Richard C. Hamelin
Affiliation : SCF
Spécialité : biotechnologie des ravageurs forestiers
Courriel : Richard.Hamelin@RNCan-NRCan.gc.ca
Projets dont Richard C. Hamelin est Collaborateur :
Publications :
- Nicolas Feau, David L. Joly, Richard C. Hamelin. 2007. Poplar leaf rusts: model pathogens for a model tree. Canadian Journal of Botany. 85(12):1127-1135 doi:10.1139/B07-102. Cet article est réalisé dans le cadre du Volet 3 TP 4
(Résumé)With the availability of the entire genome of the model tree Populus trichocarpa Torr. & A. Gray and the current genome sequencing project of its rust pathogen Melampsora larici-populina Kleb., rust-poplar interaction research has entered the genomic era. Recent genomics research on poplars has attempted to connect the genetic localizations of loci for qualitative and quantitative disease resistance with putative genes encoding resistance or signalling proteins. The interactions between these putative resistance genes and rust effectors remain unknown. Genomic resources developed for Melampsora spp. promise to contribute to our understanding of the molecular basis of pathogenicity by facilitating the isolation of pathogenicity genes. A multifaceted approach for the identification of such genes that relies largely on trimming and sequence data analysis has been developed. The strategy takes advantage of the resources available and combines EST libraries, bioinformatics data mining for extracellularly expressed secreted proteins, intra- and inter-specific comparative genomics, and testing for the presence of positive selection. It has resulted in the discovery of several putative candidate genes. In silico evidence for candidate genes will be further validated by robust experimental evidence through functional analyses.
Avec la disponibilité de la séquence complète du génome de l'arbre modèle en foresterie, Populus trichocarpa Torr. & A. Gray, et du séquençage en cours d'un de ses agents pathogènes, le Melampsora larici-populina Kleb., la recherche sur l'interaction rouille-peuplier est entrée dans l'ère de la génomique. Les recherches actuelles en génomique chez les peupliers visent à établir des liens entre les loci identifiés par cartographie génétique et des gènes potentiellement identifiés pour leur implication dans la résistance à ces agents pathogènes. Les interactions entre ces gènes de résistance et des effecteurs des rouilles restent toutefois inconnues. Dans ce contexte, les ressources en génomique développées pour les Melampsora spp. devraient conduire à la compréhension des bases moléculaires du pouvoir pathogène chez ces champignons, en facilitant l'isolation de gènes impliqués dans la pathogénicité. Une approche basée sur différents modes d'analyses de séquences a été développée et doit mener à l'identification de tels gènes. La stratégie mise en place tire avantage des ressources disponibles, en combinant les banques d'ESTs, l'exploitation de ces données de transcriptomique au moyen d'outils de bioinformatique pour la recherche de protéines sécrétées et la génomique comparative, tant au niveau intra- qu'inter-spécifique, pour la détection de sélection positive. Plusieurs gènes candidats ont pu être identifiés au moyen de cette approche. À plus long terme, ces candidats découverts in silico seront validés au moyen d'analyses fonctionnelles.
© 2007 NRC Canada - Nicolas Feau, Marie-Josée Bergeron, David L. Joly, Fabien Roussel, Richard C. Hamelin. 2007. Detection and validation of EST-derived SNPs for poplar leaf rust Melampsora medusae f. sp. deltoidae. Molecular Ecology Notes. 7:1222-1228 doi:10.1111/j.1471-8286.2007.01838.x. Cet article est réalisé dans le cadre du Volet 3 TP 4(Résumé)
We report the discovery, characterization and validation of 118 single nucleotide polymorphisms (SNPs) for poplar leaf rust Melampsora medusae f. sp. deltoidae identified using a gene-targeted approach in an expressed sequence tag (EST) library. We developed a genotyping assay using the iPLEX™ primer extension method for two multiplex assays of 28 and 22 SNPs. John Wiley & Sons, Inc. All Rights Reserved.
- Nicolas Feau, Richard C. Hamelin, Louis Bernier. 2007. Variability of Nuclear SSU-rDNA Group Introns Within Septoria Species: Incongruence with Host Sequence Phylogenies. Journal of Molecular Evolution. 64:489-499 doi:10.1007/s00239-005-0309-7. Cet article est réalisé dans le cadre du Volet 3 TP 4(Résumé)
We report structural features and distribution patterns of 26 different group I introns located at three distinct nucleotide positions in nuclear small subunit ribosomal DNA (SSU-rDNA) of 10 Septoria and 4 other anamorphic species related to the teleomorphic genus Mycosphaerella. Secondary structure and sequence characteristics assigned the introns to the common IC1 and IE groups. Intron distribution patterns and phylogenetic relationships strongly suggested that some horizontal transfer events have occurred among the closely related fungal species sampled. To test this hypothesis, we used a comparative approach of intron- and rDNA-based phylogenies through MP- and ML-based topology tests. Our results showed two statistically well-supported major incongruences between the intron and the equivalent internal transcribed spacer (ITS) tree comparisons made. Such absence of a co-evolutive history between group I introns and host sequences is discussed relatively to the intron structures, the mechanisms of intron movement, and the biology of the Mycosphaerella pathogenic fungi. © Springer
- Nicolas Feau, Richard C. Hamelin, Louis Bernier. 2006. Attributes and congruence of three molecular data sets: inferring phylogenies among Septoria-related species from woody perennials. Molecular Phylogenetics and Evolution. 40(3):808-829 doi:10.1016/j.ympev.2006.03.029. Cet article est réalisé dans le cadre du Volet 3 TP 4(Résumé)
To improve our understanding of phylogenetic relationships within the anamorphic genus Septoria, three molecular data sets representing 2417 bp of nuclear and mitochondrial genes were evaluated. Separate gene analyses and combined analyses were performed using first, the maximum parsimony criterion and second, a Bayesian framework. The homogeneity of data partitions was evaluated via a combination of homogeneity partition tests and tree topology incongruence tests before conducting combined analyses. A last incongruence re-evaluation using partitioned Bremer support was performed on the combined tree, which corroborated the previous estimates. After each separate data set attributes were examined, simple explanations were advocated as the causes of the significant incongruences detected. The analysis of multiple gene partitions showed unprecedented phylogenetic resolution within the genus Septoria that supported the results from previously published single gene phylogenies. Specifically, we have delimited distinct but closely related species representing monophyletic groups that frequently correlated with their respective host families. Conversely, the occurrence of well-supported groups including closely related but distinct molecular taxa sampled on unrelated host-plants allowed us to reject, in these particular cases, the co-evolutionary concept expected between a parasite and its host and to discuss alternative evolutionary models recently proposed for these pathogens.
Copyright © 2009 Elsevier B.V.
- Nicolas Feau, Volker Jacobi, Richard C. Hamelin, Louis Bernier. 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 doi:10.1111/j.1471-8286.2006.01230.x. Cet article est réalisé dans le cadre du Volet 3 TP 4(Résumé)
The development of an expressed sequence tag (EST) collection for the poplar pathogen Septoria musiva presented an opportunity for the development of locus-specific polymorphic markers. Five microsatellites simple sequence repeat (SSR) and six polymerase chain reaction (PCR)–restriction fragment length polymorphism (RFLP) markers were identified and tested on three S. musiva populations collected in the north-central and northeastern regions of North America. The results obtained support previously published random amplified polymorphic DNA (RAPD) data.
- Nicolas Feau, Richard C. Hamelin, C. Vandecasteele, Glen R. Stanosz, Louis Bernier. 2005. Genetic structure of Mycosphaerella populorum (anamorph Septoria musiva) populations in north central and northeastern North America. Phytopathology. 95:608-616 doi:10.1094/PHYTO-95-0608. Cet article est réalisé dans le cadre du Volet 3 TP 7(Résumé)
In order to characterize the genetic variation of the poplar pathogen Mycosphaerella populorum (anamorph Septoria musiva), we have studied seven North American populations using the polymerase chain reaction random amplified polymorphic DNA (RAPD) technique. The fungal populations were sampled in 2001 and 2002 by obtaining 352 isolates from cankers and leaf spots in hybrid poplar plantations and adjacent eastern cottonwood (Populus deltoides). A total of 21 polymorphic RAPD markers were obtained with the six RAPD primers used. A fine-level scale analysis of the genetic structure within the populations revealed that subpopulations sampled on P. deltoides and on hybrid trees were not significantly differentiated. In contrast, analyses performed on the entire data set showed high levels of haplotypic diversity and moderate to high genetic differentiation, with 20% of the expected genetic diversity found at the interpopulation level. Moreover, a high and significant correlation between genetic and geographic distances among populations was found, suggesting isolation by distance of the sampled populations. Although the occurrence of the sexual stage of this fungus remained unclear in field populations, five of the six populations were at gametic equilibrium for RAPD loci, suggesting the occurrence of recombination episodes in Septoria musiva populations. Overall, S. musiva appears to consist of differentiated subpopulations, with both asexual and sexual recombination contributing to the local level of genetic structure.