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Smenderovac E, Emilson C, Rheault K, Brazeau É, Morency MJ, Gagné P, Venier L, Martineau C. Drying as an effective method to store soil samples for DNA-based microbial community analyses: a comparative study. Sci Rep 2024; 14:1725. [PMID: 38242898 PMCID: PMC10798986 DOI: 10.1038/s41598-023-50541-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 12/21/2023] [Indexed: 01/21/2024] Open
Abstract
Soil sampling for environmental DNA in remote and semi-remote locations is often limited due to logistical constraints surrounding sample preservation, including no or limited access to a freezer. Freezing at - 20 °C is a common DNA preservation strategy, however, other methods such as desiccation, ethanol or commercial preservatives are available as potential alternative DNA preservation methods for room temperature storage. In this study, we assessed five preservation methods (CD1 solution, 95% Ethanol, Dry & Dry silica gel packs, RNAlater, LifeGuard) along with freezing at - 20 °C, against immediate extraction on organic and mineral soils for up to three weeks of preservation. We assessed direct effects on DNA concentration and quality, and used DNA metabarcoding to assess effects on bacterial and fungal communities. Drying with Dry & Dry led to no significant differences from immediate extraction. RNAlater led to lower DNA concentrations, but effects on community structures were comparable to freezing. CD1, LifeGuard and Ethanol either caused immediate significant shifts in community structure, degradation of DNA quality or changes in diversity metrics. Overall, our study supports the use of drying with silica gel packs as a cost-effective, and easily applied method for the short-term storage at room temperature for DNA-based microbial community analyses.
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Affiliation(s)
| | - Caroline Emilson
- Canadian Forest Service, Natural Resources Canada, Ottawa, Canada
| | - Karelle Rheault
- Canadian Forest Service, Natural Resources Canada, Ottawa, Canada
| | - Élodie Brazeau
- Canadian Forest Service, Natural Resources Canada, Ottawa, Canada
| | | | - Patrick Gagné
- Canadian Forest Service, Natural Resources Canada, Ottawa, Canada
| | - Lisa Venier
- Canadian Forest Service, Natural Resources Canada, Ottawa, Canada
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Samad A, Degenhardt D, Séguin A, Morency MJ, Gagné P, Martineau C. Microbial community structural and functional differentiation in capped thickened oil sands tailings planted with native boreal species. Front Microbiol 2023; 14:1168653. [PMID: 37465026 PMCID: PMC10350512 DOI: 10.3389/fmicb.2023.1168653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 06/12/2023] [Indexed: 07/20/2023] Open
Abstract
The oil sands mining operations in Alberta have produced billions of m3 of tailings which must be reclaimed and integrated into various mine closure landforms, including terrestrial landforms. Microorganisms play a central role in nutrient cycling during the reclamation of disturbed landscapes, contributing to successful vegetation restoration and long-term sustainability. However, microbial community succession and response in reconstructed and revegetated tailings remain largely unexplored. This study aimed to monitor the structural and functional responses of microbial communities in tailings subjected to different capping and vegetation strategies over two growing seasons (GS). To achieve this, a column-based greenhouse experiment was conducted to investigate microbial communities in tailings that were capped with a layer (10 or 30 cm) of peat-mineral mix (PMM) and planted with either upland or wetland communities. DNA metabarcoding analysis of the bacterial 16S rRNA gene and fungal ITS2 region as well as shotgun metagenomics were used to asses the impact of treatments on microbial taxonomy and functions, respectively. Results showed that tailings microbial diversity and community composition changed considerably after two GS compared to baseline samples, while communities in the PMM capping layer were much more stable. Likewise, several microbial functions were significantly enriched in tailings after two GS. Interestingly, the impact of capping on bacterial communities in tailings varied depending on the plant community, leading to a higher number of differentially abundant taxa and to a decrease in Shannon diversity and evenness in the upland treatment but not in the wetland treatment. Moreover, while capping in the presence of wetland vegetation increased the energy-related metabolic functions (carbon, nitrogen, and sulfur), these functions were depleted by capping in the upland treatment. Fungi represented a small proportion of the microbial community in tailings, but the relative abundance of several taxa changed over time, while the capping treatments favored the growth of some beneficial taxa, notably the root endophyte Serendipita, in both upland and wetland columns. The results suggest that selecting the right combination of capping material and vegetation type may contribute to improve below-ground microbial processes and sustain plant growth in harsh environments such as oil sands tailings.
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Affiliation(s)
- Abdul Samad
- Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, Québec City, QC, Canada
| | - Dani Degenhardt
- Natural Resources Canada, Canadian Forest Service, Northern Forestry Centre, Edmonton, AB, Canada
| | - Armand Séguin
- Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, Québec City, QC, Canada
| | - Marie-Josée Morency
- Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, Québec City, QC, Canada
| | - Patrick Gagné
- Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, Québec City, QC, Canada
| | - Christine Martineau
- Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, Québec City, QC, Canada
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Stefani F, Beguin J, Paré D, Morency MJ, Martineau C, Fortin JA, Thiffault N, Séguin A. Does wood mulch trigger microbially mediated positive plant-soil feedback in degraded boreal forest sites? A post hoc study. Front Plant Sci 2023; 14:1122445. [PMID: 37206972 PMCID: PMC10191178 DOI: 10.3389/fpls.2023.1122445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 03/15/2023] [Indexed: 05/21/2023]
Abstract
Introduction Reforestation of degraded lands in the boreal forest is challenging and depends on the direction and strength of the plant-soil feedback (PSF). Methods Using a gradient in tree productivity (null, low and high) from a long-term, spatially replicated reforestation experiment of borrow pits in the boreal forest, we investigated the interplay between microbial communities and soil and tree nutrient stocks and concentrations in relation to a positive PSF induced by wood mulch amendment. Results Three levels of mulch amendment underlie the observed gradient in tree productivity, and plots that had been amended with a continuous layer of mulch 17 years earlier showed a positive PSF with trees up to 6 m tall, a closed canopy, and a developing humus layer. The average taxonomic and functional composition of the bacterial and fungal communities differed markedly betweenlow- and high-productivity plots. Trees in high-productivity plots recruited a specialized soil microbiome that was more efficient at nutrient mobilization and acquisition. These plots showed increases in carbon (C), calcium (Ca), nitrogen (N), potassium (K), and phosphorus (P) stocks and as well as bacterial and fungal biomass. The soil microbiome was dominated by taxa from the fungal genus Cortinarius and the bacterial family Chitinophagaceae, and a complex microbial network with higher connectivity and more keystone species supported tree productivity in reforested plots compared to unproductive plots. Discussion Therefore, mulching of plots resulted in a microbially mediated PSF that enhances mineral weathering and non-symbiotic N fixation, and in turn helps transform unproductive plots into productive plots to ensure rapid restoration of the forest ecosystem in a harsh boreal environment.
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Affiliation(s)
- Franck Stefani
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, Ottawa, ON, Canada
- *Correspondence: Franck Stefani, ; David Paré,
| | - Julien Beguin
- Institut de recherche sur les forêts, Université du Québec en Abitibi-Témiscamingue, Rouyn-Noranda, QC, Canada
| | - David Paré
- Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, Québec, QC, Canada
- *Correspondence: Franck Stefani, ; David Paré,
| | - Marie-Josée Morency
- Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, Québec, QC, Canada
| | - Christine Martineau
- Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, Québec, QC, Canada
| | - J. André Fortin
- Université Laval, Faculté de foresterie, de géographie et de géomatique, Département des sciences du bois et de la forêt, Québec, QC, Canada
| | - Nelson Thiffault
- Natural Resources Canada, Canadian Forest Service, Canadian Wood Fibre Centre, Québec, QC, Canada
| | - Armand Séguin
- Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, Québec, QC, Canada
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Rheault K, Lachance D, Morency MJ, Thiffault É, Guittonny M, Isabel N, Martineau C, Séguin A. Plant Genotype Influences Physicochemical Properties of Substrate as Well as Bacterial and Fungal Assemblages in the Rhizosphere of Balsam Poplar. Front Microbiol 2020; 11:575625. [PMID: 33329437 PMCID: PMC7719689 DOI: 10.3389/fmicb.2020.575625] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 10/26/2020] [Indexed: 01/09/2023] Open
Abstract
Abandoned unrestored mines are an important environmental concern as they typically remain unvegetated for decades, exposing vast amounts of mine waste to erosion. Several factors limit the revegetation of these sites, including extreme abiotic and unfavorable biotic conditions. However, some pioneer tree species having high levels of genetic diversity, such as balsam poplar (Populus balsamifera), can naturally colonize these sites and initiate plant succession. This suggests that some tree genotypes are likely more suited for acclimation to the conditions of mine wastes. In this study, we selected two contrasting mine waste storage facilities (waste rock from a gold mine and tailings from a molybdenum mine) from the Abitibi region of Quebec (Canada), on which poplars were found to have grown naturally. First, we assessed in situ the impact of vegetation presence on each mine waste type. The presence of balsam poplars improved soil health locally by modifying the physicochemical properties (e.g., higher nutrient content and pH) of the mine wastes and causing an important shift in their bacterial and fungal community compositions, going from lithotrophic communities that dominate mine waste environments to heterotrophic communities involved in nutrient cycling. Next, in a greenhouse experiment we assessed the impact of plant genotype when grown in these mine wastes. Ten genotypes of P. balsamifera were collected locally, found growing either at the mine sites or in the surrounding natural forest. Tree growth was monitored over two growing seasons, after which the effects of genotype-by-environment interactions were assessed by measuring the physicochemical properties of the substrates and the changes in microbial community assembly. Although substrate type was identified as the main driver of rhizosphere microbiome diversity and community structure, a significant effect due to tree genotype was also detected, particularly for bacterial communities. Plant genotype also influenced aboveground tree growth and the physicochemical properties of the substrates. These results highlight the influence of balsam poplar genotype on the soil environment and the potential importance of tree genotype selection in the context of mine waste revegetation.
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Affiliation(s)
- Karelle Rheault
- Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, Quebec City, QC, Canada
| | - Denis Lachance
- Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, Quebec City, QC, Canada
| | - Marie-Josée Morency
- Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, Quebec City, QC, Canada
| | - Évelyne Thiffault
- Renewable Materials Research Centre, Department of Wood and Forest Sciences, Université Laval, Quebec City, QC, Canada
| | - Marie Guittonny
- Research Institute of Mines and Environment (RIME), Université du Québec en Abitibi-Témiscamingue, Rouyn-Noranda, QC, Canada
| | - Nathalie Isabel
- Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, Quebec City, QC, Canada
| | - Christine Martineau
- Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, Quebec City, QC, Canada
| | - Armand Séguin
- Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, Quebec City, QC, Canada
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Stefani F, Isabel N, Morency MJ, Lamothe M, Nadeau S, Lachance D, Li EHY, Greer C, Yergeau É, Pinno BD, Séguin A. The impact of reconstructed soils following oil sands exploitation on aspen and its associated belowground microbiome. Sci Rep 2018; 8:2761. [PMID: 29426844 PMCID: PMC5807544 DOI: 10.1038/s41598-018-20783-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Accepted: 01/19/2018] [Indexed: 12/02/2022] Open
Abstract
The objective of this study was to investigate the impact of different soil covers used to reclaim decommissioned oil sands mining sites on the genetic diversity of aspen and their associated belowground microbiota. Aspen genotyping showed that trees mostly originated from sexual reproduction on sites reclaimed with soil covers made of upland forest floor-mineral mix (FFMM) and lowland peat-mineral mix (PMM). In contrast, most individuals in mature and burned stands sampled as benchmarks for natural disturbances originated from vegetative reproduction. Nonetheless, aspen populations in the FFMM and PMM sites were not genetically different from those in mature and burned stands. DNA metabarcoding of bacteria and fungi in root and soil samples revealed that the diversity of the belowground microbiota associated with aspen and the relative abundance of putative symbiotic taxa in PMM were significantly lower than for FFMM and naturally disturbed sites. Despite similar aspen genetic diversity between FFMM and PMM sites, trees were not associated with the same belowground microbiota. Because the soil microbiome and more specifically the mycorrhizal communities are variable both in space and time, long-term monitoring is particularly important to better understand the ecological trajectory of these novel ecosystems.
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Affiliation(s)
- Franck Stefani
- Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, Québec, G1V4C7, Canada
- Agriculture and Agri-Food Canada, Ottawa, K1A 0C6, Canada
| | - Nathalie Isabel
- Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, Québec, G1V4C7, Canada
| | - Marie-Josée Morency
- Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, Québec, G1V4C7, Canada
| | - Manuel Lamothe
- Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, Québec, G1V4C7, Canada
| | - Simon Nadeau
- Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, Québec, G1V4C7, Canada
| | - Denis Lachance
- Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, Québec, G1V4C7, Canada
| | - Edith H Y Li
- Natural Resources Canada, Canadian Forest Service, Northern Forestry Centre, Edmonton, T6H 3S5, Canada
| | - Charles Greer
- National Research Council Canada, Energy, Mining and Environment, Montréal, H4P 2R2, Canada
| | - Étienne Yergeau
- National Research Council Canada, Energy, Mining and Environment, Montréal, H4P 2R2, Canada
- Institut national de la recherche scientifique, Centre INRS-Institut Armand-Frappier, Laval, H7V 1B7, Canada
| | - Bradley D Pinno
- Natural Resources Canada, Canadian Forest Service, Northern Forestry Centre, Edmonton, T6H 3S5, Canada
| | - Armand Séguin
- Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, Québec, G1V4C7, Canada.
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Stefani FO, Klimaszewski J, Morency MJ, Bourdon C, Labrie P, Blais M, Venier L, Séguin A. Fungal community composition in the gut of rove beetles (Coleoptera: Staphylinidae) from the Canadian boreal forest reveals possible endosymbiotic interactions for dietary needs. FUNGAL ECOL 2016. [DOI: 10.1016/j.funeco.2016.05.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Duval I, Lachance D, Giguère I, Bomal C, Morency MJ, Pelletier G, Boyle B, MacKay JJ, Séguin A. Large-scale screening of transcription factor-promoter interactions in spruce reveals a transcriptional network involved in vascular development. J Exp Bot 2014; 65:2319-33. [PMID: 24713992 PMCID: PMC4036505 DOI: 10.1093/jxb/eru116] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
This research aimed to investigate the role of diverse transcription factors (TFs) and to delineate gene regulatory networks directly in conifers at a relatively high-throughput level. The approach integrated sequence analyses, transcript profiling, and development of a conifer-specific activation assay. Transcript accumulation profiles of 102 TFs and potential target genes were clustered to identify groups of coordinately expressed genes. Several different patterns of transcript accumulation were observed by profiling in nine different organs and tissues: 27 genes were preferential to secondary xylem both in stems and roots, and other genes were preferential to phelloderm and periderm or were more ubiquitous. A robust system has been established as a screening approach to define which TFs have the ability to regulate a given promoter in planta. Trans-activation or repression effects were observed in 30% of TF-candidate gene promoter combinations. As a proof of concept, phylogenetic analysis and expression and trans-activation data were used to demonstrate that two spruce NAC-domain proteins most likely play key roles in secondary vascular growth as observed in other plant species. This study tested many TFs from diverse families in a conifer tree species, which broadens the knowledge of promoter-TF interactions in wood development and enables comparisons of gene regulatory networks found in angiosperms and gymnosperms.
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Affiliation(s)
- Isabelle Duval
- Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, Québec, QC, G1V 4C7, Canada
| | - Denis Lachance
- Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, Québec, QC, G1V 4C7, Canada
| | - Isabelle Giguère
- Centre d'Étude de la Forêt, Université Laval, Québec, QC, G1V A06, Canada
| | - Claude Bomal
- Centre d'Étude de la Forêt, Université Laval, Québec, QC, G1V A06, Canada
| | - Marie-Josée Morency
- Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, Québec, QC, G1V 4C7, Canada
| | - Gervais Pelletier
- Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, Québec, QC, G1V 4C7, Canada
| | - Brian Boyle
- Centre d'Étude de la Forêt, Université Laval, Québec, QC, G1V A06, Canada
| | - John J MacKay
- Centre d'Étude de la Forêt, Université Laval, Québec, QC, G1V A06, Canada Department of Plant Sciences, University of Oxford, Oxford, OX1 2RB, UK
| | - Armand Séguin
- Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, Québec, QC, G1V 4C7, Canada
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Hamel LP, Benchabane M, Nicole MC, Major IT, Morency MJ, Pelletier G, Beaudoin N, Sheen J, Séguin A. Stress-responsive mitogen-activated protein kinases interact with the EAR motif of a poplar zinc finger protein and mediate its degradation through the 26S proteasome. Plant Physiol 2011; 157:1379-93. [PMID: 21873571 PMCID: PMC3252155 DOI: 10.1104/pp.111.178343] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2011] [Accepted: 08/25/2011] [Indexed: 05/21/2023]
Abstract
Mitogen-activated protein kinases (MAPKs) contribute to the establishment of plant disease resistance by regulating downstream signaling components, including transcription factors. In this study, we identified MAPK-interacting proteins, and among the newly discovered candidates was a Cys-2/His-2-type zinc finger protein named PtiZFP1. This putative transcription factor belongs to a family of transcriptional repressors that rely on an ERF-associated amphiphilic repression (EAR) motif for their repression activity. Amino acids located within this repression motif were also found to be essential for MAPK binding. Close examination of the primary protein sequence revealed a functional bipartite MAPK docking site that partially overlaps with the EAR motif. Transient expression assays in Arabidopsis (Arabidopsis thaliana) protoplasts suggest that MAPKs promote PtiZFP1 degradation through the 26S proteasome. Since features of the MAPK docking site are conserved among other EAR repressors, our study suggests a novel mode of defense mechanism regulation involving stress-responsive MAPKs and EAR repressors.
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Côté CL, Boileau F, Roy V, Ouellet M, Levasseur C, Morency MJ, Cooke JEK, Séguin A, MacKay JJ. Gene family structure, expression and functional analysis of HD-Zip III genes in angiosperm and gymnosperm forest trees. BMC Plant Biol 2010; 10:273. [PMID: 21143995 PMCID: PMC3017839 DOI: 10.1186/1471-2229-10-273] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2010] [Accepted: 12/11/2010] [Indexed: 05/03/2023]
Abstract
BACKGROUND Class III Homeodomain Leucine Zipper (HD-Zip III) proteins have been implicated in the regulation of cambium identity, as well as primary and secondary vascular differentiation and patterning in herbaceous plants. They have been proposed to regulate wood formation but relatively little evidence is available to validate such a role. We characterised and compared HD-Zip III gene family in an angiosperm tree, Populus spp. (poplar), and the gymnosperm Picea glauca (white spruce), representing two highly evolutionarily divergent groups. RESULTS Full-length cDNA sequences were isolated from poplar and white spruce. Phylogenetic reconstruction indicated that some of the gymnosperm sequences were derived from lineages that diverged earlier than angiosperm sequences, and seem to have been lost in angiosperm lineages. Transcript accumulation profiles were assessed by RT-qPCR on tissue panels from both species and in poplar trees in response to an inhibitor of polar auxin transport. The overall transcript profiles HD-Zip III complexes in white spruce and poplar exhibited substantial differences, reflecting their evolutionary history. Furthermore, two poplar sequences homologous to HD-Zip III genes involved in xylem development in Arabidopsis and Zinnia were over-expressed in poplar plants. PtaHB1 over-expression produced noticeable effects on petiole and primary shoot fibre development, suggesting that PtaHB1 is involved in primary xylem development. We also obtained evidence indicating that expression of PtaHB1 affected the transcriptome by altering the accumulation of 48 distinct transcripts, many of which are predicted to be involved in growth and cell wall synthesis. Most of them were down-regulated, as was the case for several of the poplar HD-Zip III sequences. No visible physiological effect of over-expression was observed on PtaHB7 transgenic trees, suggesting that PtaHB1 and PtaHB7 likely have distinct roles in tree development, which is in agreement with the functions that have been assigned to close homologs in herbaceous plants. CONCLUSIONS This study provides an overview of HD-zip III genes related to woody plant development and identifies sequences putatively involved in secondary vascular growth in angiosperms and in gymnosperms. These gene sequences are candidate regulators of wood formation and could be a source of molecular markers for tree breeding related to wood properties.
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Affiliation(s)
- Caroline L Côté
- Département des Sciences du Bois et de la Forêt, Université Laval, 2405 rue de la Terrasse, Québec, QC G1V0A6, Canada
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10
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Pitre FE, Lafarguette F, Boyle B, Pavy N, Caron S, Dallaire N, Poulin PL, Ouellet M, Morency MJ, Wiebe N, Ly Lim E, Urbain A, Mouille G, Cooke JEK, Mackay JJ. High nitrogen fertilization and stem leaning have overlapping effects on wood formation in poplar but invoke largely distinct molecular pathways. Tree Physiol 2010; 30:1273-89. [PMID: 20739427 DOI: 10.1093/treephys/tpq073] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Previous studies indicated that high nitrogen fertilization may impact secondary xylem development and alter fibre anatomy and composition. The resulting wood shares some resemblance with tension wood, which has much thicker cell walls than normal wood due to the deposition of an additional layer known as the G-layer. This report compares the short-term effects of high nitrogen fertilization and tree leaning to induce tension wood, either alone or in combination, upon wood formation in young trees of Populus trichocarpa (Torr. & Gray) × P. deltoides Bartr. ex Marsh. Fibre anatomy, chemical composition and transcript profiles were examined in newly formed secondary xylem. Each of the treatments resulted in thicker cell walls relative to the controls. High nitrogen and tree leaning had overlapping effects on chemical composition based on Fourier transform infrared analysis, specifically indicating that secondary cell wall composition was shifted in favour of cellulose and hemicelluloses relative to lignin content. In contrast, the high-nitrogen trees had shorter fibres, whilst the leaning trees had longer fibres that the controls. Microarray transcript profiling carried out after 28 days of treatment identified 180 transcripts that accumulated differentially in one or more treatments. Only 10% of differentially expressed transcripts were affected in all treatments relative to the controls. Several of the affected transcripts were related to carbohydrate metabolism, secondary cell wall formation, nitrogen metabolism and osmotic stress. RT-qPCR analyses at 1, 7 and 28 days showed that several transcripts followed very different accumulation profiles in terms of rate and level of accumulation, depending on the treatment. Our findings suggest that high nitrogen fertilization and tension wood induction elicit largely distinct and molecular pathways with partial overlap. When combined, the two types of environmental cue yielded additive effects.
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Affiliation(s)
- Frederic E Pitre
- ARBOREA, Centre for Forest Research, Universite Laval, Quebec QC, Canada G1K 7P4
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Bomal C, Bedon F, Caron S, Mansfield SD, Levasseur C, Cooke JEK, Blais S, Tremblay L, Morency MJ, Pavy N, Grima-Pettenati J, Séguin A, Mackay J. Involvement of Pinus taeda MYB1 and MYB8 in phenylpropanoid metabolism and secondary cell wall biogenesis: a comparative in planta analysis. J Exp Bot 2008; 59:3925-39. [PMID: 18805909 PMCID: PMC2576632 DOI: 10.1093/jxb/ern234] [Citation(s) in RCA: 125] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2008] [Revised: 08/15/2008] [Accepted: 08/19/2008] [Indexed: 05/18/2023]
Abstract
The involvement of two R2R3-MYB genes from Pinus taeda L., PtMYB1 and PtMYB8, in phenylpropanoid metabolism and secondary cell wall biogenesis was investigated in planta. These pine MYBs were constitutively overexpressed (OE) in Picea glauca (Moench) Voss, used as a heterologous conifer expression system. Morphological, histological, chemical (lignin and soluble phenols), and transcriptional analyses, i.e. microarray and reverse transcription quantitative PCR (RT-qPCR) were used for extensive phenotyping of MYB-overexpressing spruce plantlets. Upon germination of somatic embryos, root growth was reduced in both transgenics. Enhanced lignin deposition was also a common feature but ectopic secondary cell wall deposition was more strongly associated with PtMYB8-OE. Microarray and RT-qPCR data showed that overexpression of each MYB led to an overlapping up-regulation of many genes encoding phenylpropanoid enzymes involved in lignin monomer synthesis, while misregulation of several cell wall-related genes and other MYB transcription factors was specifically associated with PtMYB8-OE. Together, the results suggest that MYB1 and MYB8 may be part of a conserved transcriptional network involved in secondary cell wall deposition in conifers.
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Affiliation(s)
- Claude Bomal
- Centre d'Etude de Forêt, Université Laval, Québec (QC), Canada G1V 0A6.
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Nicole MC, Hamel LP, Morency MJ, Beaudoin N, Ellis BE, Séguin A. MAP-ping genomic organization and organ-specific expression profiles of poplar MAP kinases and MAP kinase kinases. BMC Genomics 2006; 7:223. [PMID: 16945144 PMCID: PMC1574314 DOI: 10.1186/1471-2164-7-223] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2006] [Accepted: 08/31/2006] [Indexed: 11/30/2022] Open
Abstract
Background As in other eukaryotes, plant mitogen-activated protein kinase (MAPK) cascades are composed of three classes of hierarchically organized protein kinases, namely MAPKKKs, MAPKKs, and MAPKs. These modules rapidly amplify and transduce extracellular signals into various appropriate intracellular responses. While extensive work has been conducted on the post-translational regulation of specific MAPKKs and MAPKs in various plant species, there has been no systematic investigation of the genomic organization and transcriptional regulation of these genes. Results Ten putative poplar MAPKK genes (PtMKKs) and 21 putative poplar MAPK genes (PtMPKs) have been identified and located within the poplar (Populus trichocarpa) genome. Analysis of exon-intron junctions and of intron phase inside the predicted coding region of each candidate gene has revealed high levels of conservation within and between phylogenetic groups. Expression profiles of all members of these two gene families were also analyzed in 17 different poplar organs, using gene-specific primers directed at the 3'-untranslated region of each candidate gene and real-time quantitative PCR. Most PtMKKs and PtMPKs were differentially expressed across this developmental series. Conclusion This analysis provides a complete survey of MAPKK and MAPK gene expression profiles in poplar, a large woody perennial plant, and thus complements the extensive expression profiling data available for the herbaceous annual Arabidopsis thaliana. The poplar genome is marked by extensive segmental and chromosomal duplications, and within both kinase families, some recently duplicated paralogous gene pairs often display markedly different patterns of expression, consistent with the rapid evolution of specialized protein functions in this highly adaptive species.
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Affiliation(s)
- Marie-Claude Nicole
- Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, 1055 du P.E.P.S., P.O. Box 10380, Stn. Sainte-Foy, Quebec, Quebec, G1V 4C7, Canada
| | - Louis-Philippe Hamel
- Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, 1055 du P.E.P.S., P.O. Box 10380, Stn. Sainte-Foy, Quebec, Quebec, G1V 4C7, Canada
- Département de biologie, Université de Sherbrooke, Sherbrooke, Quebec, J1K 2R1, Canada
| | - Marie-Josée Morency
- Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, 1055 du P.E.P.S., P.O. Box 10380, Stn. Sainte-Foy, Quebec, Quebec, G1V 4C7, Canada
| | - Nathalie Beaudoin
- Département de biologie, Université de Sherbrooke, Sherbrooke, Quebec, J1K 2R1, Canada
| | - Brian E Ellis
- Michael Smith Laboratories, University of British Columbia, 2185 East Mall, Vancouver, British Columbia, V6T 1Z4, Canada
| | - Armand Séguin
- Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, 1055 du P.E.P.S., P.O. Box 10380, Stn. Sainte-Foy, Quebec, Quebec, G1V 4C7, Canada
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Hamel LP, Nicole MC, Sritubtim S, Morency MJ, Ellis M, Ehlting J, Beaudoin N, Barbazuk B, Klessig D, Lee J, Martin G, Mundy J, Ohashi Y, Scheel D, Sheen J, Xing T, Zhang S, Seguin A, Ellis BE. Ancient signals: comparative genomics of plant MAPK and MAPKK gene families. Trends Plant Sci 2006; 11:192-8. [PMID: 16537113 DOI: 10.1016/j.tplants.2006.02.007] [Citation(s) in RCA: 320] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2005] [Revised: 01/05/2006] [Accepted: 02/27/2006] [Indexed: 05/07/2023]
Abstract
MAPK signal transduction modules play crucial roles in regulating many biological processes in plants, and their components are encoded by highly conserved genes. The recent availability of genome sequences for rice and poplar now makes it possible to examine how well the previously described Arabidopsis MAPK and MAPKK gene family structures represent the broader evolutionary situation in plants, and analysis of gene expression data for MPK and MKK genes in all three species allows further refinement of those families, based on functionality. The Arabidopsis MAPK nomenclature appears sufficiently robust to allow it to be usefully extended to other well-characterized plant systems.
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Affiliation(s)
- Louis-Philippe Hamel
- Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, 1055 du PEPS, Sainte-Foy, Québec, Canada G1V 4C7
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14
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Richard S, Morency MJ, Drevet C, Jouanin L, Séguin A. Isolation and characterization of a dehydrin gene from white spruce induced upon wounding, drought and cold stresses. Plant Mol Biol 2000; 43:1-10. [PMID: 10949369 DOI: 10.1023/a:1006453811911] [Citation(s) in RCA: 45] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
A cDNA clone encoding a dehydrin gene was isolated from a cDNA library prepared from white spruce (Picea glauca) needle mRNAs. The cDNA, designated PgDhn1, is 1159 nucleotides long and has an open reading frame of 735 bp with a deduced amino acid sequence of 245 residues. The PgDhn1 amino acid sequence is highly hydrophilic and possesses four conserved repeats of the characterized lysine-rich K-segment (EKKGIMD-KIKEKLPG), and an 8-serine residue stretch prior to the first lysine-rich repeat that is common to many dehydrins. The DEYGNP conserved motif is, however, absent in the PgDhn1 sequence. In unstressed plants, the highest level of transcripts was detected in stem tissue and not fully expanded vegetative buds. PgDhn1 expression was also clearly detected in reproductive buds, at various stages of development. The mRNAs corresponding to PgDhn1 cDNA were induced upon wounding and by jasmonic acid (JA) and methyl jasmonate (MeJa) treatments. Upon drought stress, increased transcript accumulation was observed in needle tissue reaching a maximum level 48 h after treatment. Treatments of seedlings with abscisic acid or ethephon also resulted in high levels of transcript accumulation in needle tissue. Finally, cold induction of PgDhn1 transcripts was also detected as early as 8 h after treatment.
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MESH Headings
- Abscisic Acid/pharmacology
- Acetates/pharmacology
- Cold Temperature
- Cyclopentanes/pharmacology
- DNA, Complementary/chemistry
- DNA, Complementary/genetics
- DNA, Complementary/isolation & purification
- Gene Expression Regulation, Developmental/drug effects
- Gene Expression Regulation, Plant/drug effects
- Molecular Sequence Data
- Organophosphorus Compounds/pharmacology
- Oxylipins
- Plant Growth Regulators/pharmacology
- Plant Proteins/genetics
- RNA, Plant/drug effects
- RNA, Plant/genetics
- RNA, Plant/metabolism
- Sequence Analysis, DNA
- Stress, Mechanical
- Transcription, Genetic/drug effects
- Trees/genetics
- Trees/growth & development
- Water/pharmacology
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Affiliation(s)
- S Richard
- Centre de recherche en biologie forestière, Pavillon C.-E.-Marchand, Université Laval, Sainte-Foy, Québec, Canada
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15
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Gagnon S, Morency MJ, Bourbeau D, Levesque RC. Toxoplasma gondii: structure and characterization of the 26S ribosomal RNA and peptidyl transferase domain. Exp Parasitol 1996; 83:346-51. [PMID: 8823251 DOI: 10.1006/expr.1996.0082] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The 26S, 5.8S, and the intergenic spacer ribosomal DNAs (rDNA) of Toxoplasma gondii have been cloned and completely sequenced from both DNA strands. The length of the large subunit was found to be 3487 nucleotides and the 5.8S was 153 nucleotides long. These formed the large rRNA subunit of Toxoplasma and were mapped in the rDNA unit known to be repeated 110 times in a head-to-tail fashion in the genome. Primer extension analysis and multiple alignments localized the 5' end point of the two rRNAs. Comparisons with Toxoplasma rDNA by nucleic acid homology studies gave 76% similarity with the dinoflagellate Prorocentrum micans, 66% with yeast Saccharomyces cerevisiae, and 64% with the ciliate Tetrahymena thermophila. Similarity was apparent in the conserved core structure of the large subunit rRNA and divergent sequences were identified in the so-called divergent domains. Construction of a secondary structure model of the peptidyl transferase center of the large rRNA revealed similarities with the same domain from other life forms.
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Affiliation(s)
- S Gagnon
- Pavillon Charles-Eugène Marchand et Faculté de Médecine, Université Laval, Ste-Foy, Québec, Canada
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16
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Liao X, Charlebois I, Ouellet C, Morency MJ, Dewar K, Lightfoot J, Foster J, Siehnel R, Schweizer H, Lam JS, Hancock REW, Levesque RC. Physical mapping of 32 genetic markers on the Pseudomonas aeruginosa PAO1 chromosome. Microbiology (Reading) 1996; 142 ( Pt 1):79-86. [PMID: 8581173 DOI: 10.1099/13500872-142-1-79] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
The Pseudomonas aeruginosa chromosome was fractionated with the enzymes SpeI and DpnI, and genomic fragments were separated by PFGE and used for mapping a collection of 40 genes. This permitted the localization of 8 genes previously mapped and of 32 genes which had not been mapped. We showed that a careful search of databases and identification of sequences that were homologous to known genes could be used to design and synthesize DNA probes for the mapping of P. aeruginosa homologues by Southern hybridization with genomic fragments, resulting in definition of the locations of the aro-2, dapB, envA, mexA, groEL, oprH, oprM, oprP, ponA, rpoB and rpoH genetic markers. In addition, a combination of distinct DNA sources were utilized as radioactively labelled probes, including specific restriction fragments of the cloned genes (glpD, opdE, oprH, oprO, oprP, phoS), DNA fragments prepared by PCR, and single-stranded DNA prepared from phagemid libraries that had been randomly sequenced. We used a PCR approach to clone fragments of the putative yhhF, sucC, sucD, cypH, pbpB, murE, pbpC, soxR, ftsA, ftsZ and envA genes. Random sequencing of P. aeruginosa DNA from phagemid libraries and database searching permitted the cloning of sequences from the acoA, catR, hemD, pheS, proS, oprD, pyo and rpsB gene homologues. The described genomic methods permit the rapid mapping of the P. aeruginosa genome without linkage analysis.
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MESH Headings
- Base Sequence
- Chromosomes, Bacterial/genetics
- Cloning, Molecular
- DNA, Bacterial/genetics
- DNA, Bacterial/metabolism
- DNA, Complementary/genetics
- Deoxyribonucleases, Type II Site-Specific/metabolism
- Electrophoresis, Gel, Pulsed-Field
- Gene Expression
- Genes, Bacterial
- Genetic Markers
- Molecular Sequence Data
- Oligonucleotide Probes
- Polymerase Chain Reaction
- Pseudomonas aeruginosa/genetics
- Restriction Mapping
- Sequence Analysis, DNA
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Affiliation(s)
- Xiaowen Liao
- Department of Microbiology and Immunology, University of British Columbia, 300-6174 University Boulevard, Vancouver BC, Canada V6T 1Z3
| | - Isabelle Charlebois
- Microbiologie Moléculaire et Génie des Protéines, Département de Microbiologie, Faculté de Médecine, Pavillon Charles-Eugène-Marchand, Université Laval, Ste-Foy, Québec, Canada G1K 7P4
| | - Catherine Ouellet
- Microbiologie Moléculaire et Génie des Protéines, Département de Microbiologie, Faculté de Médecine, Pavillon Charles-Eugène-Marchand, Université Laval, Ste-Foy, Québec, Canada G1K 7P4
| | - Marie-Josée Morency
- Microbiologie Moléculaire et Génie des Protéines, Département de Microbiologie, Faculté de Médecine, Pavillon Charles-Eugène-Marchand, Université Laval, Ste-Foy, Québec, Canada G1K 7P4
| | - Ken Dewar
- Microbiologie Moléculaire et Génie des Protéines, Département de Microbiologie, Faculté de Médecine, Pavillon Charles-Eugène-Marchand, Université Laval, Ste-Foy, Québec, Canada G1K 7P4
| | - Jeff Lightfoot
- Microbiologie Moléculaire et Génie des Protéines, Département de Microbiologie, Faculté de Médecine, Pavillon Charles-Eugène-Marchand, Université Laval, Ste-Foy, Québec, Canada G1K 7P4
| | - Jennifer Foster
- Department of Microbiology, University of Guelph, Guelph, Ontario, Canada N1G 2W1
| | - Richard Siehnel
- Department of Microbiology and Immunology, University of British Columbia, 300-6174 University Boulevard, Vancouver BC, Canada V6T 1Z3
| | - Herbert Schweizer
- Department of Medical Microbiology and Infectious Diseases, University of Calgary, Calgary, Alberta, Canada T2N 4N1
| | - Joseph S Lam
- Department of Microbiology, University of Guelph, Guelph, Ontario, Canada N1G 2W1
| | - Robert E W Hancock
- Department of Microbiology and Immunology, University of British Columbia, 300-6174 University Boulevard, Vancouver BC, Canada V6T 1Z3
| | - Roger C Levesque
- Microbiologie Moléculaire et Génie des Protéines, Département de Microbiologie, Faculté de Médecine, Pavillon Charles-Eugène-Marchand, Université Laval, Ste-Foy, Québec, Canada G1K 7P4
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17
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Guay JM, Dubois D, Morency MJ, Gagnon S, Mercier J, Levesque RC. Detection of the pathogenic parasite Toxoplasma gondii by specific amplification of ribosomal sequences using comultiplex polymerase chain reaction. J Clin Microbiol 1993; 31:203-7. [PMID: 8432803 PMCID: PMC262736 DOI: 10.1128/jcm.31.2.203-207.1993] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Amplification of DNA sequences from ribosomal DNA (rDNA) was tested as a specific and sensitive method for the detection of small numbers of Toxoplasma gondii tachyzoite cells. We applied the polymerase chain reaction (PCR) on the basis of detection of the 110-fold repetitive rDNA as a target by using (i) DNA sequences within the small ribosomal subunit known to be universal and conserved in all eukaryotes and (ii) small ribosomal subunit and intergenic spacer rDNA sequences known to be T. gondii species specific. The level of sensitivity obtained from a crude cell lysate allowed the detection of as few as one parasite visualized directly as a specific PCR product in agarose gels. By using a combination of universal and T. gondii species-specific primers, we propose a comultiplex-based PCR approach as a new diagnostic tool. The combination of sensitivity, specificity, and built-in positive and negative PCR controls should make detection of the rDNA sequences by comultiplex PCR a useful clinical test for the diagnosis of toxoplasmosis and for epidemiological studies. Finally, the idea of a built-in positive control to support or counter the T. gondii-specific PCR result is novel and is a notable advance.
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Affiliation(s)
- J M Guay
- Département de Microbiologie, Faculté de Médecine, Université Laval, Ste-Foy, Québec, Canada
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