The Experts below are selected from a list of 249 Experts worldwide ranked by ideXlab platform

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

  • Exploration de la diversité et richesse virale dans des communautés végétales de Poacées contrastées
    2020
    Co-Authors: Maclot François, Filloux Denis, Candresse Thierry, Malmstrom Carolyn, Massart Sébastien
    Abstract:

    audience: researcherPrior to plant domestication, it is hypothesized that plant viruses were co-evolving with uncultivated plants growing in mixed species communities, thereby resulting in complex interactions (antagonism, commensalism, mutualism). Development of agriculture further deeply modified natural ecosystems, land use and dynamics of virus-plant interactions, which has fostered occurrence of virus disease emergence events. 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 plant species diversity on the virome (e.g. the genomes of viral community) of Poaceae in contrasted plant communities (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 plant community (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 bioinformatic analyses revealed 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. Alphaflexiviridae, Luteoviridae, Partitiviridae, Totiviridae), infecting a large range of hosts within Poaceae and transmitted by different vectors (insects, mites, nematods) or seed-borne. More than 30 virus species were detected in the different plots and at least half of them are candidates for new virus species, revealing that virome in Poaceae-based agroecosystems and its impact on the dynamic of plant communities remain largely unexplored.Impact of ecosystem diversity on Poaceae virom

  • Exploration de la diversité et richesse virale dans des communautés végétales de Poacées contrastées
    2020
    Co-Authors: Maclot François, Filloux Denis, Candresse Thierry, Malmstrom Carolyn, Massart Sébastien
    Abstract:

    Prior to plant domestication, it is hypothesized that plant viruses were co-evolving with uncultivated plants growing in mixed species communities, thereby resulting in complex interactions (antagonism, commensalism, mutualism). Development of agriculture further deeply modified natural ecosystems, land use and dynamics of virus-plant interactions, which has fostered occurrence of virus disease emergence events. 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 plant species diversity on the virome (e.g. the genomes of viral community) of Poaceae in contrasted plant communities (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 plant community (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 bioinformatic analyses revealed 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. Alphaflexiviridae, Luteoviridae, Partitiviridae, Totiviridae), infecting a large range of hosts within Poaceae and transmitted by different vectors (insects, mites, nematods) or seed-borne. More than 30 virus species were detected in the different plots and at least half of them are candidates for new virus species, revealing that virome in Poaceae-based agroecosystems and its impact on the dynamic of plant communities remain largely unexplored

  • Exploring the virus richness and diversity in contrasted plant communities of Poaceae
    2019
    Co-Authors: Maclot François, Filloux Denis, Candresse Thierry, Malmstrom Carolyn, Massart Sébastien
    Abstract:

    audience: researcherPrior to the domestication of plants, it is hypothesized that plant viruses were only co-evolving with uncultivated plants growing in mixed species communities, thereby resulting 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. 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 on the virome of Poaceae communities 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. Alphaflexiviridae, 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, mycoviruses (Chrysovirus and Totivirus genera) were found in all ecosystems, in particular wheat and barley fields. Out of the 23 virus species detected in the different plots, ten of them are condidates for new virus species, revealing that virome in Poaceae-based agroecosystems remains unexplored. To confirm these results and determine the virus incidence in the different ecosystems, total RNA extraction and RT-PCR were implemented on 600 individual plants, targeting five viruses: three viruses detected in several ecosystems (Barley yellow dwarf virus, Lolium latent virus, Ryegrass mosaic virus) and two candidates for new virus species (belonging to Nepovirus and Waikavirus genera). The preliminary results are presented here.Impact of ecosystem diversity on Poaceae virom

  • Exploring the virus richness and diversity in contrasted plant communities of Poaceae
    2019
    Co-Authors: Maclot François, Filloux Denis, Candresse Thierry, Malmstrom Carolyn, Massart Sébastien
    Abstract:

    Prior to the domestication of plants, it is hypothesized that plant viruses were only co-evolving with uncultivated plants growing in mixed species communities, thereby resulting 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. 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 on the virome of Poaceae communities 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. Alphaflexiviridae, 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, mycoviruses (Chrysovirus and Totivirus genera) were found in all ecosystems, in particular wheat and barley fields. Out of the 23 virus species detected in the different plots, ten of them are condidates for new virus species, revealing that virome in Poaceae-based agroecosystems remains unexplored. To confirm these results and determine the virus incidence in the different ecosystems, total RNA extraction and RT-PCR were implemented on 600 individual plants, targeting five viruses: three viruses detected in several ecosystems (Barley yellow dwarf virus, Lolium latent virus, Ryegrass mosaic virus) and two candidates for new virus species (belonging to Nepovirus and Waikavirus genera). The preliminary results are presented here

  • 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

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

  • Exploration de la diversité et richesse virale dans des communautés végétales de Poacées contrastées
    2020
    Co-Authors: Maclot François, Filloux Denis, Candresse Thierry, Malmstrom Carolyn, Massart Sébastien
    Abstract:

    audience: researcherPrior to plant domestication, it is hypothesized that plant viruses were co-evolving with uncultivated plants growing in mixed species communities, thereby resulting in complex interactions (antagonism, commensalism, mutualism). Development of agriculture further deeply modified natural ecosystems, land use and dynamics of virus-plant interactions, which has fostered occurrence of virus disease emergence events. 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 plant species diversity on the virome (e.g. the genomes of viral community) of Poaceae in contrasted plant communities (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 plant community (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 bioinformatic analyses revealed 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. Alphaflexiviridae, Luteoviridae, Partitiviridae, Totiviridae), infecting a large range of hosts within Poaceae and transmitted by different vectors (insects, mites, nematods) or seed-borne. More than 30 virus species were detected in the different plots and at least half of them are candidates for new virus species, revealing that virome in Poaceae-based agroecosystems and its impact on the dynamic of plant communities remain largely unexplored.Impact of ecosystem diversity on Poaceae virom

  • Exploration de la diversité et richesse virale dans des communautés végétales de Poacées contrastées
    2020
    Co-Authors: Maclot François, Filloux Denis, Candresse Thierry, Malmstrom Carolyn, Massart Sébastien
    Abstract:

    Prior to plant domestication, it is hypothesized that plant viruses were co-evolving with uncultivated plants growing in mixed species communities, thereby resulting in complex interactions (antagonism, commensalism, mutualism). Development of agriculture further deeply modified natural ecosystems, land use and dynamics of virus-plant interactions, which has fostered occurrence of virus disease emergence events. 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 plant species diversity on the virome (e.g. the genomes of viral community) of Poaceae in contrasted plant communities (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 plant community (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 bioinformatic analyses revealed 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. Alphaflexiviridae, Luteoviridae, Partitiviridae, Totiviridae), infecting a large range of hosts within Poaceae and transmitted by different vectors (insects, mites, nematods) or seed-borne. More than 30 virus species were detected in the different plots and at least half of them are candidates for new virus species, revealing that virome in Poaceae-based agroecosystems and its impact on the dynamic of plant communities remain largely unexplored

  • Exploring the virus richness and diversity in contrasted plant communities of Poaceae
    2019
    Co-Authors: Maclot François, Filloux Denis, Candresse Thierry, Malmstrom Carolyn, Massart Sébastien
    Abstract:

    audience: researcherPrior to the domestication of plants, it is hypothesized that plant viruses were only co-evolving with uncultivated plants growing in mixed species communities, thereby resulting 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. 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 on the virome of Poaceae communities 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. Alphaflexiviridae, 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, mycoviruses (Chrysovirus and Totivirus genera) were found in all ecosystems, in particular wheat and barley fields. Out of the 23 virus species detected in the different plots, ten of them are condidates for new virus species, revealing that virome in Poaceae-based agroecosystems remains unexplored. To confirm these results and determine the virus incidence in the different ecosystems, total RNA extraction and RT-PCR were implemented on 600 individual plants, targeting five viruses: three viruses detected in several ecosystems (Barley yellow dwarf virus, Lolium latent virus, Ryegrass mosaic virus) and two candidates for new virus species (belonging to Nepovirus and Waikavirus genera). The preliminary results are presented here.Impact of ecosystem diversity on Poaceae virom

  • Exploring the virus richness and diversity in contrasted plant communities of Poaceae
    2019
    Co-Authors: Maclot François, Filloux Denis, Candresse Thierry, Malmstrom Carolyn, Massart Sébastien
    Abstract:

    Prior to the domestication of plants, it is hypothesized that plant viruses were only co-evolving with uncultivated plants growing in mixed species communities, thereby resulting 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. 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 on the virome of Poaceae communities 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. Alphaflexiviridae, 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, mycoviruses (Chrysovirus and Totivirus genera) were found in all ecosystems, in particular wheat and barley fields. Out of the 23 virus species detected in the different plots, ten of them are condidates for new virus species, revealing that virome in Poaceae-based agroecosystems remains unexplored. To confirm these results and determine the virus incidence in the different ecosystems, total RNA extraction and RT-PCR were implemented on 600 individual plants, targeting five viruses: three viruses detected in several ecosystems (Barley yellow dwarf virus, Lolium latent virus, Ryegrass mosaic virus) and two candidates for new virus species (belonging to Nepovirus and Waikavirus genera). The preliminary results are presented here

  • 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

Maclot François - One of the best experts on this subject based on the ideXlab platform.

  • Exploration de la diversité et richesse virale dans des communautés végétales de Poacées contrastées
    2020
    Co-Authors: Maclot François, Filloux Denis, Candresse Thierry, Malmstrom Carolyn, Massart Sébastien
    Abstract:

    audience: researcherPrior to plant domestication, it is hypothesized that plant viruses were co-evolving with uncultivated plants growing in mixed species communities, thereby resulting in complex interactions (antagonism, commensalism, mutualism). Development of agriculture further deeply modified natural ecosystems, land use and dynamics of virus-plant interactions, which has fostered occurrence of virus disease emergence events. 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 plant species diversity on the virome (e.g. the genomes of viral community) of Poaceae in contrasted plant communities (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 plant community (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 bioinformatic analyses revealed 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. Alphaflexiviridae, Luteoviridae, Partitiviridae, Totiviridae), infecting a large range of hosts within Poaceae and transmitted by different vectors (insects, mites, nematods) or seed-borne. More than 30 virus species were detected in the different plots and at least half of them are candidates for new virus species, revealing that virome in Poaceae-based agroecosystems and its impact on the dynamic of plant communities remain largely unexplored.Impact of ecosystem diversity on Poaceae virom

  • Exploration de la diversité et richesse virale dans des communautés végétales de Poacées contrastées
    2020
    Co-Authors: Maclot François, Filloux Denis, Candresse Thierry, Malmstrom Carolyn, Massart Sébastien
    Abstract:

    Prior to plant domestication, it is hypothesized that plant viruses were co-evolving with uncultivated plants growing in mixed species communities, thereby resulting in complex interactions (antagonism, commensalism, mutualism). Development of agriculture further deeply modified natural ecosystems, land use and dynamics of virus-plant interactions, which has fostered occurrence of virus disease emergence events. 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 plant species diversity on the virome (e.g. the genomes of viral community) of Poaceae in contrasted plant communities (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 plant community (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 bioinformatic analyses revealed 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. Alphaflexiviridae, Luteoviridae, Partitiviridae, Totiviridae), infecting a large range of hosts within Poaceae and transmitted by different vectors (insects, mites, nematods) or seed-borne. More than 30 virus species were detected in the different plots and at least half of them are candidates for new virus species, revealing that virome in Poaceae-based agroecosystems and its impact on the dynamic of plant communities remain largely unexplored

  • Exploring the virus richness and diversity in contrasted plant communities of Poaceae
    2019
    Co-Authors: Maclot François, Filloux Denis, Candresse Thierry, Malmstrom Carolyn, Massart Sébastien
    Abstract:

    audience: researcherPrior to the domestication of plants, it is hypothesized that plant viruses were only co-evolving with uncultivated plants growing in mixed species communities, thereby resulting 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. 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 on the virome of Poaceae communities 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. Alphaflexiviridae, 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, mycoviruses (Chrysovirus and Totivirus genera) were found in all ecosystems, in particular wheat and barley fields. Out of the 23 virus species detected in the different plots, ten of them are condidates for new virus species, revealing that virome in Poaceae-based agroecosystems remains unexplored. To confirm these results and determine the virus incidence in the different ecosystems, total RNA extraction and RT-PCR were implemented on 600 individual plants, targeting five viruses: three viruses detected in several ecosystems (Barley yellow dwarf virus, Lolium latent virus, Ryegrass mosaic virus) and two candidates for new virus species (belonging to Nepovirus and Waikavirus genera). The preliminary results are presented here.Impact of ecosystem diversity on Poaceae virom

  • Exploring the virus richness and diversity in contrasted plant communities of Poaceae
    2019
    Co-Authors: Maclot François, Filloux Denis, Candresse Thierry, Malmstrom Carolyn, Massart Sébastien
    Abstract:

    Prior to the domestication of plants, it is hypothesized that plant viruses were only co-evolving with uncultivated plants growing in mixed species communities, thereby resulting 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. 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 on the virome of Poaceae communities 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. Alphaflexiviridae, 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, mycoviruses (Chrysovirus and Totivirus genera) were found in all ecosystems, in particular wheat and barley fields. Out of the 23 virus species detected in the different plots, ten of them are condidates for new virus species, revealing that virome in Poaceae-based agroecosystems remains unexplored. To confirm these results and determine the virus incidence in the different ecosystems, total RNA extraction and RT-PCR were implemented on 600 individual plants, targeting five viruses: three viruses detected in several ecosystems (Barley yellow dwarf virus, Lolium latent virus, Ryegrass mosaic virus) and two candidates for new virus species (belonging to Nepovirus and Waikavirus genera). The preliminary results are presented here

  • 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

Miguel A. Aranda - One of the best experts on this subject based on the ideXlab platform.

  • stable and broad spectrum cross protection against pepino mosaic virus attained by mixed infection
    Frontiers in Plant Science, 2018
    Co-Authors: Jesús Agüero, Julio Garciavillalba, Jorge Garcianunez, Raquel Navarro Sempere, Cristina Gomezaix, Yolanda Hernando, Miguel A. Aranda
    Abstract:

    While recent Pepino mosaic virus (PepMV; genus Potexvirus, family Alphaflexiviridae) epidemics seem to be predominantly caused by isolates of the Ch2 genotype, PepMV epidemics in Spain are caused by both Ch2 and EU isolates that co-circulate, representing a challenge in terms of control, including cross-protection. In this work, we hypothesized that mixed infections with two mild isolates of the EU and Ch2 genotypes (PepMV-Sp13 and -PS5, respectively) may be useful in PepMV cross-protection in Spanish epidemics, providing protection against a broad range of aggressive isolates. Thus, we performed a range of field trials and an experimental evolution assay to determine the phenotypic and genetic stability of PepMV-Sp13 and -PS5 mixed infections, as well as their cross-protective efficiency. Our results showed that (i) the phenotype of PepMV-Sp13 and -PS5 mixed infections was mild and did not change significantly when infecting different tomato cultivars or under different environmental conditions, (ii) PepMV-Sp13 and -PS5 mixed infections provided more efficient protection against aggressive EU and Ch2 isolates than single infections, and (iii) PepMV-Sp13 and -PS5, either in single or in mixed infections, were at least as genetically stable as other PepMV isolates occurring naturally in PepMV epidemics.

  • Stable and Broad Spectrum Cross-Protection Against Pepino Mosaic Virus Attained by Mixed Infection
    Frontiers Media S.A., 2018
    Co-Authors: Jesús Agüero, Yolanda Hernando, Cristina Gómez-aix, Raquel N. Sempere, Julio García-villalba, Jorge García-núñez, Miguel A. Aranda
    Abstract:

    While recent pepino mosaic virus (PepMV; species Pepino mosaic virus, genus Potexvirus, family Alphaflexiviridae) epidemics seem to be predominantly caused by isolates of the CH2 strain, PepMV epidemics in intensive tomato crops in Spain are caused by both CH2 and EU isolates that co-circulate, representing a challenge in terms of control, including cross-protection. In this work, we hypothesized that mixed infections with two mild isolates of the EU and CH2 strains (PepMV-Sp13 and -PS5, respectively) may be useful in PepMV cross-protection in Spanish epidemics, providing protection against a broad range of aggressive isolates. Thus, we performed a range of field trials and an experimental evolution assay to determine the phenotypic and genetic stability of PepMV-Sp13 and -PS5 mixed infections, as well as their cross-protective efficiency. Our results showed that: (i) the phenotype of PepMV-Sp13 and -PS5 mixed infections was mild and did not change significantly when infecting different tomato cultivars or under different environmental conditions in Spain, (ii) PepMV-Sp13 and -PS5 mixed infections provided more efficient protection against two aggressive EU and CH2 isolates than single infections, and (iii) PepMV-Sp13 and -PS5, either in single or in mixed infections, were less variable than other two PepMV isolates occurring naturally in PepMV epidemics in Spain

  • Image_1_Stable and Broad Spectrum Cross-Protection Against Pepino Mosaic Virus Attained by Mixed Infection.tif
    2018
    Co-Authors: Jesús Agüero, Yolanda Hernando, Cristina Gómez-aix, Raquel N. Sempere, Julio García-villalba, Jorge García-núñez, Miguel A. Aranda
    Abstract:

    While recent pepino mosaic virus (PepMV; species Pepino mosaic virus, genus Potexvirus, family Alphaflexiviridae) epidemics seem to be predominantly caused by isolates of the CH2 strain, PepMV epidemics in intensive tomato crops in Spain are caused by both CH2 and EU isolates that co-circulate, representing a challenge in terms of control, including cross-protection. In this work, we hypothesized that mixed infections with two mild isolates of the EU and CH2 strains (PepMV-Sp13 and -PS5, respectively) may be useful in PepMV cross-protection in Spanish epidemics, providing protection against a broad range of aggressive isolates. Thus, we performed a range of field trials and an experimental evolution assay to determine the phenotypic and genetic stability of PepMV-Sp13 and -PS5 mixed infections, as well as their cross-protective efficiency. Our results showed that: (i) the phenotype of PepMV-Sp13 and -PS5 mixed infections was mild and did not change significantly when infecting different tomato cultivars or under different environmental conditions in Spain, (ii) PepMV-Sp13 and -PS5 mixed infections provided more efficient protection against two aggressive EU and CH2 isolates than single infections, and (iii) PepMV-Sp13 and -PS5, either in single or in mixed infections, were less variable than other two PepMV isolates occurring naturally in PepMV epidemics in Spain.

  • Table_1_Stable and Broad Spectrum Cross-Protection Against Pepino Mosaic Virus Attained by Mixed Infection.DOCX
    2018
    Co-Authors: Jesús Agüero, Yolanda Hernando, Cristina Gómez-aix, Raquel N. Sempere, Julio García-villalba, Jorge García-núñez, Miguel A. Aranda
    Abstract:

    While recent pepino mosaic virus (PepMV; species Pepino mosaic virus, genus Potexvirus, family Alphaflexiviridae) epidemics seem to be predominantly caused by isolates of the CH2 strain, PepMV epidemics in intensive tomato crops in Spain are caused by both CH2 and EU isolates that co-circulate, representing a challenge in terms of control, including cross-protection. In this work, we hypothesized that mixed infections with two mild isolates of the EU and CH2 strains (PepMV-Sp13 and -PS5, respectively) may be useful in PepMV cross-protection in Spanish epidemics, providing protection against a broad range of aggressive isolates. Thus, we performed a range of field trials and an experimental evolution assay to determine the phenotypic and genetic stability of PepMV-Sp13 and -PS5 mixed infections, as well as their cross-protective efficiency. Our results showed that: (i) the phenotype of PepMV-Sp13 and -PS5 mixed infections was mild and did not change significantly when infecting different tomato cultivars or under different environmental conditions in Spain, (ii) PepMV-Sp13 and -PS5 mixed infections provided more efficient protection against two aggressive EU and CH2 isolates than single infections, and (iii) PepMV-Sp13 and -PS5, either in single or in mixed infections, were less variable than other two PepMV isolates occurring naturally in PepMV epidemics in Spain.

  • multifaceted capsid proteins multiple interactions suggest multiple roles for pepino mosaic virus capsid protein
    Molecular Plant-microbe Interactions, 2014
    Co-Authors: Matthaios M Mathioudakis, Luis Rodriguezmoreno, Miguel A. Aranda, Raquel Navarro Sempere, Ioannis Livieratos
    Abstract:

    Pepino mosaic virus (PepMV) (family Alphaflexiviridae, genus Potexvirus) is a mechanically transmitted tomato pathogen that, over the last decade, has evolved from emerging to endemic worldwide. Here, two heat-shock cognate (Hsc70) isoforms were identified as part of the coat protein (CP)/Hsc70 complex in vivo, following full-length PepMV and CP agroinoculation. PepMV accumulation was severely reduced in Hsp70 virus-induced gene silenced and in quercetin-treated Nicotiana benthamiana plants. Similarly, in vitro–transcribed as well as virion RNA input levels were reduced in quercetin-treated protoplasts, suggesting an essential role for Hsp70 in PepMV replication. As for Potato virus X, the PepMV CP and triple gene-block protein 1 (TGBp1) self-associate and interact with each other in vitro but, unlike in the prototype, both PepMV proteins represent suppressors of transgene-induced RNA silencing with different modes of action; CP is a more efficient suppressor of RNA silencing, sequesters the silencing sig...

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  • Small-RNA Deep Sequencing Reveals Arctium tomentosum as a Natural Host of Alstroemeria virus X and a New Putative Emaravirus
    PloS one, 2012
    Co-Authors: Arthur K. Tugume, Jari P. T. Valkonen
    Abstract:

    Background Arctium species (Asteraceae) are distributed worldwide and are used as food and rich sources of secondary metabolites for the pharmaceutical industry, e.g., against avian influenza virus. RNA silencing is an antiviral defense mechanism that detects and destroys virus-derived double-stranded RNA, resulting in accumulation of virus-derived small RNAs (21–24 nucleotides) that can be used for generic detection of viruses by small-RNA deep sequencing (SRDS). Methodology/Principal Findings SRDS was used to detect viruses in the biennial wild plant species Arctium tomentosum (woolly burdock; family Asteraceae) displaying virus-like symptoms of vein yellowing and leaf mosaic in southern Finland. Assembly of the small-RNA reads resulted in contigs homologous to Alstroemeria virus X (AlsVX), a positive/single-stranded RNA virus of genus Potexvirus (family Alphaflexiviridae), or related to negative/single-stranded RNA viruses of the genus Emaravirus. The coat protein gene of AlsVX was 81% and 89% identical to the two AlsVX isolates from Japan and Norway, respectively. The deduced, partial nucleocapsid protein amino acid sequence of the emara-like virus was only 78% or less identical to reported emaraviruses and showed no variability among the virus isolates characterized. This virus—tentatively named as Woolly burdock yellow vein virus—was exclusively associated with yellow vein and leaf mosaic symptoms in woolly burdock, whereas AlsVX was detected in only one of the 52 plants tested. Conclusions/Significance These results provide novel information about natural virus infections in Acrtium species and reveal woolly burdock as the first natural host of AlsVX besides Alstroemeria (family Alstroemeriaceae). Results also revealed a new virus related to the recently emerged Emaravirus genus and demonstrated applicability of SRDS to detect negative-strand RNA viruses. SRDS potentiates virus surveys of wild plants, a research area underrepresented in plant virology, and helps reveal natural reservoirs of viruses that cause yield losses in cultivated plants.

  • Small-RNA deep sequencing reveals Arctium tomentosum as a natural host of Alstroemeria virus X and a new putative Emaravirus.
    Public Library of Science (PLoS), 2026
    Co-Authors: Arthur K. Tugume, Jari P. T. Valkonen
    Abstract:

    Arctium species (Asteraceae) are distributed worldwide and are used as food and rich sources of secondary metabolites for the pharmaceutical industry, e.g., against avian influenza virus. RNA silencing is an antiviral defense mechanism that detects and destroys virus-derived double-stranded RNA, resulting in accumulation of virus-derived small RNAs (21-24 nucleotides) that can be used for generic detection of viruses by small-RNA deep sequencing (SRDS).SRDS was used to detect viruses in the biennial wild plant species Arctium tomentosum (woolly burdock; family Asteraceae) displaying virus-like symptoms of vein yellowing and leaf mosaic in southern Finland. Assembly of the small-RNA reads resulted in contigs homologous to Alstroemeria virus X (AlsVX), a positive/single-stranded RNA virus of genus Potexvirus (family Alphaflexiviridae), or related to negative/single-stranded RNA viruses of the genus Emaravirus. The coat protein gene of AlsVX was 81% and 89% identical to the two AlsVX isolates from Japan and Norway, respectively. The deduced, partial nucleocapsid protein amino acid sequence of the emara-like virus was only 78% or less identical to reported emaraviruses and showed no variability among the virus isolates characterized. This virus--tentatively named as Woolly burdock yellow vein virus--was exclusively associated with yellow vein and leaf mosaic symptoms in woolly burdock, whereas AlsVX was detected in only one of the 52 plants tested.These results provide novel information about natural virus infections in Acrtium species and reveal woolly burdock as the first natural host of AlsVX besides Alstroemeria (family Alstroemeriaceae). Results also revealed a new virus related to the recently emerged Emaravirus genus and demonstrated applicability of SRDS to detect negative-strand RNA viruses. SRDS potentiates virus surveys of wild plants, a research area underrepresented in plant virology, and helps reveal natural reservoirs of viruses that cause yield losses in cultivated plants