The Experts below are selected from a list of 360 Experts worldwide ranked by ideXlab platform

Marc Fuchs - One of the best experts on this subject based on the ideXlab platform.

  • identification of protein interactions of grapevine fanleaf virus rna dependent rna polymerase during infection of nicotiana benthamiana by affinity purification and tandem mass spectrometry
    Journal of General Virology, 2021
    Co-Authors: Larissa J. Osterbaan, Victoria Hoyle, Michelle Curtis, Stacy L Deblasio, Keith D Rivera, Michelle Heck, Marc Fuchs
    Abstract:

    The RNA-dependent RNA polymerase (1EPol) is involved in replication of grapevine fanleaf virus (GFLV, Nepovirus, Secoviridae) and causes vein clearing symptoms in Nicotiana benthamiana. Information on protein 1EPol interaction with other viral and host proteins is scarce. To study protein 1EPol biology, three GFLV infectious clones, i.e. GHu (a symptomatic wild-type strain), GHu-1EK802G (an asymptomatic GHu mutant) and F13 (an asymptomatic wild-type strain), were engineered with protein 1EPol fused to a V5 epitope tag at the C-terminus. Following Agrobacterium tumefaciens-mediated delivery of GFLV clones in N. benthamiana and protein extraction at seven dpi, when optimal 1EPol:V5 accumulation was detected, two viral and six plant putative interaction partners of V5-tagged protein 1EPol were identified for the three GFLV clones by affinity purification and tandem mass spectrometry. This study provides insights into the protein interactome of 1EPol during GFLV systemic infection in N. benthamiana and lays the foundation for validation work.

  • Grapevine viruses: a multitude of diverse species with simple but overall poorly adopted management solutions in the vineyard
    Journal of Plant Pathology, 2020
    Co-Authors: Marc Fuchs
    Abstract:

    Eighty-six viruses have been isolated to date from grapevines worldwide. Some of these viruses are associated with economically damaging diseases such as leaf mottling and deformation, vein clearing, leafroll, degeneration and red blotch. They belong to the families Betaflexiviridae , Caulimoviridae , Closteroviridae , Secoviridae and Geminiviridae , and are transmitted by diverse vectors such as mealybugs (Hemiptera: Pseudococcidae), soft scale insects (Hemiptera: Coccidae), an aphid (Hemiptera: Aphididae), dagger nematodes (Nematoda: Longidoridae), a treehopper (Hemiptera: Membracidae) and eriophyid mites (Acari: Eriophyidae). Management of these viruses primarily relies on preventive measures to limit their presence in the propagation and planting material. In the vineyard, specific disease scenario-based strategies such as rogueing in combination with agrochemical applications to limit vector populations, if appropriate, and the removal of entire parcels and their replacement with clean planting material, including vector tolerant rootstocks, if opportune, are implemented to reduce their incidence, prevent their spread and mitigate their impact. These solutions are simple but their implementation is often suboptimal and their adoption is largely low. Some of the uncertainties that hinder their endorsement are captured here, and options to refine them and to enhance their adoption are discussed.

  • Proposed revision of the family Secoviridae taxonomy to create three subgenera, “Satsumavirus”, “Stramovirus” and “Cholivirus”, in the genus Sadwavirus
    Archives of Virology, 2020
    Co-Authors: Indranil Dasgupta, Alexander Karasev, Marc Fuchs, Jeremy R. Thompson, Ioannis Tzanetakis, Thierry Wetzel, Karel Petrzik, René Vlugt, Nobuyuki Yoshikawa
    Abstract:

    We present a taxonomic proposal for revision of the family Secoviridae , a taxon of plant viruses in the order Picornavirales . We propose the reorganization of the genus Sadwavirus to create three new subgenera and to update the classification of five existing species. The proposed subgenera are “ Satsumavirus ” (one species: Satsuma dwarf virus ), “ Stramovirus ” (two species: Strawberry mottle virus and Black raspberry necrosis virus ) and “ Cholivirus ” (two species: Chocolate lily virus A and Dioscorea mosaic associated virus ).

  • The Identity of a Single Residue of the RNA-Dependent RNA Polymerase of Grapevine Fanleaf Virus Modulates Vein Clearing in Nicotiana benthamiana
    Molecular Plant-Microbe Interactions, 2019
    Co-Authors: Larissa J. Osterbaan, Emmanuelle Vigne, Michelle Heck, Corinne Schmitt-keichinger, Jiyeong Choi, Jaimie Kenney, Madison Flasco, Ana Rita Rebelo, Marc Fuchs
    Abstract:

    The mechanisms underlying host plant symptom development upon infection by viruses of the genus Nepovirus in the family Secoviridae, including grapevine fanleaf virus (GFLV), are poorly understood. In the systemic host Nicotiana benthamiana, GFLV strain GHu produces characteristic symptoms of vein clearing in apical leaves, unlike other GFLV strains such as F13, which cause an asymptomatic infection. In this study, we expanded on earlier findings and used reverse genetics to identify residue 802 (lysine, K) of the GFLV-GHu RNA1-encoded RNA-dependent RNA polymerase (1EPol) as a modulator of vein-clearing symptom development in N. benthamiana. Mutations to this site abolished (K to G, A, or Q) or attenuated (K to N or P) symptom expression. Noteworthy, residue 802 is necessary but not sufficient for vein clearing, as GFLV-F13 RNA1 carrying K802 remained asymptomatic in N. benthamiana. No correlation was found between symptom expression and RNA1 accumulation, as shown by reverse transcription-quantitative polymerase chain reaction. Additionally, the involvement of RNA silencing of vein clearing was ruled out by virus-induced gene silencing experiments and structure predictions for protein 1EPol suggested that residue 802 is flanked by strongly predicted stable secondary structures, including a conserved motif of unknown function (805LLKT/AHLK/RT/ALR814). Together, these results reveal the protein nature of the GFLV-GHu symptom determinant in N. benthamiana and provide a solid basis for probing and determining the virus-host proteome network for symptoms of vein clearing.

  • ICTV Virus Taxonomy Profile: Secoviridae.
    Journal of General Virology, 2017
    Co-Authors: Jeremy R. Thompson, Alexander Karasev, Marc Fuchs, Ioannis E. Tzanetakis, Toru Iwanami, Karel Petrzik, René Vlugt, Indranil Dasgupta, Thierry Wetzel
    Abstract:

    Members of the family Secoviridae are non-enveloped viruses with mono- or bipartite (RNA-1 and RNA-2) linear positive-sense ssRNA genomes with the size of the RNAs combined ranging from 9 to 13.7 kb. They are related to picornaviruses and are classified in the order Picornavirales. The majority of known members infect dicotyledonous plants and many are important plant pathogens (e.g. grapevine fanleaf virus and rice tungro spherical virus). This is a summary of the current International Committee on Taxonomy of Viruses (ICTV) report on the taxonomy of the family Secoviridae available at www.ictv.global/report/Secoviridae.

Filloux Denis - One of the best experts on this subject based on the ideXlab platform.

  • Identification, molecular and biological characterization of two novel secovirids in wild grass species in Belgium
    'Elsevier BV', 2021
    Co-Authors: Maclot François, Filloux Denis, Debue Virginie, Blouin Arnaud, Fontdevila Pareta Núria, Tamisier Lucie, Massart Sébastien
    Abstract:

    International audienceHigh throughput sequencing was performed on virion-associated nucleic acids (VANA) from a pool of fifty asymptomatic rough bluegrasses (Poa trivialis L.) collected in a Belgian grazed pasture. Bioinformatics analyses produced some contigs presenting similarities with secovirid genomes, in particular nepoviruses and waikaviruses. Three distinct positive-sense single-stranded RNAs including 5? and 3? UTR were reconstructed and they represented two novel viruses infecting rough bluegrass, for which the provisional names poaceae Liege nepovirus A (PoLNVA, 7298 nt for RNA1 and 4263 nt for RNA2) and poaceae Liege virus 1 (PoLV1, 11,623 nt) were proposed. Compared to other Secoviridae members, the highest amino acid identity reached 90.7 % and 66.7 % between PoLNVA and nepoviruses for the Pro-Pol and CP regions respectively, while PoLV1 presented the highest amino acid identity with waikaviruses but with lower identities, i.e. 41.2 % for Pro-Pol and 25.8 % for CP regions, far below the ICTV demarcation criteria for novel secovirid. Based on sequence identity and phylogenetic analyses, PoLNVA was proposed to belong to the genus Nepovirus and PoLV1 as an unclassified secovirids. Detection of the two novel viruses was confirmed in high prevalence in rough bluegrass and ten other wild Poaceae species (Agropyron repens, Agrostis capillaris, Apera spica-venti, Anthoxanthum odoratum, Cynosorus cristatus, Festuca rubra, Holcus lanatus, Lolium perenne, Phleum bertolini and Phleum pratense) by RT-PCR and Sanger sequencing, revealing a diverse host range within Poaceae for these novel secovirids. Seed transmission was evaluated and confirmed for PoLNVA

  • Identification, molecular and biological characterization of two novel secovirids in wild grass species in Belgium
    2021
    Co-Authors: Maclot François, Filloux Denis, Debue Virginie, Blouin Arnaud, Fontdevila Pareta Núria, Tamisier Lucie, Massart Sébastien
    Abstract:

    High throughput sequencing was performed on virion-associated nucleic acids (VANA) from a pool of fifty asymptomatic rough bluegrasses (Poa trivialis L.) collected in a Belgian grazed pasture. Bioinformatics analyses produced some contigs presenting similarities with secovirid genomes, in particular nepoviruses and waikaviruses. Three distinct positive-sense single-stranded RNAs including 5’ and 3’ UTR were reconstructed and they represented two novel viruses infecting rough bluegrass, for which the provisional names poaceae Liege nepovirus A (PoLNVA, 7298 nt for RNA1 and 4263 nt for RNA2) and poaceae Liege virus 1 (PoLV1, 11,623 nt) were proposed. Compared to other Secoviridae members, the highest amino acid identity reached 90.7 % and 66.7 % between PoLNVA and nepoviruses for the Pro-Pol and CP regions respectively, while PoLV1 presented the highest amino acid identity with waikaviruses but with lower identities, i.e. 41.2 % for Pro-Pol and 25.8 % for CP regions, far below the ICTV demarcation criteria for novel secovirid. Based on sequence identity and phylogenetic analyses, PoLNVA was proposed to belong to the genus Nepovirus and PoLV1 as an unclassified secovirids. Detection of the two novel viruses was confirmed in high prevalence in rough bluegrass and ten other wild Poaceae species (Agropyron repens, Agrostis capillaris, Apera spica-venti, Anthoxanthum odoratum, Cynosorus cristatus, Festuca rubra, Holcus lanatus, Lolium perenne, Phleum bertolini and Phleum pratense) by RT-PCR and Sanger sequencing, revealing a diverse host range within Poaceae for these novel secovirids. Seed transmission was evaluated and confirmed for PoLNVA.Peer reviewe

  • Identification, molecular and biological characterization of two novel secovirids in wild grass species in Belgium
    'Elsevier BV', 2021
    Co-Authors: Maclot François, Filloux Denis, Debue Virginie, Tamisier Lucie, Blouin, Arnaud G., Fontdevilla Pareta Núria, Massart Sébastien
    Abstract:

    High throughput sequencing was performed on virion-associated nucleic acids (VANA) from a pool of fifty asymptomatic rough bluegrasses (Poa trivialis L.) collected in a Belgian grazed pasture. Bioinformatics analyses produced some contigs presenting similarities with secovirid genomes, in particular nepoviruses and waikaviruses. Three distinct positive-sense single-stranded RNAs including 5' and 3' UTR were reconstructed and they represented two novel viruses infecting rough bluegrass, for which the provisional names poaceae Liege nepovirus A (PoLNVA, 7298 nt for RNA1 and 4263 nt for RNA2) and poaceae Liege virus 1 (PoLV1, 11,623 nt) were proposed. Compared to other Secoviridae members, the highest amino acid identity reached 90.7 % and 66.7 % between PoLNVA and nepoviruses for the Pro-Pol and CP regions respectively, while PoLV1 presented the highest amino acid identity with waikaviruses but with lower identities, i.e. 41.2 % for Pro-Pol and 25.8 % for CP regions, far below the ICTV demarcation criteria for novel secovirid. Based on sequence identity and phylogenetic analyses, PoLNVA was proposed to belong to the genus Nepovirus and PoLV1 as an unclassified secovirids. Detection of the two novel viruses was confirmed in high prevalence in rough bluegrass and ten other wild Poaceae species (Agropyron repens, Agrostis capillaris, Apera spica-venti, Anthoxanthum odoratum, Cynosorus cristatus, Festuca rubra, Holcus lanatus, Lolium perenne, Phleum bertolini and Phleum pratense) by RT-PCR and Sanger sequencing, revealing a diverse host range within Poaceae for these novel secovirids. Seed transmission was evaluated and confirmed for PoLNVA

  • Les espèces végétales minoritaires peuvent jouer un rôle clé dans le virome des Poaceae à l'échelle des agroécosystèmes
    2019
    Co-Authors: Maclot François, Filloux Denis, Candresse Thierry, Roumagnac Philippe, Massart Sébastien
    Abstract:

    Prior to the domestication of plants, it is hypothesized that plant viruses were co-evolving with uncultivated plants growing in mixed species communities, which probably resulted in complex interactions (antagonism, commensalism, mutualism). The development of agriculture further deeply modified natural ecosystems and land use, creating agroecosystems composed by both cultivated and uncultivated areas. It is postulated that the advent of agriculture has modified the dynamics of virus-plant interactions, which has fostered the occurrence of virus disease emergence events. At the level of natural ecosystems, the relationships between plant communities’ diversity and plant virus diversity, the distribution of plant viruses and the interactions between viruses and their uncultivated hosts, have just started to be explored. In this context, we are conducting a study in the Natural Park “Burdinale-Mehaigne” (Belgium) using high throughput sequencing technologies in order to characterize the virome of Poaceae communities, including minor species, in contrasted agricultural ecosystems (cereal monocultures, grazed pastures and natural grasslands). We adapted a virion-associated nucleic acids (VANA) metagenomics protocol to sequence at high throughput pools of 50 plant samples per ecosystem (50 samples reflecting plant species composition) and per plant species. Over two years, about 4,300 Poaceae plants (corresponding to 24 species) were sampled and processed using the VANA metagenomics approach. The bioinformatic analyses revealed the presence of diverse viral communities in wild and cultivated Poaceae, even though they did not present any symptoms. These viruses belong to diverse families (e.g. Endornaviridae, Luteoviridae, Partitiviridae, Potyviridae, Reoviridae, Secoviridae), infecting a large range of hosts within the Poaceae and transmitted by different vectors (aphids, planthoppers, mites, nematods) or seed-borne. Interestingly, minor Poaceae species studied in grasslands contained a wide virus richness, sometimes greater than ecosystemic pools containing 8-11 major plant species. Moreover, some virus genera (e.g. Amalgavirus, Alphaendornavirus, Potyvirus, Sobemovirus) were found only in minor species, underlining the importance of minor plant species as virus reservoirs in wild ecosystems such as grasslands

  • Les espèces végétales minoritaires peuvent jouer un rôle clé dans le virome des Poaceae à l'échelle des agroécosystèmes
    2019
    Co-Authors: Maclot François, Filloux Denis, Candresse Thierry, Roumagnac Philippe, Massart Sébastien
    Abstract:

    audience: researcherPrior to the domestication of plants, it is hypothesized that plant viruses were co-evolving with uncultivated plants growing in mixed species communities, which probably resulted in complex interactions (antagonism, commensalism, mutualism). The development of agriculture further deeply modified natural ecosystems and land use, creating agroecosystems composed by both cultivated and uncultivated areas. It is postulated that the advent of agriculture has modified the dynamics of virus-plant interactions, which has fostered the occurrence of virus disease emergence events. At the level of natural ecosystems, the relationships between plant communities’ diversity and plant virus diversity, the distribution of plant viruses and the interactions between viruses and their uncultivated hosts, have just started to be explored. In this context, we are conducting a study in the Natural Park “Burdinale-Mehaigne” (Belgium) using high throughput sequencing technologies in order to characterize the virome of Poaceae communities, including minor species, in contrasted agricultural ecosystems (cereal monocultures, grazed pastures and natural grasslands). We adapted a virion-associated nucleic acids (VANA) metagenomics protocol to sequence at high throughput pools of 50 plant samples per ecosystem (50 samples reflecting plant species composition) and per plant species. Over two years, about 4,300 Poaceae plants (corresponding to 24 species) were sampled and processed using the VANA metagenomics approach. The bioinformatic analyses revealed the presence of diverse viral communities in wild and cultivated Poaceae, even though they did not present any symptoms. These viruses belong to diverse families (e.g. Endornaviridae, Luteoviridae, Partitiviridae, Potyviridae, Reoviridae, Secoviridae), infecting a large range of hosts within the Poaceae and transmitted by different vectors (aphids, planthoppers, mites, nematods) or seed-borne. Interestingly, minor Poaceae species studied in grasslands contained a wide virus richness, sometimes greater than ecosystemic pools containing 8-11 major plant species. Moreover, some virus genera (e.g. Amalgavirus, Alphaendornavirus, Potyvirus, Sobemovirus) were found only in minor species, underlining the importance of minor plant species as virus reservoirs in wild ecosystems such as grasslands

Massart Sébastien - One of the best experts on this subject based on the ideXlab platform.

  • Identification, molecular and biological characterization of two novel secovirids in wild grass species in Belgium
    'Elsevier BV', 2021
    Co-Authors: Maclot François, Filloux Denis, Debue Virginie, Blouin Arnaud, Fontdevila Pareta Núria, Tamisier Lucie, Massart Sébastien
    Abstract:

    International audienceHigh throughput sequencing was performed on virion-associated nucleic acids (VANA) from a pool of fifty asymptomatic rough bluegrasses (Poa trivialis L.) collected in a Belgian grazed pasture. Bioinformatics analyses produced some contigs presenting similarities with secovirid genomes, in particular nepoviruses and waikaviruses. Three distinct positive-sense single-stranded RNAs including 5? and 3? UTR were reconstructed and they represented two novel viruses infecting rough bluegrass, for which the provisional names poaceae Liege nepovirus A (PoLNVA, 7298 nt for RNA1 and 4263 nt for RNA2) and poaceae Liege virus 1 (PoLV1, 11,623 nt) were proposed. Compared to other Secoviridae members, the highest amino acid identity reached 90.7 % and 66.7 % between PoLNVA and nepoviruses for the Pro-Pol and CP regions respectively, while PoLV1 presented the highest amino acid identity with waikaviruses but with lower identities, i.e. 41.2 % for Pro-Pol and 25.8 % for CP regions, far below the ICTV demarcation criteria for novel secovirid. Based on sequence identity and phylogenetic analyses, PoLNVA was proposed to belong to the genus Nepovirus and PoLV1 as an unclassified secovirids. Detection of the two novel viruses was confirmed in high prevalence in rough bluegrass and ten other wild Poaceae species (Agropyron repens, Agrostis capillaris, Apera spica-venti, Anthoxanthum odoratum, Cynosorus cristatus, Festuca rubra, Holcus lanatus, Lolium perenne, Phleum bertolini and Phleum pratense) by RT-PCR and Sanger sequencing, revealing a diverse host range within Poaceae for these novel secovirids. Seed transmission was evaluated and confirmed for PoLNVA

  • Identification, molecular and biological characterization of two novel secovirids in wild grass species in Belgium
    2021
    Co-Authors: Maclot François, Filloux Denis, Debue Virginie, Blouin Arnaud, Fontdevila Pareta Núria, Tamisier Lucie, Massart Sébastien
    Abstract:

    High throughput sequencing was performed on virion-associated nucleic acids (VANA) from a pool of fifty asymptomatic rough bluegrasses (Poa trivialis L.) collected in a Belgian grazed pasture. Bioinformatics analyses produced some contigs presenting similarities with secovirid genomes, in particular nepoviruses and waikaviruses. Three distinct positive-sense single-stranded RNAs including 5’ and 3’ UTR were reconstructed and they represented two novel viruses infecting rough bluegrass, for which the provisional names poaceae Liege nepovirus A (PoLNVA, 7298 nt for RNA1 and 4263 nt for RNA2) and poaceae Liege virus 1 (PoLV1, 11,623 nt) were proposed. Compared to other Secoviridae members, the highest amino acid identity reached 90.7 % and 66.7 % between PoLNVA and nepoviruses for the Pro-Pol and CP regions respectively, while PoLV1 presented the highest amino acid identity with waikaviruses but with lower identities, i.e. 41.2 % for Pro-Pol and 25.8 % for CP regions, far below the ICTV demarcation criteria for novel secovirid. Based on sequence identity and phylogenetic analyses, PoLNVA was proposed to belong to the genus Nepovirus and PoLV1 as an unclassified secovirids. Detection of the two novel viruses was confirmed in high prevalence in rough bluegrass and ten other wild Poaceae species (Agropyron repens, Agrostis capillaris, Apera spica-venti, Anthoxanthum odoratum, Cynosorus cristatus, Festuca rubra, Holcus lanatus, Lolium perenne, Phleum bertolini and Phleum pratense) by RT-PCR and Sanger sequencing, revealing a diverse host range within Poaceae for these novel secovirids. Seed transmission was evaluated and confirmed for PoLNVA.Peer reviewe

  • Identification, molecular and biological characterization of two novel secovirids in wild grass species in Belgium
    'Elsevier BV', 2021
    Co-Authors: Maclot François, Filloux Denis, Debue Virginie, Tamisier Lucie, Blouin, Arnaud G., Fontdevilla Pareta Núria, Massart Sébastien
    Abstract:

    High throughput sequencing was performed on virion-associated nucleic acids (VANA) from a pool of fifty asymptomatic rough bluegrasses (Poa trivialis L.) collected in a Belgian grazed pasture. Bioinformatics analyses produced some contigs presenting similarities with secovirid genomes, in particular nepoviruses and waikaviruses. Three distinct positive-sense single-stranded RNAs including 5' and 3' UTR were reconstructed and they represented two novel viruses infecting rough bluegrass, for which the provisional names poaceae Liege nepovirus A (PoLNVA, 7298 nt for RNA1 and 4263 nt for RNA2) and poaceae Liege virus 1 (PoLV1, 11,623 nt) were proposed. Compared to other Secoviridae members, the highest amino acid identity reached 90.7 % and 66.7 % between PoLNVA and nepoviruses for the Pro-Pol and CP regions respectively, while PoLV1 presented the highest amino acid identity with waikaviruses but with lower identities, i.e. 41.2 % for Pro-Pol and 25.8 % for CP regions, far below the ICTV demarcation criteria for novel secovirid. Based on sequence identity and phylogenetic analyses, PoLNVA was proposed to belong to the genus Nepovirus and PoLV1 as an unclassified secovirids. Detection of the two novel viruses was confirmed in high prevalence in rough bluegrass and ten other wild Poaceae species (Agropyron repens, Agrostis capillaris, Apera spica-venti, Anthoxanthum odoratum, Cynosorus cristatus, Festuca rubra, Holcus lanatus, Lolium perenne, Phleum bertolini and Phleum pratense) by RT-PCR and Sanger sequencing, revealing a diverse host range within Poaceae for these novel secovirids. Seed transmission was evaluated and confirmed for PoLNVA

  • Les espèces végétales minoritaires peuvent jouer un rôle clé dans le virome des Poaceae à l'échelle des agroécosystèmes
    2019
    Co-Authors: Maclot François, Filloux Denis, Candresse Thierry, Roumagnac Philippe, Massart Sébastien
    Abstract:

    Prior to the domestication of plants, it is hypothesized that plant viruses were co-evolving with uncultivated plants growing in mixed species communities, which probably resulted in complex interactions (antagonism, commensalism, mutualism). The development of agriculture further deeply modified natural ecosystems and land use, creating agroecosystems composed by both cultivated and uncultivated areas. It is postulated that the advent of agriculture has modified the dynamics of virus-plant interactions, which has fostered the occurrence of virus disease emergence events. At the level of natural ecosystems, the relationships between plant communities’ diversity and plant virus diversity, the distribution of plant viruses and the interactions between viruses and their uncultivated hosts, have just started to be explored. In this context, we are conducting a study in the Natural Park “Burdinale-Mehaigne” (Belgium) using high throughput sequencing technologies in order to characterize the virome of Poaceae communities, including minor species, in contrasted agricultural ecosystems (cereal monocultures, grazed pastures and natural grasslands). We adapted a virion-associated nucleic acids (VANA) metagenomics protocol to sequence at high throughput pools of 50 plant samples per ecosystem (50 samples reflecting plant species composition) and per plant species. Over two years, about 4,300 Poaceae plants (corresponding to 24 species) were sampled and processed using the VANA metagenomics approach. The bioinformatic analyses revealed the presence of diverse viral communities in wild and cultivated Poaceae, even though they did not present any symptoms. These viruses belong to diverse families (e.g. Endornaviridae, Luteoviridae, Partitiviridae, Potyviridae, Reoviridae, Secoviridae), infecting a large range of hosts within the Poaceae and transmitted by different vectors (aphids, planthoppers, mites, nematods) or seed-borne. Interestingly, minor Poaceae species studied in grasslands contained a wide virus richness, sometimes greater than ecosystemic pools containing 8-11 major plant species. Moreover, some virus genera (e.g. Amalgavirus, Alphaendornavirus, Potyvirus, Sobemovirus) were found only in minor species, underlining the importance of minor plant species as virus reservoirs in wild ecosystems such as grasslands

  • Les espèces végétales minoritaires peuvent jouer un rôle clé dans le virome des Poaceae à l'échelle des agroécosystèmes
    2019
    Co-Authors: Maclot François, Filloux Denis, Candresse Thierry, Roumagnac Philippe, Massart Sébastien
    Abstract:

    audience: researcherPrior to the domestication of plants, it is hypothesized that plant viruses were co-evolving with uncultivated plants growing in mixed species communities, which probably resulted in complex interactions (antagonism, commensalism, mutualism). The development of agriculture further deeply modified natural ecosystems and land use, creating agroecosystems composed by both cultivated and uncultivated areas. It is postulated that the advent of agriculture has modified the dynamics of virus-plant interactions, which has fostered the occurrence of virus disease emergence events. At the level of natural ecosystems, the relationships between plant communities’ diversity and plant virus diversity, the distribution of plant viruses and the interactions between viruses and their uncultivated hosts, have just started to be explored. In this context, we are conducting a study in the Natural Park “Burdinale-Mehaigne” (Belgium) using high throughput sequencing technologies in order to characterize the virome of Poaceae communities, including minor species, in contrasted agricultural ecosystems (cereal monocultures, grazed pastures and natural grasslands). We adapted a virion-associated nucleic acids (VANA) metagenomics protocol to sequence at high throughput pools of 50 plant samples per ecosystem (50 samples reflecting plant species composition) and per plant species. Over two years, about 4,300 Poaceae plants (corresponding to 24 species) were sampled and processed using the VANA metagenomics approach. The bioinformatic analyses revealed the presence of diverse viral communities in wild and cultivated Poaceae, even though they did not present any symptoms. These viruses belong to diverse families (e.g. Endornaviridae, Luteoviridae, Partitiviridae, Potyviridae, Reoviridae, Secoviridae), infecting a large range of hosts within the Poaceae and transmitted by different vectors (aphids, planthoppers, mites, nematods) or seed-borne. Interestingly, minor Poaceae species studied in grasslands contained a wide virus richness, sometimes greater than ecosystemic pools containing 8-11 major plant species. Moreover, some virus genera (e.g. Amalgavirus, Alphaendornavirus, Potyvirus, Sobemovirus) were found only in minor species, underlining the importance of minor plant species as virus reservoirs in wild ecosystems such as grasslands

Candresse Thierry - One of the best experts on this subject based on the ideXlab platform.

  • Les espèces végétales minoritaires peuvent jouer un rôle clé dans le virome des Poaceae à l'échelle des agroécosystèmes
    2019
    Co-Authors: Maclot François, Filloux Denis, Candresse Thierry, Roumagnac Philippe, Massart Sébastien
    Abstract:

    audience: researcherPrior to the domestication of plants, it is hypothesized that plant viruses were co-evolving with uncultivated plants growing in mixed species communities, which probably resulted in complex interactions (antagonism, commensalism, mutualism). The development of agriculture further deeply modified natural ecosystems and land use, creating agroecosystems composed by both cultivated and uncultivated areas. It is postulated that the advent of agriculture has modified the dynamics of virus-plant interactions, which has fostered the occurrence of virus disease emergence events. At the level of natural ecosystems, the relationships between plant communities’ diversity and plant virus diversity, the distribution of plant viruses and the interactions between viruses and their uncultivated hosts, have just started to be explored. In this context, we are conducting a study in the Natural Park “Burdinale-Mehaigne” (Belgium) using high throughput sequencing technologies in order to characterize the virome of Poaceae communities, including minor species, in contrasted agricultural ecosystems (cereal monocultures, grazed pastures and natural grasslands). We adapted a virion-associated nucleic acids (VANA) metagenomics protocol to sequence at high throughput pools of 50 plant samples per ecosystem (50 samples reflecting plant species composition) and per plant species. Over two years, about 4,300 Poaceae plants (corresponding to 24 species) were sampled and processed using the VANA metagenomics approach. The bioinformatic analyses revealed the presence of diverse viral communities in wild and cultivated Poaceae, even though they did not present any symptoms. These viruses belong to diverse families (e.g. Endornaviridae, Luteoviridae, Partitiviridae, Potyviridae, Reoviridae, Secoviridae), infecting a large range of hosts within the Poaceae and transmitted by different vectors (aphids, planthoppers, mites, nematods) or seed-borne. Interestingly, minor Poaceae species studied in grasslands contained a wide virus richness, sometimes greater than ecosystemic pools containing 8-11 major plant species. Moreover, some virus genera (e.g. Amalgavirus, Alphaendornavirus, Potyvirus, Sobemovirus) were found only in minor species, underlining the importance of minor plant species as virus reservoirs in wild ecosystems such as grasslands

  • Les espèces végétales minoritaires peuvent jouer un rôle clé dans le virome des Poaceae à l'échelle des agroécosystèmes
    2019
    Co-Authors: Maclot François, Filloux Denis, Candresse Thierry, Roumagnac Philippe, Massart Sébastien
    Abstract:

    Prior to the domestication of plants, it is hypothesized that plant viruses were co-evolving with uncultivated plants growing in mixed species communities, which probably resulted in complex interactions (antagonism, commensalism, mutualism). The development of agriculture further deeply modified natural ecosystems and land use, creating agroecosystems composed by both cultivated and uncultivated areas. It is postulated that the advent of agriculture has modified the dynamics of virus-plant interactions, which has fostered the occurrence of virus disease emergence events. At the level of natural ecosystems, the relationships between plant communities’ diversity and plant virus diversity, the distribution of plant viruses and the interactions between viruses and their uncultivated hosts, have just started to be explored. In this context, we are conducting a study in the Natural Park “Burdinale-Mehaigne” (Belgium) using high throughput sequencing technologies in order to characterize the virome of Poaceae communities, including minor species, in contrasted agricultural ecosystems (cereal monocultures, grazed pastures and natural grasslands). We adapted a virion-associated nucleic acids (VANA) metagenomics protocol to sequence at high throughput pools of 50 plant samples per ecosystem (50 samples reflecting plant species composition) and per plant species. Over two years, about 4,300 Poaceae plants (corresponding to 24 species) were sampled and processed using the VANA metagenomics approach. The bioinformatic analyses revealed the presence of diverse viral communities in wild and cultivated Poaceae, even though they did not present any symptoms. These viruses belong to diverse families (e.g. Endornaviridae, Luteoviridae, Partitiviridae, Potyviridae, Reoviridae, Secoviridae), infecting a large range of hosts within the Poaceae and transmitted by different vectors (aphids, planthoppers, mites, nematods) or seed-borne. Interestingly, minor Poaceae species studied in grasslands contained a wide virus richness, sometimes greater than ecosystemic pools containing 8-11 major plant species. Moreover, some virus genera (e.g. Amalgavirus, Alphaendornavirus, Potyvirus, Sobemovirus) were found only in minor species, underlining the importance of minor plant species as virus reservoirs in wild ecosystems such as grasslands

  • Effet de la composition spécifique sur la diversité du virome dans des écosystèmes variés de Poaceae
    2019
    Co-Authors: Maclot François, Filloux Denis, Candresse Thierry, Massart Sébastien
    Abstract:

    audience: researcherBefore the domestication of plants, it is hypothesized that plant viruses were co-evolving with wild plants growing in mixed species communities, thereby resulting in complex interactions (antagonism, commensalism, mutualism). The development of agriculture deeply modified ecosystems, which is postulated to have altered the dynamics of virus-plant pathosystems and accelerated the rate of virus evolution and emergence. In this context, we are conducting a study in the Natural Park “Burdinale-Mehaigne” (Belgium) using high throughput sequencing technologies in order to examine the impact of species diversity (in terms of richness and density) on the virome of Poaceae communities in contrasted agricultural ecosystems (cereal monocultures, grazed pastures and natural grasslands). We developed a metagenomic approach consisting in virus particles purification, virion-associated nucleic acids (VANA) extraction and library preparation for Illumina sequencing and applied it on pools of 50 plant samples per ecosystem (50 samples reflecting plant species composition) or plant species (50 individual plants). Over two years, 4096 Poaceae plants were thus sampled and the bioinformatic analysis revealed the presence of diverse viral communities in wild and cultivated Poaceae, even though they did not present any symptoms. These viruses belong to diverse families (e.g. Endornaviridae, Luteoviridae, Partitiviridae, Potyviridae, Reoviridae, Secoviridae), infecting a large range of hosts within the Poaceae and transmitted by different vectors (aphids, planthoppers, mites, nematods) or seeds-bornes. Virus richness was compared between ecosystems: limited viral diversity (e.g. Hordeum vulgare endornavirus, Brome mosaic virus) were detected in barley and wheat field s, whereas a larger diversity was found in less anthropic ecosystems. Lolium latent virus (Alphaflexiviridae) and Ryegrass mosaic virus (Potyviridae) were strongly present in grazed pastures, particularly in Lolium perenne L. Several tentative new virus species belonging to the Nepovirus genus and the Partitiviridae family were found in natural grasslands

  • Effet de la composition spécifique sur la diversité du virome dans des écosystèmes variés de Poaceae
    2019
    Co-Authors: Maclot François, Filloux Denis, Candresse Thierry, Massart Sébastien
    Abstract:

    Before the domestication of plants, it is hypothesized that plant viruses were co-evolving with wild plants growing in mixed species communities, thereby resulting in complex interactions (antagonism, commensalism, mutualism). The development of agriculture deeply modified ecosystems, which is postulated to have altered the dynamics of virus-plant pathosystems and accelerated the rate of virus evolution and emergence. In this context, we are conducting a study in the Natural Park “Burdinale-Mehaigne” (Belgium) using high throughput sequencing technologies in order to examine the impact of species diversity (in terms of richness and density) on the virome of Poaceae communities in contrasted agricultural ecosystems (cereal monocultures, grazed pastures and natural grasslands). We developed a metagenomic approach consisting in virus particles purification, virion-associated nucleic acids (VANA) extraction and library preparation for Illumina sequencing and applied it on pools of 50 plant samples per ecosystem (50 samples reflecting plant species composition) or plant species (50 individual plants). Over two years, 4096 Poaceae plants were thus sampled and the bioinformatic analysis revealed the presence of diverse viral communities in wild and cultivated Poaceae, even though they did not present any symptoms. These viruses belong to diverse families (e.g. Endornaviridae, Luteoviridae, Partitiviridae, Potyviridae, Reoviridae, Secoviridae), infecting a large range of hosts within the Poaceae and transmitted by different vectors (aphids, planthoppers, mites, nematods) or seeds-bornes. Virus richness was compared between ecosystems: limited viral diversity (e.g. Hordeum vulgare endornavirus, Brome mosaic virus) were detected in barley and wheat field s, whereas a larger diversity was found in less anthropic ecosystems. Lolium latent virus (Alphaflexiviridae) and Ryegrass mosaic virus (Potyviridae) were strongly present in grazed pastures, particularly in Lolium perenne L. Several tentative new virus species belonging to the Nepovirus genus and the Partitiviridae family were found in natural grasslands

  • Effect of species composition on virome diversity in various ecosystemic communities of Poaceae
    INRA, 2019
    Co-Authors: Maclot François, Filloux Denis, Candresse Thierry, Massart Sébastien
    Abstract:

    Before the domestication of plants, it is hypothesized that plant viruses were co-evolving with wild plants growing in mixed species communities, thereby resulting in complex interactions (antagonism, commensalism, mutualism). The development of agriculture deeply modified ecosystems, which is postulated to have altered the dynamics of virus-plant pathosystems and accelerated the rate of virus evolution and emergence. In this context, we are conducting a study in the Natural Park “Burdinale-Mehaigne” (Belgium) using high throughput sequencing technologies in order to examine the impact of species diversity (in terms of richness and density) on the virome of Poaceae communities in contrasted agricultural ecosystems (cereal monocultures, grazed pastures and natural grasslands).We developed a metagenomic approach consisting in virus particles purification, virion-associated nucleic acids (VANA) extraction and library preparation for Illumina sequencing and applied it on pools of 50 plant samples per ecosystem (50 samples reflecting plant species composition) or plant species (50 individual plants). Over two years, 4096 Poaceae plants were thus sampled and the bioinformatic analysis revealed the presence of diverse viral communities in wild and cultivated Poaceae, even though they did not present any symptoms. These viruses belong to diverse families (e.g. Endornaviridae, Luteoviridae, Partitiviridae, Potyviridae, Reoviridae, Secoviridae), infecting a large range of hosts within the Poaceae and transmitted by different vectors (aphids, planthoppers, mites, nematods) or seeds-bornes. Virus richness was compared between ecosystems: limited viral diversity (e.g. Hordeum vulgare endornavirus, Brome mosaic virus) were detected in barley and wheat fields, whereas a larger diversity was found in less anthropic ecosystems. Lolium latent virus (Alphaflexiviridae) and Ryegrass mosaic virus (Potyviridae) were strongly present in grazed pastures, particularly in Lolium perenne L. Several tentative new virus species belonging to the Nepovirus genus and the Partitiviridae family were found in natural grasslands

Emmanuelle Vigne - One of the best experts on this subject based on the ideXlab platform.

  • The Identity of a Single Residue of the RNA-Dependent RNA Polymerase of Grapevine Fanleaf Virus Modulates Vein Clearing in Nicotiana benthamiana
    Molecular Plant-Microbe Interactions, 2019
    Co-Authors: Larissa J. Osterbaan, Emmanuelle Vigne, Michelle Heck, Corinne Schmitt-keichinger, Jiyeong Choi, Jaimie Kenney, Madison Flasco, Ana Rita Rebelo, Marc Fuchs
    Abstract:

    The mechanisms underlying host plant symptom development upon infection by viruses of the genus Nepovirus in the family Secoviridae, including grapevine fanleaf virus (GFLV), are poorly understood. In the systemic host Nicotiana benthamiana, GFLV strain GHu produces characteristic symptoms of vein clearing in apical leaves, unlike other GFLV strains such as F13, which cause an asymptomatic infection. In this study, we expanded on earlier findings and used reverse genetics to identify residue 802 (lysine, K) of the GFLV-GHu RNA1-encoded RNA-dependent RNA polymerase (1EPol) as a modulator of vein-clearing symptom development in N. benthamiana. Mutations to this site abolished (K to G, A, or Q) or attenuated (K to N or P) symptom expression. Noteworthy, residue 802 is necessary but not sufficient for vein clearing, as GFLV-F13 RNA1 carrying K802 remained asymptomatic in N. benthamiana. No correlation was found between symptom expression and RNA1 accumulation, as shown by reverse transcription-quantitative polymerase chain reaction. Additionally, the involvement of RNA silencing of vein clearing was ruled out by virus-induced gene silencing experiments and structure predictions for protein 1EPol suggested that residue 802 is flanked by strongly predicted stable secondary structures, including a conserved motif of unknown function (805LLKT/AHLK/RT/ALR814). Together, these results reveal the protein nature of the GFLV-GHu symptom determinant in N. benthamiana and provide a solid basis for probing and determining the virus-host proteome network for symptoms of vein clearing.

  • a strain specific segment of the rna dependent rna polymerase of grapevine fanleaf virus determines symptoms in nicotiana species
    Journal of General Virology, 2013
    Co-Authors: Veronique Komar, Emmanuelle Vigne, Corinne Schmittkeichinger, J Gottula, Lea Ackerer, Lorene Belval, Lalaina Rakotomalala
    Abstract:

    Factors involved in symptom expression of viruses from the genus Nepovirus in the family Secoviridae such as grapevine fanleaf virus (GFLV) are poorly characterized. To identify symptom determinants encoded by GFLV, infectious cDNA clones of RNA1 and RNA2 of strain GHu were developed and used alongside existing infectious cDNA clones of strain F13 in a reverse genetics approach. In vitro transcripts of homologous combinations of RNA1 and RNA2 induced systemic infection in Nicotiana benthamiana and Nicotiana clevelandii with identical phenotypes to WT virus strains, i.e. vein clearing and chlorotic spots on N. benthamiana and N. clevelandii for GHu, respectively, and lack of symptoms on both hosts for F13. The use of assorted transcripts mapped symptom determinants on RNA1 of GFLV strain GHu, in particular within the distal 408 nt of the RNA-dependent RNA polymerase (1E(Pol)), as shown by RNA1 transcripts for which coding regions or fragments derived thereof were swapped. Semi-quantitative analyses indicated no significant differences in virus titre between symptomatic and asymptomatic plants infected with various recombinants. Also, unlike the nepovirus tomato ringspot virus, no apparent proteolytic cleavage of GFLV protein 1E(Pol) was detected upon virus infection or transient expression in N. benthamiana. In addition, GFLV protein 1E(Pol) failed to suppress silencing of EGFP in transgenic N. benthamiana expressing EGFP or to enhance GFP expression in patch assays in WT N. benthamiana. Together, our results suggest the existence of strain-specific functional domains, including a symptom determinant module, on the RNA-dependent RNA polymerase of GFLV.

  • a stretch of 11 amino acids in the βb βc loop of the coat protein of grapevine fanleaf virus is essential for transmission by the nematode xiphinema index
    Journal of Virology, 2010
    Co-Authors: Marc Fuchs, Pascale Schellenberger, Marc Bergdoll, Olivier Lemaire, Emmanuelle Vigne, Aurelie Marmonier, P Andretlink, Corinne Schmittkeichinger, Gerard Demangeat
    Abstract:

    Grapevine fanleaf virus (GFLV) and Arabis mosaic virus (ArMV) from the genus Nepovirus, family Secoviridae, cause a severe degeneration of grapevines. GFLV and ArMV have a bipartite RNA genome and are transmitted specifically by the ectoparasitic nematodes Xiphinema index and Xiphinema diversicaudatum, respectively. The transmission specificity of both viruses maps to their respective RNA2-encoded coat protein (CP). To further delineate the GFLV CP determinants of transmission specificity, three-dimensional (3D) homology structure models of virions and CP subunits were constructed based on the crystal structure of Tobacco ringspot virus, the type member of the genus Nepovirus. The 3D models were examined to predict amino acids that are exposed at the external virion surface, highly conserved among GFLV isolates but divergent between GFLV and ArMV. Five short amino acid stretches that matched these topographical and sequence conservation criteria were selected and substituted in single and multiple combinations by their ArMV counterparts in a GFLV RNA2 cDNA clone. Among the 21 chimeric RNA2 molecules engineered, transcripts of only three of them induced systemic plant infection in the presence of GFLV RNA1. Nematode transmission assays of the three viable recombinant viruses showed that swapping a stretch of (i) 11 residues in the βB-βC loop near the icosahedral 3-fold axis abolished transmission by X. index but was insufficient to restore transmission by X. diversicaudatum and (ii) 7 residues in the βE-αB loop did not interfere with transmission by the two Xiphinema species. This study provides new insights into GFLV CP determinants of nematode transmission.

  • Genetic structure and molecular variability of Grapevine fanleaf virus populations
    Virus Research, 2010
    Co-Authors: J. E. Olivier, Emmanuelle Vigne, Marc Fuchs
    Abstract:

    To gain insights into the evolutionary mechanisms of Grapevine fanleaf virus (GFLV) from the genus Nepovirus, family Secoviridae, the sequences of the complete coding region of RNA2, including genes 2AHP, 2BMP and 2CCP, and partial sequence from the RNA1-encoded gene 1EPol of 14 GFLV isolates from three naturally infected California vineyards were characterized. Phylogenetic analyses suggested two to three evolutionarily divergent lineages that did not reflect the vineyard origin of the isolates or an association with rootstock genotype or scion cultivar. Examination of the genetic variability of the California isolates alongside isolates worldwide, for which three RNA1 and 44 RNA2 coding sequences are available, revealed similar patterns of molecular evolution for the different regions within the GFLV genome but distinct selection constraints with the strongest pressure exerted on genes 2CCP and 2BMP, an intermediate level of pressure exerted on gene 1EPol, and the weakest pressure exerted on gene 2AHP. Some of the California isolates resulted from interspecies recombination events between GFLV and Arabis mosaic virus with crossover sites suspected in gene 1EPol and identified in genes 2AHP and 2BMP; and intraspecies recombination events inferred in the four target genes but most frequently observed within gene 2CCP. This study suggested that purifying selection and recombination are important evolutionary mechanisms in the genetic diversification of GFLV.