Biology subjects

Brochu, A.-S.

Publications and source records attributed to Brochu, A.-S..

6 recordsLinked to original sources

bioRxiv2024

Telomere-to-telomere genome assembly of the clubroot pathogen Plasmodiophora brassicae

Plasmodiophora brassicae (Woronin, 1877), a biotrophic, obligate parasite, is the causal agent of clubroot disease in brassicas. The clubroot pathogen has been reported in more than 80 countries worldwide, causing economic losses of hundreds of millions every year. Despite its widespread impact, very little is known about the molecular strategies it employs to induce the characteristic clubs in the roots of susceptible hosts during infection, nor about the mechanisms it uses to overcome genetic resistance. Here, we provide the first telomere-to-telomere complete genome of Plasmodiophora brassicae. We generated [~] 27 Gb of Illumina, Oxford Nanopore, and PacBio HiFi data from resting spores of strain Pb3A and produced a 25.3 Mb assembly comprising 20 chromosomes, with an N50 of 1.37 Mb. The BUSCO score, the highest reported for any member of the group Rhizaria (Eukaryota: 88.2%), highlights the limitations within the Eukaryota database for members of this lineage. Using available transcriptomic data and protein evidence, we annotated the Pb3A genome, identifying 10,521 protein-coding gene models. This high-quality, complete genome of Plasmodiophora brassicae will serve as a crucial resource for the plant pathology community to advance the much-needed understanding of the evolution of the clubroot pathogen. SIGNIFICANCEPlasmodiophora brassicae (Woronin, 1877) is a devastating plant pathogen, member of the Rhizaria group, and is putting at risk the oilseed rape and cruciferous vegetable industry worldwide. Here, we present the first telomere-to-telomere genome of P. brassicae, and the first complete genome for a member of the Rhizaria taxon. We also provide a high-quality genome annotation featuring an enhanced gene model relative to previous studies. This complete genome will be of great interest to researchers focused on the ecology and evolution of the clubroot pathogen, as well as those studying other members of the Rhizaria group.

microbiology↗

bioRxiv2023

A new multiplex TaqMan qPCR targeting Clavibacter michiganensis virulence-related genes

Bacterial canker of tomato caused by Clavibacter michiganensis (Cm) is one of the most devastating bacterial diseases affecting the tomato industry worldwide. As the result of Cm colonization of the xylem, the susceptible host shows typical symptoms of wilt, marginal leaf necrosis, stem cankers, and ultimately plant death. However, is the ability of Cm to infect seeds and plants without causing symptoms what makes it an even more dangerous pathogen. Unfortunately, there are no resistant cultivars or effective chemical or biological control methods available to growers against Cm. Its control relies heavily on prevention. The implementation of a rapid and accurate detection tool is imperative to monitor the presence of Cm and prevent its spread. In this study, we developed a specific and sensitive multiplex TaqMan qPCR assay to detect Cm and distinguish it from related bacterial species that affect tomato plants. Two Cm chromosomal virulence-related genes, rhuM and tomA, were used as specific targets. The plant internal control tubulin alpha-3 was included in each of the multiplexes to improve the reliability of the assay. Specificity was evaluated with 37 bacterial strains and more than 120 samples, including other Clavibacter spp. and related and unrelated bacterial pathogens from different geographic locations affecting a wide variety of hosts. Results showed that the assay was able to screen all Cm strains against other related bacteria. The assay was validated on tissue and seed samples following artificial infection and all tested samples accurately detected the presence of Cm. The tool described here is highly specific, sensitive, and reliable for the detection of Cm and allows the quantification of Cm in seeds, roots, stems, and leaves, finding a lower abundance of Cm in the roots compared to the other parts of the plant. The diagnostic assay can also be adapted for multiple purposes such as seed certification programs, surveillance, biosafety, the effectiveness of control methods, border protection, and epidemiological studies.

microbiology↗

bioRxiv2023

Can leafhoppers help us trace the impact of climate change on agriculture?

SUMMARYClimate change is reshaping agriculture and insect biodiversity worldwide. With rising temperatures, insect species with narrow thermal margins are expected to be pushed beyond their thermal limits, and losses related to herbivory and diseases transmitted by them will be experienced in new regions. Several previous studies have investigated this phenomenon in tropical and temperate regions, locally and globally; however, here, it is proposed that climate changes impact on agriculture can be traced through the study of Nearctic migratory insects, specifically leafhoppers. To test this hypothesis, leafhoppers in strawberry fields located in the province of Quebec, eastern Canada, were evaluated. The strawberry-leafhopper pathosystem offers a unique opportunity because leafhoppers can transmit, among other diseases, strawberry green petal disease (SbGP), which is associated with pathogenic phytoplasmas. Here, we found that in the last ten years, the number of leafhoppers has been increasing in correspondence with the number of SbGP cases detected in eastern Canada, reporting for the first time ten species new to eastern Canada and two to the country, although the leafhopper diversity has been seriously affected. Our model using more than 34 000 leafhoppers showed that their abundance is influenced by temperature, a factor that we found also influences the microbiome associated with Macrosteles quadrilineatus, which was one of the most abundant leafhoppers we observed. One of our most striking findings is that none of the insecticides used by strawberry growers can control leafhopper incidence, which could be linked to microbiome changes induced by changing temperatures. We suggest that Nearctic leafhoppers can be used as sentinels to trace the multilayered effects of climate change in agriculture. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=185 SRC="FIGDIR/small/544773v1_ufig1.gif" ALT="Figure 1"> View larger version (77K): org.highwire.dtl.DTLVardef@e984eorg.highwire.dtl.DTLVardef@3146a9org.highwire.dtl.DTLVardef@1160b9aorg.highwire.dtl.DTLVardef@53c39c_HPS_FORMAT_FIGEXP M_FIG C_FIG IN BRIEFThe current climate crisis is reshaping insect biodiversity and abundance, but little is known about the direct effect of this phenomenon on agriculture. In this study, we explored leafhoppers, a group of agriculturally important insect pests and disease vectors, as sentinels of the effect of climate change on agriculture. Our findings indicate that this group of insects can help us to understand the effect of the current climate crisis on insect invasions, diversity, abundance, disease dynamics and insecticide resistance and to take quick action to ensure food security while achieving more sustainable agriculture. HIGHLIGHTSO_LIMigratory leafhoppers benefit from temperature increases C_LIO_LILeafhopper-transmitted diseases have increased in the last decade C_LIO_LINew non-migratory leafhoppers can be found now in Nearctic regions C_LIO_LILeafhopper insecticide resistance could be linked to the insect microbiome C_LI

ecology↗

bioRxiv2023

A Hydroponic-Based Bioassay to Facilitate Plasmodiophora brassicae Phenotyping

Clubroot, caused by the obligate parasite Plasmodiophora brassicae, is one of the most devastating diseases affecting the canola/oilseed rape (Brassica napus) industry worldwide. Currently, the planting of clubroot-resistant (CR) cultivars is the most effective strategy used to restrict the spread and the economic losses linked to the disease. However, virulent P. brassicae isolates have been able to infect many of the currently available CR cultivars, and the options to manage the disease are becoming limited. Another challenge has been achieving consistency in evaluating host reactions to P. brassicae infection, with most bioassays conducted in soil and/or potting medium, which requires significant space and can be labour intensive. Visual scoring of clubroot symptom development can also be influenced by user bias. Here, we have developed a hydroponic bioassay using well-characterized P. brassicae single-spore isolates representative of clubroot virulence in Canada, as well as field isolates from three Canadian provinces, in combination with canola inbred homozygous lines carrying resistance genetics representative of CR cultivars available to growers in Canada. To improve the efficiency and consistency of disease assessment, symptom severity scores were compared with clubroot evaluations based on the scanned root area. According to the results, this bioassay offers a reliable, less expensive, and reproducible option to evaluate P. brassicae virulence, as well as a means to identify which canola resistance profile(s) may be effective against particular isolates. This bioassay will contribute to the breeding of new CR canola cultivars and the identification of virulence genes in P. brassicae that could trigger resistance and have been very elusive to this day.

microbiology↗

bioRxiv2023

Diet and injection, our recommendation to characterize Clavibacter michiganensis- tomato interactions

Tomato (Solanum lycopersicum L.) is one of the most important vegetables in the world. Its extensive cultivation has made this plant the target of many viral, fungal, and bacterial diseases. Among them, the bacterial canker of tomato caused by Clavibacter michiganensis (Cm) has been named one of the most devastating diseases affecting the tomato industry worldwide. It can significantly reduce the yields and profitability of this crop. One of the big challenges we found when working with Cm and trying to characterize the virulence of different isolates was the lack of a consensus methodology to inoculate tomato plants, how to fertilize them and characterize Cm virulence. This research aimed to identify an artificial inoculation method to induce bacterial canker on tomato plants in greenhouse conditions to homogenize the results of different studies with Cm. We compared two inoculation methods, including the scalpel and syringe method with two levels of fertilization, low and high fertilization. After evaluating several variables like the percentage of necrotic leaves and the height of the plants, the results showed that the syringe inoculation with low fertilization was the most effective inoculation method allowing the development of a multilevel scale that can be used to study the interaction between tomato plants and Cm isolates.

microbiology↗

bioRxiv2023

A decade of hidden phytoplasmas unveiled through citizen science

Climate change is impacting agriculture in many ways, and a contribution from all is required to reduce the imminent loses related to it. Recently, it has been showed that citizen science could be a way to trace the impact of climate change. However, how can citizen science be applied in plant pathology? Here, using as an example a decade of phytoplasma-related diseases reported by growers, agronomists, citizens in general, and confirmed by a government laboratory, we explore a new way of valuing plant pathogens monitoring data deriving from land-users or stakeholders. Through this collaboration we found that in the last decade thirty-four hosts have been affected by phytoplasmas, nine, thirteen and five of these plants were, for the first time, reported phytoplasma hosts in Eastern Canada, in Canada and worldwide, respectively. Another finding of great impact is the first report of a Ca. P. phoenicium-related strain in Canada, while Ca. P. pruni and Ca. P. pyri was reported for the first time in Eastern Canada. These findings will have a great impact in the management of phytoplasmas and their insect vectors. Using these insect-vectored bacterial pathogens, we show the needs of new strategies that allow a fast and accurate communication between concerned citizens and those institutions confirming their observations. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=200 SRC="FIGDIR/small/524422v1_ufig1.gif" ALT="Figure 1"> View larger version (107K): org.highwire.dtl.DTLVardef@f676eborg.highwire.dtl.DTLVardef@f964bforg.highwire.dtl.DTLVardef@14576acorg.highwire.dtl.DTLVardef@1721bfb_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗