Publications

In Press

• Ojeda, D.I., Dhillon, B., Tsui, C.K.M. and Hamelin, R.C. SNP discovery in Leptographium longiclavatum, a mountain pine beetle-associated symbiotic fungus, using whole-genome resequencing. Molecular Ecology Resources (in press)

2013

• Porth, Ilga, Jaroslav Klapste, Athena D. McKown, Jon La Mantia, Richard C. Hamelin, Oleksandr Skyba, Faride Unda et al. 2013. Extensive functional pleiotropy of REVOLUTA substantiated through forward genetics. Plant physiology: pp. 113.228783.
• La Mantia, J., Klápště, J., El-Kassaby, Y.A., Azam, S., Guy, R.D. Douglas, C.J., Mansfield, S.D., and Hamelin, R.C. Temporal and expression validation of SNPs associated with poplar leaf rust resistance. PLoS-One 8:e78423
• Winder, R.S., J. Lamarche, C.P. Constabel, and R.C.  Hamelin. 2013. The effects of high-tannin leaf litter from transgenic poplars on microbial communities in microcosm soils. Frontiers in Microbiology 4 : 290.
• Tsui, C. K-M., DiGuistini, S. Wang, Y. Feau, N., Dhillon, Braham, Bohlmann, J. and Hamelin, R.C. 2013. Unequal Recombination and Evolution of the Mating-Type (MAT) Loci in the Pathogenic Fungus Grosmannia clavigera and Relatives. G3: Genes| Genomes| Genetics 3: 465-480.
• Boutigny, A.-L., Guinet, C., Vialle, A., Hamelin, R.C., Andrieux, A., Frey, P., Husson, C., and Ioos, R. 2013. Optimization of a real-time PCR assay for the detection of the quarantine pathogen Melampsora medusae f. sp. deltoidae. Fungal Biology (available on-line, May 2013)
• Boutigny, A. L, Guinet, C., Vialle, A. Hamelin, R.C., Frey, P., and Ioos, R. 2013. A sensitive real-time PCR assay for the detection of the two Melampsora medusae formae speciales on infected poplar leaves. European Journal of Plant Pathology 1-9.

2012

• Ohm, R.A., Feau, N., Henrissat, B., Schoch, C.L., Horwitz, B.A., Barry, K.W., Hamelin, R.C. and others. 2012. Diverse Lifestyles and Strategies of Plant Pathogenesis Encoded in the Genomes of Eighteen Dothideomycetes Fungi. PLoS Pathogen 8: e1003037 EP
• de Wit PJGM, van der Burgt A, Ökmen B, Stergiopoulos I, Abd-Elsalam KA, Aerts AL, Bahkali AH, Beenen HG, Chettri P, Cox MP, Datema E, de Vries RP, Dhillon B, Ganley AR, Griffiths SA, Guo Y, Hamelin RC, Henrissat B, Kabir MS, Jashni MK, Kema G, Klaubauf S, Lapidus A, Levasseur A, Lindquist E, Mehrabi R, Ohm RA, Owen TJ, Salamov A, Schwelm A, et al. 2012. The Genomes of the Fungal Plant Pathogens Cladosporium fulvum and Dothistroma septosporum Reveal Adaptation to Different Hosts and Lifestyles But Also Signatures of Common Ancestry. PLoS Genet, 8:e1003088.
• Conrad L. Schoch, Keith A. Seifert, Sabine Huhndorf, Vincent Robert, John L. Spouge, C. André Levesque, Wen Chen, Hamelin, R.C. and Fungal Barcoding Consortium. 2012. Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi. Proceedings of the National Academy of Sciences of the United States of America 109 (16) 6241-6246
• Vialle, A., Feau, N., Frey, P., Bernier, L. and Hamelin, R. C. 2012. Phylogenetic species recognition reveals host speciation among poplar rust fungi. Molecular Phylogeny and Evolution: 66:628–644
• Hamelin, R. C. 2012. Contributions of genomics to forest pathology. Canadian Journal of Plant Pathology, 34(1), 20–28
• Hacquard, S., Joly, D.L., Lin, Y.C., Tisserant, E., Feau, N., Delaruelle, C., Legue, V., Kohler, A., Tanguay, P., Petre, B., Frey, P., Van De Peer, Y., Rouze, P., Martin, F., Hamelin, R.C. & Duplessis, S. 2012. A Comprehensive Analysis of Genes Encoding Small Secreted Proteins Identifies Candidate Effectors in Melampsora larici-populina (Poplar Leaf Rust). Molecular Plant-Microbe Interactions 25: 279-293.
• Tsui, C.K., Roe, A.D., El-Kassaby, Y.A., Rice, A.V., Alamouti, S.M., Sperling, F.A., Cooke, J.E., Bohlmann, J. and Hamelin, R.C. 2012. Population structure and migration pattern of a conifer pathogen, Grosmannia clavigera, as influenced by its symbiont, the mountain pine beetle. Molecular Ecology 21: 71-86.

2011

• Vialle, A., Frey, P., Hambleton, S., & Bernier, L. 2011. Poplar rust systematics and refinement of Melampsora species delineation. Fungal Diversity 50: 227-248
• James, P.M., Coltman, D.W., Murray, B.W., Hamelin, R.C. and Sperling, F.A. 2011. Spatial genetic structure of a symbiotic beetle-fungal system: toward multi-taxa integrated landscape genetics. PLoS ONE, 6: e25359.
• Bergeron, M. J., I. Leal, B. Foord, G. Ross, C. Davis, B. Slippers, P. de Groot and Hamelin, R.C. 2011. Putative origin of clonal lineages of Amylostereum areolatum, the fungal symbiont associated with Sirex noctilio, retrieved from Pinus sylvestris, in eastern Canada. Fungal Biology 115: 750-758.
• Alamouti, S.M., Wang, V., Diguistini, S., Six, D.L., Bohlmann, J., Hamelin, R.C., Feau, N. and Breuil, C. 2011. Gene genealogies reveal cryptic species and host preferences for the pine fungal pathogen Grosmannia clavigera. Molecular Ecology, 20: 2581-2602.
• Lamarche, J., Stefani, F.O., Seguin, A. and Hamelin, R.C. 2011. Impact of endochitinase-transformed white spruce on soil fungal communities under greenhouse conditions. FEMS Microbiology and Ecology, 76: 199-208.
• Feau, N., Vialle, A., Allaire, M., Maier, W. and Hamelin, R.C. 2011. DNA barcoding in the rust genus Chrysomyxa and its implications for the phylogeny of the genus. Mycologia 103: 1250-1266.
• Duplessis, S., C. A. Cuomo, Y. C. Lin, A. Aerts, E. Tisserant, C. Veneault-Fourrey, D. L. Joly, S. Hacquard, J. Amselem, B. L. Cantarel, R. Chiu, P. M. Coutinho, N. Feau, M. Field, P. Frey, E. Gelhaye, J. Goldberg, M. G. Grabherr, C. D. Kodira, A. Kohler, U. Kues, E. A. Lindquist, S. M. Lucas, R. Mago, E. Mauceli, E. Morin, C. Murat, J. L. Pangilinan, R. Park, M. Pearson, H. Quesneville, N. Rouhier, S. Sakthikumar, A. A. Salamov, J. Schmutz, B. Selles, H. Shapiro, P. Tanguay, G. A. Tuskan, B. Henrissat, Y. Van de Peer, P. Rouze, J. G. Ellis, P. N. Dodds, J. E. Schein, S. B. Zhong, Hamelin, R.C., I. V. Grigoriev, L. J. Szabo and F. Martin. 2011. Obligate biotrophy features unraveled by the genomic analysis of rust fungi. Proceedings of the National Academy of Sciences of the United States of America 108: 9166-9171.
• DiGuistini, S., Y. Wang, N. Y. Liao, G. Taylor, P. Tanguay, N. Feau, B. Henrissat, S. K. Chan, U. Hesse-Orce, S. M. Alamouti, C. K. M. Tsui, R. T. Docking, A. Levasseur, S. Haridas, G. Robertson, I. Birol, R. A. Holt, M. A. Marra, Hamelin, R.C., M. Hirst, S. J. M. Jones, J. Bohlmann and C. Breuil. 2011. Genome and transcriptome analyses of the mountain pine beetle-fungal symbiont Grosmannia clavigera, a lodgepole pine pathogen. Proceedings of the National Academy of Sciences of the United States of America 108: 2504-2509.
• Hintz, W., Pinchback, M., la Bastide, de, P., Burgess, S., Jacobi, V., Hamelin, R. C., Breuil, C. and L. Bernier. 2011. Functional categorization of unique expressed sequence tags obtained from the yeast-like growth phase of the elm pathogen Ophiostoma novo-ulmi. BMC Genomics 431. doi:10.1186/1471-2164-12-431

2010

• Feau, N., Mottet, M.-J., Périnet, P., Hamelin, R. C. and Bernier, L. 2010. Recent advances related to poplar leaf spot and canker caused by Septoria musiva, Canadian Journal of Plant Pathology, 32: 122-134
• Stefani, F.O.P. and Hamelin, R. C. 2010. Current state of genetically modified plant impact on target and non-target fungi. Environmental Reviews. 18: 441-475.
• Clement K.M. Tsui, Bin Wang, Lily Khadempour, Sepideh Massoumi Alamouti, Jorg Bohlmann, Brent W. Murray, Richard C. Hamelin. 2010. Rapid identification and detection of pine pathogenic fungi associated with mountain pine beetles by padlock probes. Journal of Microbiological Methods, Volume 83:26-33.
• Lily Khadempour, Sepideh Massoumi Alamouti, Richard Hamelin, Jorg Bohlmann, Colette Breuil. 2010.  Target-specific PCR primers can detect and differentiate ophiostomatoid fungi from microbial communities associated with the mountain pine beetle Dendroctonus ponderosae. Fungal Biology, Volume 114: 825-833.
• Joly, D. L., Feau, N., Tanguay, P. and Hamelin, R. C. 2010. Comparative analysis of secreted protein evolution using expressed sequence tags from four poplar leaf rusts (Melampsora spp.). BMC Genomics, 11: 422 (doi:10.1186/1471-2164-11-422).
• Stefani, F. O. P., Sokolski, S., Piché, Y., Hamelin, R. C and Bérubé, J. A. 2010. Morchella tomentosa: a unique belowground structure and a new clade of morels. Mycologia 102:1082-1088.
• Stefani, F. O. P., Tanguay, P., Pelletier, G., Piche, Y, and Hamelin, R. C. 2010. Impact of Endochitinase-Transformed White Spruce on Soil Fungal Biomass and Ectendomycorrhizal Symbiosis. Applied and Environmental Microbiology 76: 2607-2614

2009

• Stefani, F. O. P., Moncalvo, J-M. Seguin, A., Berube, J. A. and Hamelin, R. C. 2009. Impact of an 8-Year-Old Transgenic Poplar Plantation on the Ectomycorrhizal Fungal Community. Applied and Environmental Microbiology 75: 7527-7536.
• Bilodeau, G. B., Pelletier, G., Pelletier, F., Lévesque, C. A. and Hamelin, R. C. 2009. Multiplex Real-Time PCR for Detection of Phytophthora ramorum, the Causal Agent of Sudden Oak Death. Canadian Journal of Plant Pathology 31: 195–210.
• Germain, H., Bergeron, M.-J., Bernier, L., Laflamme, G. and Hamelin, R. C. 2009. Patterns of colonization and spread in the fungal spruce pathogen Onnia tomentosus. Molecular Ecology 18, 4422–4433.
• Diguistini, S., Liao, N. Y., Platt, D., Robertson, G., Seidel, M., Chan, S. K., Docking, T. R., Birol, I., Holt, R. A., Hirst, M., Mardis, E., Marra, M. A., Hamelin, R. C., Bohlmann, J., Breuil C., Jones, S. J. 2009. De novo genome sequence assembly of a filamentous fungus using Sanger, 454 and Illumina sequence data. Genome Biology: Volume 10, Issue 9, Article R94.
• Grünwald, N. J., Goss, E. M., Ivors, K., Garbelotto, M., Martin, F. N., Prospero, S., Hansen, E., Bonants, P. J., Hamelin, R. C., Chastagner, G., Werres, S., Rizzo, D. M., Abad, G., Beales, P., Bilodeau, G. J., Blomquist, C. L., Brasier, C., Brière, S. C., Chandelier, A., Davidson, J. M., Denman, S., Elliott, M., Frankel, S. J., Goheen, E. M., de Gruyter, H., Heungens, K., James, D., Kanaskie, A., McWilliams, M. G., Man in ‘t Veld, W., Moralejo, E., Osterbauer, N. K., Palm, M. E., Parke, J. L., Sierra, A. M., Shamoun, S. F., Shishkoff, N., Tooley, P. W., Vettraino, A. M., Webber, J., Widmer, T. L. 2009. Standardizing the nomenclature for clonal lineages of the Sudden Oak Death pathogen, Phytophthora ramorum. Phytopathology 99: 792 – 795.
• Tsui, C.K.M., Feau, N., Ritland, C.E., Massoumi Alamouti, S., DiGuistini, S., Khadempour, L., Bohlmann, J., Breuil, C., and Hamelin, R. C. 2009. Characterization of microsatellite loci in the fungus, Grosmannia clavigera, a pine pathogen associated with the mountain pine beetle. Molecular Ecology Resources, Volume 9, Issue 6, pages 1500–1503.
• Vialle, A., Feau, N., Allaire, M., Didukh, M., Martin, F., Moncalvo, J.M., and Hamelin, R. C. 2009. Evaluation of mitochondrial genes as DNA barcode for Basidiomycota. Molecular Ecology Resources, 9: 99-113.
• Feau, N., Vialle, A., Allaire, M., Tanguay, P., Joly, D.L., Frey, P., Callan, B.E., and Hamelin, R. C. 2009. Fungal pathogen (mis-) identifications: A case study with DNA barcodes on Melampsora rusts of aspen and white poplar. Mycol. Res., 113:713-724.

2008

• Martin, F.N., Coffey, M.D., Zeller, K., Hamelin, R. C., Tooley, P., Garbelotto, M., Hughes, K.J.D., Kubisiak, T., Bilodeau, G.J., Levy, L., Blomquist, C. and Berger, P.H. 2008. Evaluation of molecular markers for Phytophthora ramorum detection and identification; testing for specificity using a standardized library of isolates. Phytopathology 99:390-403
• Bergeron, M.-J., Hamelin, R. C., Leal, I., Davis, C., and de Groot, P. 2008. First report of Amylostereum areolatum, the fungal symbiont of Sirex noctilio, on Pinus spp. in Canada. Plant Disease 92:1138.
• Oliver, K. L., Hamelin, R. C., and Hintz, W. E. 2008. Effects of transgenic hybrid aspen overexpressing polyphenol oxidase on rhizosphere diversity. Applied and Environmental Microbiology 74:5340-5348.

2007

• Bilodeau, G. J., Lévesque, C.A., de Cock, A.W.A.M., Brière, S.C. and Hamelin, R. C. 2007. Differentiation of European and North American genotypes of Phytophthora ramorum by real-time PCR primer extension. Canadian Journal of Plant Pathology 29:408-420.
• Feau, N., Joly, D. L., and Hamelin, R. C. 2007. Poplar leaf rusts: model pathogens for a model tree. Canadian Journal of Botany 85: 1127-1135
• Feau, N., Hamelin, R. C., and Bernier, L. 2007. Variability of nuclear SSU-rDNA group introns within Septoria species: Incongruence with host sequence phylogenies. Journal of Molecular Evolution 64:489-499.
• Bilodeau, G. J., Levesque, C. A., de Cock, A. W. A. M., Duchaine, C., Briere, S., Uribe, P., Martin, F. N., and Hamelin, R. C. 2007. Molecular detection of Phytophthora ramorum by real-time polymerase chain reaction using TaqMan, SYBR Green, and molecular beacons. Phytopathology 97:632-642.
• Feau, N., Bergeron, M. J., Joly, D. L., Roussel, F., and Hamelin, R. C. 2007. Detection and validation of EST-derived SNPs for poplar leaf rust Melampsora medusae f. sp deltoidae. Molecular Ecology Notes 7:1222-1228.
• Bourassa, M., Bernier, L., and Hamelin, R. C. 2007. Genetic diversity in poplar leaf rust (Melampsora medusae f. sp deltoidae) in the zones of host sympatry and allopatry. Phytopathology 97:603-610.
• Lee, S., Hamelin, R. C., Six, D. L., and Breuil, C. 2007. Genetic diversity and the presence of two distinct groups in Ophiostoma clavigerum associated with Dendroctonus ponderosae in British Columbia and the northern Rocky Mountains. Phytopathology 97:1177-1185.
• Lamarche, J., and Hamelin, R. C. 2007. No evidence of an impact on the rhizosphere diazotroph community by the expression of Bacillus thuringiensis Cry1Ab toxin by Bt white spruce. Applied and Environmental Microbiology 73 (20):6577-6583.
• Cayer, M. P., Veillette, M., Pageau, P., Hamelin, R. C., Bergeron, M.-J., Meriaux, A., Cormier, Y., and Duchaine, C. 2007. Identification of mycobacteria in peat moss processing plants: application of molecular biology approaches. Canadian Journal of Microbiology 53 (1): 92-99.
• LeBlanc, P. M., Hamelin, R. C., and Filion, M. 2007. Alteration of soil rhizosphere communities following genetic transformation of white spruce. Applied and Environmental Microbiology 73 (13):4128-4134.
• Vujanovic, V., Hamelin, R. C., Bernier, L., Vujanovic, G., and St-Arnaud, M. 2007. Fungal diversity, dominance, and community structure in the rhizosphere of clonal Picea mariana plants throughout nursery production chronosequences. Microbial Ecology 54 (4):672-684.

2006

• Hamelin, R. C. 2006. Molecular epidemiology of forest pathogens: from genes to landscape. Canadian Journal of Plant Pathology 28:167-181.
• Feau, N., Hamelin, R. C. and Bernier, L. 2006. Attributes and congruence of three molecular data sets: Inferring phylogenies among Septoria-related species from woody perennial plants. Molecular Phylogenetics and Evolution 40:808-829.
• Feau, N., Jacobi, V., Hamelin, R. C., and Bernier, L. 2006. Screening of ESTs from Septoria musiva (teleomorph Mycosphaerella populorum) for detection of SSR and PCR-RFLP markers. Molecular Ecology Notes 6 (2):356-358.
• Joly, D. L., Langor, D. W. and Hamelin, R. C. 2006. Molecular and morphological evidence for interspecific hybridization between Cronartium ribicola and C. comandrae on Pinus flexilis in southwestern Alberta. Plant Disease 90:1552-1552.