Kalman, Z., Nawrath, Ch., Bakkeren, G., Crameri, A., Angelis, K., Redei, G., Schell, J., Hohn, B. and Koncz, C. (1991) T-DNA integration: a mode of illegitimate recombination in plants. EMBO J, 10, 697-704. [Abstract] [PDF]


Bakkeren, G., Koukolíková-Nicola, Z., Grimsley, N. and Hohn, B. (1989) Recovery of Agrobacterium tumefaciens T-DNA molecules from whole plants early after transfer. Cell, 57, 847-857. [Abstract] [PDF]


Hohn, B., Koukolíková-Nicola, Z., Bakkeren, G. and Grimsley, N. (1989) Agrobacterium-mediated gene transfer to monocots and dicots. Genome, 31, 987-993. [Abstract] [PDF]


Cornelissen, A.W.C.A., Bakkeren, G.A.M., Barry, J.D., Michels, P.A.M. and Borst, P. (1985) Characteristics of Trypanosome variant antigen genes active in the tsetse fly. Nucl Acid Res, 13, 4661-4676. [Abstract] [PDF]


Schetgens, T.M.P., Bakkeren, G., van Dun, C., Hontelez, J.G.J., van den Bos, R.C. and van Kammen, A. (1984) Molecular cloning and functional characterization of Rhizobium leguminosarum structural nif -genes by site-directed transposon mutagenesis and expression in E.coli minicells. J Molec Appl Gen, 2, 406-421. [Abstract]



Chapters in conference proceedings:

Bakkeren, G., Song, X., Panwar, V., Linning, R., Wang, X., Rampitsch, C., McCallum, B., Fellers, J., and Saville, B. 2012. Functional genomic approaches in cereal rusts. Can J Plant Pathol. 34. 3-12. (Symposium “Contributions of Genomics to Plant Pathology” at the Joint Meeting of the Canadian Phytopathological Society and Pacific Division of the American Phytopathological Society, University of British Columbia, Vancouver, BC, June 20-23, 2010) [Abstract] [PDF]


Kronstad, J., Gold, S., Yee, A., Laity, C., Bakkeren, G., Duncan, G., Barrett, K., Giasson, L., Campbell, R. and Athwal, G. (1995) Control of filamentous growth by mating and cyclic-AMP in Ustilago. Proceedings of the 5th International Mycology Congress, Can J Bot, 73, 258-265. [Abstract] [PDF]


Kronstad, J., Yee, A., Bakkeren, G., Gold, S., Barrett, K. and Giasson, L. (1993) The genetics of dimorphism in the smut fungi. In: Advances in Molecular Genetics of Plant-Microbe Interactions, Vol.2, E.W. Nester and D.P.S. Verma, eds (Dordrecht, Kluwer), pp. 325-333. [Abstract] [PDF]


Hohn, B., Koukolíková-Nicola, Z., Dürrenberger, F., Bakkeren, G. and Koncz, C. (1991) The T-DNA on its way from Agrobacterium tumefaciens to the plant. In: Advances in Molecular Genetics of Plant-Microbe Interactions, Vol.1, H. Hennecke and D.P.S. Verma, eds. (Dordrecht, Kluwer), pp. 19-27.


Bakkeren, G., Gal, S. and Hohn, B. (1990) Involvement of Agrobacterium tumefaciens Virulence E and C proteins in T-DNA transfer. In: Proceedings of the 6th International Symposium on Genetics of Industrial Microorganisms, Vol. II., H. Heslot, J. Davies, J. Florent, L. Bobichon, G. Durand, L. Penasse, eds (Strassbourg, Société Francaise de Microbiologie), pp. 809-817.


Hohn, B., Gietl, C., Dürrenberger, F., Bakkeren, G., Grimsley, N. and Koukolíková-Nicola, Z. (1988) The mechanism of T-DNA transfer from Agrobacterium to dicotyledonous and monocotyledonous plants. In: Molecular Genetics of Plant-Microbe Interactions 1988., R. Palacios and D.P.S. Verma, eds (St.Paul, Minnesota, APS press), pp. 289-290.


Schetgens, T. M. P., Bakkeren, G., van Dun, C., Hontelez, J. G. J., van Kammen, A. and van den Bos, R. C. 1984. Identification and analysis of the expression of Rhizobium leguminosarum presymbiotic genes. Advances in Agricultural Biotechnology 4(4): 699


Van den Bos, R.C, T.M.P. Schetgens, J.G.J. Hontelez, G. Bakkeren, C. van Dun, . 1983. Expression of nodule specific genes in both partners in the Rhizobium legume symbiosis. Endocytobiology, Vol. 2: Intracellular space as oligogenetic ecosystem: proceedings 2nd International colloquium on endocytobiology, Tübingen, Germany, April 10-15, Eds.: Hainfried E.A. Schenk, Werner Schwemmler, Walter de Gruyter & Co., Berlin - New York, ISBN 3110086603



Ph.D. thesis, University of Basel, Switzerland.

Bakkeren, G. (1989) An analysis of interkingdom movement of genetic information by rescue of Agrobacterium tumefaciens T-DNA molecules from plants. [Abstract]