Biology subjects

Lemoyne, P.

Publications and source records attributed to Lemoyne, P..

3 recordsLinked to original sources

bioRxiv2025

Exploring the mycovirome: novel and diverse mycoviruses in Botrytis cinerea

Botrytis cinerea is a necrotrophic fungal pathogen that causes significant economic losses to many crops, including vegetables, fruits, and ornamental plants. The management of B. cinerea is difficult due to a rise in fungicide resistance. Harnessing mycoviruses that cause reduced virulence (hypovirulence) in B. cinerea is a promising alternative. Over 100 mycoviruses have been identified in Botrytis spp. to date, including several hypovirulence-inducing mycoviruses. This research aimed to further explore, for the first time in Canada, the mycovirome of B. cinerea and identify potential hypovirulence-inducing mycoviruses. Isolates of B. cinerea were collected from fruits and vegetables in the province of Quebec. Fitness and pathogenicity criteria, including sclerotia production, colony morphotype, and lesion size were evaluated. A double-stranded RNA (dsRNA) extraction protocol tailored to the detection of mycoviruses was used to sequence dsRNA from 45 isolates with low fitness/pathogenicity, and an in-house bioinformatics workflow was used to profile the mycovirome. Mycoviruses were identified in 44/45 isolates. Most of these had positive single-stranded RNA or dsRNA genomes, and a small number had negative single-stranded RNA, single-stranded DNA, or reverse transcriptase RNA genomes. Following deep analysis of RNA-dependent RNA polymerase and replication initiation proteins, a total of 62 unique contigs were identified belonging to new strains of mycovirus species. Furthermore, four putative novel mycovirus species belonging to Endornaviridae, Botybirnaviridae, Peribunyaviridae, and Bunyavirales taxa were identified. Several mycovirus species positively and/or negatively co-occurred with B. cinerea isolates collected from strawberry or raspberry. This study revealed a high degree of diversity in the mycovirome of B. cinerea. Species accumulation curve analysis indicated that, with the number of isolates characterized, we were unable to capture the full extent of expected diversity. Nevertheless, we identified potential hypovirulence-inducing mycoviruses, including Botrytis cinerea mitovirus 1, Botrytis cinerea hypovirus 1, and Botrytis porri botybirnavirus 1. Some of these novel mycoviruses belonged to taxa known to produce viral particles, which can be an interesting feature for their use as biocontrol agents (BCA). ImportanceThis study provides the first comprehensive profiling of mycoviruses infecting Botrytis cinerea in Canada, a significant step in understanding how these viruses can naturally limit crop disease. Due to growing resistance against conventional fungicides, new biological methods to control B. cinerea are crucial. By profiling mycoviruses in fungal samples collected in Quebec, we identified several novel viruses that appear to reduce the pathogenicity of B. cinerea. These viruses, known as hypovirulence-inducing mycoviruses, could be used to develop biocontrol agents (BCA), offering a more sustainable disease management alternative. Notably, we found virus families with extracellular potential, which may enable easier application as BCAs in agriculture. This research not only broadens the understanding of fungal virology but also holds promise for innovative, eco-friendly approaches to managing Botrytis cinerea in Canada.

genomics↗

bioRxiv2023

From Asymptomatic to Symptomatic: Multiomics profiling of the temporal response of grapevine viral-mixed infection

Mixed viral infections are common in grapevines. However, our understanding of the factors and signaling pathways that influence the expression of viral symptoms in mixed infections is still incomplete. In a previous study, we revealed that the presence of grapevine leafroll-associated virus species in mixed infections was randomly associated with the devel-opment of virus-like symptoms. To understand what drives the timing of these virus-like symptoms in mixed infections, we used dsRNA and total RNA sequencing and metabolomic analysis to profile the viromes, metabolites, and transcripts of grapevine leaves collected at two different times of the year (summer and autumn). We demonstrated that neither viral titre nor virome composition changes were associated with symptom expression in autumn. The total phenolic content and antioxidant capacity increased in most plants except for those with early onset symptoms. According to the results of differential gene expression analysis, cell wall biosynthesis pathways were significantly downregulated in all grapevine plants infected with grapevine leafroll-associated virus 3, grapevine asteroid mosaic-associated virus, and grape-vine Pinot gris virus. In addition, polyketide pathways were significantly upregulated in all cultivars, while flavonoid precursor (e.g. abscisic acid) production was significantly reduced in plants that expressed strong virus-like symptoms. In the Vidal cultivar, an uncharacterized double-stranded RNA-binding protein (DRB) appears to play a critical role in the plants an-tiviral defences, supporting the recent hypothesis that DRBs make an important contribution to dominant antiviral responses in plants. The seasonality of the expression virus-like symptoms appears to be a consequence of the dynamic interactions between antiviral factors and viral counter-defences that occur at different developmental stages of grapevine.

plant biology↗

bioRxiv2023

Nanovirseq: dsRNA sequencing for plant virus and viroid detection by Nanopore sequencing

Worldwide, there is a need for certified clean plant materials to limit viral diseases spread. In order to design a robust and proactive viral-like disease certification, diagnostics, and management program, it is essential to have a fast, inexpensive, and user-friendly tool. The purpose of this study was to determine whether dsRNA-based nanopore sequencing can be a reliable method for the detection of viruses and viroids in grapevines or not. Compared to direct RNA sequencing from rRNA-depleted total RNA (rdTotalRNA), direct-cDNA sequencing from dsRNA (dsRNAcD) yielded more viral reads and detected all grapevine viruses and viroids detected using Illumina MiSeq sequencing (dsRNA-MiSeq). With dsRNAcD sequencing it was possible to detect low abundance viruses (e.g., Grapevine red globe virus) where rdTotalRNA sequencing failed to detect them. Indeed, even after removing rRNA, rdTotalRNA sequencing yielded low viral read numbers. rdTotalRNA sequencing was not sensitive enough to detect all the viruses detected by dsRNA-MiSeq. In addition, there was a false positive identification of a viroid in the rdTotalRNA sequencing that was due to misannotation of a host-driven read. For quick and accurate reads classification, two different taxonomical classification workflows based on protein and nucleotide homology were evaluated in this study, namely DIAMOND&MEGAND (DIA&MEG) and Centrifuge&Recentrifuge (Cent&Rec), respectively. Virome profiles from both workflows were similar except for grapevine endophyte endornavirus (GEEV), which was only detected using DIA&MEG. However, because DIA&MEGs classification is based on protein homology, it cannot detect viroid infection despite giving more robust results. Even though Cent&Recs virus and viroid detection workflow was faster (30 minutes) than DIA&MEGs (two hours), it could not provide the details and information DIA&MEG was able to provide. As demonstrated in our study, nanopore dsRNAcD sequencing and the proposed data analysis workflows are suitable and reliable for viruses and viroids detection, especially in grapevine where viral mixed infection is common.

pathology↗