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Dive into the research topics where Benjamin Mimee is active.

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Featured researches published by Benjamin Mimee.


Molecular Phylogenetics and Evolution | 2013

Genetic diversity of the golden potato cyst nematode Globodera rostochiensis and determination of the origin of populations in Quebec, Canada.

Annie Christine Boucher; Benjamin Mimee; Josselin Montarry; Sylvie Bardou-Valette; Guy Bélair; Peter Moffett; Eric Grenier

The golden cyst nematode (Globodera rostochiensis), native to South America, has been introduced in many parts of the world, including Europe and North America. Recently, it was found for the first time in the province of Quebec, Canada in the locality of St. Amable near Montreal. To date, very few studies have examined the population genetics of this pest. Consequently, there is a lack of knowledge about the genetic structure and evolution of this nematode. In this study, twelve new microsatellite markers were developed in order to explore these questions. These markers were used to genotype fifteen populations originating from different regions of the world, including five from Canada. Within populations, the highest genetic diversity was consistently observed in the populations from Bolivia, the postulated region of origin of the golden nematode, and the lowest in populations from British Columbia (Canada) and New York (USA). The two Quebec populations were very similar to each other and to the population found in Newfoundland, but surprisingly, they were significantly different from three other North American populations including those from New York and British Columbia. Based on our results, we conclude that the golden cyst nematode has been introduced in North America at least twice from distinct regions of the world.


Molecular Ecology Resources | 2015

A new method for studying population genetics of cyst nematodes based on Pool-Seq and genomewide allele frequency analysis

Benjamin Mimee; Marc-Olivier Duceppe; Pierre-Yves Véronneau; Joël Lafond-Lapalme; Martine Jean; François Belzile; Guy Bélair

Cyst nematodes are important agricultural pests responsible for billions of dollars of losses each year. Plant resistance is the most effective management tool, but it requires a close monitoring of population genetics. Current technologies for pathotyping and genotyping cyst nematodes are time‐consuming, expensive and imprecise. In this study, we capitalized on the reproduction mode of cyst nematodes to develop a simple population genetic analysis pipeline based on genotyping‐by‐sequencing and Pool‐Seq. This method yielded thousands of SNPs and allowed us to study the relationships between populations of different origins or pathotypes. Validation of the method on well‐characterized populations also demonstrated that it was a powerful and accurate tool for population genetics. The genomewide allele frequencies of 23 populations of golden nematode, from nine countries and representing the five known pathotypes, were compared. A clear separation of the pathotypes and fine genetic relationships between and among global populations were obtained using this method. In addition to being powerful, this tool has proven to be very time‐ and cost‐efficient and could be applied to other cyst nematode species.


Bioinformatics | 2016

A new method for decontamination of de novo transcriptomes using a hierarchical clustering algorithm.

Joël Lafond-Lapalme; Marc-Olivier Duceppe; Shengrui Wang; Peter Moffett; Benjamin Mimee

Motivation: The identification of contaminating sequences in a de novo assembly is challenging because of the absence of information on the target species. For sample types where the target organism is impossible to isolate from its matrix, such as endoparasites, endosymbionts and soil‐harvested samples, contamination is unavoidable. A few post‐assembly decontamination methods are currently available but are based only on alignments to databases, which can lead to poor decontamination. Results: We present a new decontamination method based on a hierarchical clustering algorithm called MCSC. This method uses frequent patterns found in sequences to create clusters. These clusters are then linked to the target species or tagged as contaminants using classic alignment tools. The main advantage of this decontamination method is that it allows sequences to be tagged correctly even if they are unknown or misaligned to a database. Availability and Implementation: Scripts and documentation about the MCSC decontamination method are available at https://github.com/Lafond‐LapalmeJ/MCSC_Decontamination. Contact : [email protected] Supplementary information: Supplementary data are available at Bioinformatics online.


Scientific Reports | 2017

Analysis of survival and hatching transcriptomes from potato cyst nematodes, Globodera rostochiensis and G . pallida

Marc-Olivier Duceppe; Joël Lafond-Lapalme; Juan E. Palomares-Rius; Michael Sabeh; Vivian C. Blok; Peter Moffett; Benjamin Mimee

Potato cyst nematodes (PCNs), Globodera rostochiensis and G. pallida, cause important economic losses. They are hard to manage because of their ability to remain dormant in soil for many years. Although general knowledge about these plant parasitic nematodes has considerably increased over the past decades, very little is known about molecular events involved in cyst dormancy and hatching, two key steps of their development. Here, we have studied the progression of PCN transcriptomes from dry cysts to hatched juveniles using RNA-Seq. We found that several cell detoxification-related genes were highly active in the dry cysts. Many genes linked to an increase of calcium and water uptake were up-regulated during transition from dormancy to hydration. Exposure of hydrated cysts to host plant root exudates resulted in different transcriptional response between species. After 48 h of exposure, G. pallida cysts showed no significant modulation of gene expression while G. rostochiensis had 278 differentially expressed genes. The first G. rostochiensis significantly up-regulated gene was observed after 8 h and was coding for a transmembrane metalloprotease. This enzyme is able to activate/inactivate peptide hormones and could be involved in a cascade of events leading to hatching. Several known effector genes were also up-regulated during hatching.


Canadian Journal of Plant Pathology-revue Canadienne De Phytopathologie | 2016

Evaluation of cultural methods for the management of the golden nematode (Globodera rostochiensis) in Quebec, Canada

Guy Bélair; Nathalie Dauphinais; Benjamin Mimee

Abstract Potato cyst nematodes are a major threat to potato production worldwide. In 2006, the isolation of the golden nematode, Globodera rostochiensis, in Quebec, Canada, led to the establishment of a quarantine area and the initiation of a research programme for the sustainable management of this regulated pest. In this study, the field efficacy of crop rotations and soil amendments was assessed in microplots for their potential to reduce populations of G. rostochiensis in the quarantine area. Crop rotation with a resistant potato cultivar was very effective in decreasing the population density of G. rostochiensis in soil. A single year with a cultivar carrying the H1 resistance gene reduced nematode populations by 62–95%. After 3 consecutive years of cropping to resistant potato, the number of viable eggs was zero in several microplots, and the overall population reduction was around 95%. Natural population decline with the cultivation of a non-host crop such as corn was around 30% per year. Trap cropping also showed reduced G. rostochiensis populations with results similar to the resistant cultivar. Sticky nightshade could not be established under Quebec’s climatic conditions and therefore was not a viable alternative for managing golden nematode in Quebec. Soil amendment with high rates of urea provided some reduction in populations but was not an economically viable option for managing potato cyst nematodes. Chicken manure and pig slurry did not provide a significant reduction of G. rostochiensis under Quebec field conditions.


bioRxiv | 2018

The genome of the soybean cyst nematode (Heterodera glycines) reveals complex patterns of duplications involved in the evolution of parasitism genes

Rick E. Masonbrink; Thomas R. Maier; Usha Muppirala; Arun S. Seetharam; Etienne Lord; Parijat S. Juvale; Jeremy Schmutz; Nathan T. Johnson; Dmitry Korkin; Melissa G. Mitchum; Benjamin Mimee; Sebastian Eves-van den Akker; Matthew E. Hudson; Andrew J. Severin; Thomas J. Baum

Heterodera glycines, commonly referred to as the soybean cyst nematode (SCN), is an obligatory and sedentary plant parasite that causes over a billion-dollar yield loss to soybean production annually. Although there are genetic determinants that render soybean plants resistant to certain nematode genotypes, resistant soybean cultivars are increasingly ineffective because their multi-year usage has selected for virulent H. glycines populations. The parasitic success of H. glycines relies on the comprehensive re-engineering of an infection site into a syncytium, as well as the long-term suppression of host defense to ensure syncytial viability. At the forefront of these complex molecular interactions are effectors, the proteins secreted by H. glycines into host root tissues. The mechanisms of effector acquisition, diversification, and selection need to be understood before effective control strategies can be developed, but the lack of an annotated genome has been a major roadblock. Here, we use PacBio long-read technology to assemble a H. glycines genome of 738 contigs into 123Mb with annotations for 29,769 genes. The genome contains significant numbers of repeats (34%), tandem duplicates (18.7Mb), and horizontal gene transfer events (151 genes). Using previously published effector sequences, the newly generated H. glycines genome, and comparisons to other nematode genomes, we investigate the evolutionary mechanisms responsible for the emergence and diversification of effector genes.


Scientific Reports | 2018

Genetic diversity and phylogeny of South African Meloidogyne populations using genotyping by sequencing

Milad Rashidifard; Hendrika Fourie; Pierre-Yves Véronneau; Mariette Marais; M. Daneel; Benjamin Mimee

Meloidogyne species cause great crop losses worldwide. Although genetic host plant resistance is an effective control strategy to minimize damage caused by Meloidogyne, some resistant genes are ineffective against virulent species such as Meloidogyne enterolobii. Detailed knowledge about the genetic composition of Meloidogyne species is thus essential. This study focused on genotyping-by-sequencing (GBS) and Pool-Seq to elucidate the genetic relation between South African M. enterolobii, M. incognita and M. javanica populations. Hence, 653 common single nucleotide polymorphisms (SNPs) were identified and used to compare these species at genetic level. Allele frequencies of 34 SNPs consistently differed between the three Meloidogyne species studied. Principal component and phylogenetic analyses grouped the M. enterolobii populations in one clade, showing a distant relation to the M. javanica populations. These two species also shared genetic links with the M. incognita populations studied. GBS has been used successfully in this study to identify SNPs that discriminated among the three Meloidogyne species investigated. Alleles, only occurring in the genome of M. enterolobii and located in genes involved in virulence in other animal species (e.g. a serine/threonine phosphatase and zinc finger) have also been identified, accentuating the value of GBS in future studies of this nature.


PLOS ONE | 2018

Transcriptome-wide selection of a reliable set of reference genes for gene expression studies in potato cyst nematodes (Globodera spp.)

Michael Sabeh; Marc-Olivier Duceppe; Marc St-Arnaud; Benjamin Mimee

Relative gene expression analyses by qRT-PCR (quantitative reverse transcription PCR) require an internal control to normalize the expression data of genes of interest and eliminate the unwanted variation introduced by sample preparation. A perfect reference gene should have a constant expression level under all the experimental conditions. However, the same few housekeeping genes selected from the literature or successfully used in previous unrelated experiments are often routinely used in new conditions without proper validation of their stability across treatments. The advent of RNA-Seq and the availability of public datasets for numerous organisms are opening the way to finding better reference genes for expression studies. Globodera rostochiensis is a plant-parasitic nematode that is particularly yield-limiting for potato. The aim of our study was to identify a reliable set of reference genes to study G. rostochiensis gene expression. Gene expression levels from an RNA-Seq database were used to identify putative reference genes and were validated with qRT-PCR analysis. Three genes, GR, PMP-3, and aaRS, were found to be very stable within the experimental conditions of this study and are proposed as reference genes for future work.


Frontiers in Plant Science | 2018

Genome Scans Reveal Homogenization and Local Adaptations in Populations of the Soybean Cyst Nematode

Anne-Frédérique Gendron St-Marseille; Etienne Lord; Pierre-Yves Véronneau; Jacques Brodeur; Benjamin Mimee

Determining the adaptive potential of alien invasive species in a new environment is a key concern for risk assessment. As climate change is affecting local climatic conditions, widespread modifications in species distribution are expected. Therefore, the genetic mechanisms underlying local adaptations must be understood in order to predict future species distribution. The soybean cyst nematode (SCN), Heterodera glycines Ichinohe, is a major pathogen of soybean that was accidentally introduced in most soybean-producing countries. In this study, we explored patterns of genetic exchange between North American populations of SCN and the effect of isolation by geographical distance. Genotyping-by-sequencing was used to sequence and compare 64 SCN populations from the United States and Canada. At large scale, only a weak correlation was found between genetic distance (Wrights fixation index, FST) and geographic distance, but local effects were strong in recently infested states. Our results also showed a high level of genetic differentiation within some populations, allowing them to adapt to new environments and become established in new soybean-producing areas. Bayesian genome scan methods identified 15 loci under selection for climatic or geographic co-variables. Among these loci, two non-synonymous mutations were detected in SMAD-4 (mothers against decapentaplegic homolog 4) and DOP-3 (dopamine receptor 3). High-impact variants linked to these loci by genetic hitchhiking were also highlighted as putatively involved in local adaptation of SCN populations to new environments. Overall, it appears that strong selective pressure by resistant cultivars is causing a large scale homogenization with virulent populations.


Plant Disease | 2017

Development and application of a multiplex qPCR method for the simultaneous detection and quantification of Pratylenchus alleni and P. penetrans in Quebec, Canada

Nathalie Dauphinais; Myriam Vandal; Annie-Ève Gagnon; Guy Bélair; Pierre-Yves Véronneau; Benjamin Mimee

Root lesion nematodes are very common plant-parasitic nematodes that affect a wide range of plants. More than one species can be found simultaneously in a field, and each has a different impact on crop yield. Unfortunately, identifying them using classical morphometric criteria is very difficult and time consuming. The species Pratylenchus alleni was recently observed for the first time in Canada, associated with severe damage in a soybean field in the province of Quebec. The major species, P. penetrans, is also known to be endemic in Quebec but no data exist on its distribution in field crops. This prompted the development of a multiplex quantitative polymerase chain reaction (PCR) assay for the simultaneous detection and quantification of P. alleni and P. penetrans. The method was found to be specific and sensitive, systematically detecting a single larva in a 100-cm3 soil sample with no cross-amplification with other species, even when they outnumbered the target species. An exogenous internal positive control was included in the test to avoid false negatives due to the presence of PCR inhibitors. This assay was used to study the distribution of P. alleni and P. penetrans in 185 soybean fields in the major soybean-producing areas of Quebec during a 3-year survey. Overall, P. penetrans was found in 42% of the fields, P. alleni in 8%, and both species in 4%. The population density of P. alleni in positive fields was still very low, with only a few larvae detected. However, densities of P. penetrans were much higher: the provincial mean was 51.7 nematodes per 100 cm3 of soil (in positive samples), and 8% of the fields (15 of 185) exceeded the theoretical economic threshold. The presence of P. penetrans was also strongly correlated with soil texture, with lighter soil being the most favorable.

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Guy Bélair

Agriculture and Agri-Food Canada

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Pierre-Yves Véronneau

Agriculture and Agri-Food Canada

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Marc-Olivier Duceppe

Agriculture and Agri-Food Canada

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Nathalie Dauphinais

Agriculture and Agri-Food Canada

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Joël Lafond-Lapalme

Agriculture and Agri-Food Canada

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Michael Sabeh

Agriculture and Agri-Food Canada

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Peter Moffett

Université de Sherbrooke

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Etienne Lord

Agriculture and Agri-Food Canada

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