Viral treasure hunt in European outermost territories: how metagenomics boosts the discovery of novel viral species in tropical and sub-tropical crops germplasm. [O.18]
A comparative assay of 8 viral metagenomic protocols based on next generation sequencing (NGS) was performed on 6 tropical and subtropical crops (banana, garlic, sugarcane, sweet potato, vanilla and yam) originating from the Azores, Guadeloupe, Madeira and Réunion. Roche 454-based sequencing of purified dsRNA and virion-associated nucleic acids (VANA) proved the best strategies for recovering plant virus sequences following a first screening performed on a set of 96 plant samples. These two metagenomics approaches were further used on a total of 740 plant samples of the 6 targeted crops. Following demultiplexing, reads were either mapped against viral references or assembled into contigs and annotated using Blast analyses, leading to the identification and molecular characterization of 5 new viral species in garlic, 10 in yams, 7 in sugarcane, and 3 in vanilla. Sequences hinting at the possible presence of additional novel agents were also identified. In addition, a systematic search was performed on publicly available EST resources for the 6 targeted crops in order to identify yet uncharacterized viral agents. For all newly identified viruses, corresponding EST sequences were downloaded, assembled in contigs and taxonomic relationships were established. Sequences assembled from NGS reads and EST datamining were used to design specific primers for the detection of the novel viral species, allowing studies of their prevalence and diversity in germplasm collections conserved in European outermost regions and providing insights into transmission modes of some of these novel viruses. The potential of metagenomics for plant virus discovery and diagnostics will be discussed, together with the risk of complicating the exchange of plant materiel following the discovery of new virus species in conserved plant germplasm.
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dig-cirad-fr-5758122022-05-24T16:03:21Z http://agritrop.cirad.fr/575812/ http://agritrop.cirad.fr/575812/ Viral treasure hunt in European outermost territories: how metagenomics boosts the discovery of novel viral species in tropical and sub-tropical crops germplasm. [O.18]. Teycheney Pierre-Yves, Bandou Eric, Gomez Rose-Marie, Lange David, Pavis Claudie, Umber Marie, Acina Manbole Isabelle Nina, Bonheur Lydiane, Daugrois Jean-Heinrich, Fernandez Emmanuel, Filloux Denis, Julian Charlotte, Roumagnac Philippe, Grisoni Michel, Pierret Alycia, Rubington Margot, Candresse Thierry, Contreras Sandy, Faure Chantal, Marais Armelle, Theil Sébastien, Da Câmara Machado Artur, Mendonça Duarte, Pinheiro de Carvalho Miguel A.A., Silva Emanuel. 2015. In : 15èmes Rencontres de Virologie Végétale, Aussois, France, 18-22 janvier 2015. CIRAD ; IRD. s.l. : s.n., Résumé, 30. Rencontres de virologie végétale. 15, Aussois, France, 18 Janvier 2015/22 Janvier 2015. Researchers Viral treasure hunt in European outermost territories: how metagenomics boosts the discovery of novel viral species in tropical and sub-tropical crops germplasm. [O.18] Teycheney, Pierre-Yves Bandou, Eric Gomez, Rose-Marie Lange, David Pavis, Claudie Umber, Marie Acina Manbole, Isabelle Nina Bonheur, Lydiane Daugrois, Jean-Heinrich Fernandez, Emmanuel Filloux, Denis Julian, Charlotte Roumagnac, Philippe Grisoni, Michel Pierret, Alycia Rubington, Margot Candresse, Thierry Contreras, Sandy Faure, Chantal Marais, Armelle Theil, Sébastien Da Câmara Machado, Artur Mendonça, Duarte Pinheiro de Carvalho, Miguel A.A. Silva, Emanuel eng 2015 s.n. 15èmes Rencontres de Virologie Végétale, Aussois, France, 18-22 janvier 2015 H20 - Maladies des plantes A comparative assay of 8 viral metagenomic protocols based on next generation sequencing (NGS) was performed on 6 tropical and subtropical crops (banana, garlic, sugarcane, sweet potato, vanilla and yam) originating from the Azores, Guadeloupe, Madeira and Réunion. Roche 454-based sequencing of purified dsRNA and virion-associated nucleic acids (VANA) proved the best strategies for recovering plant virus sequences following a first screening performed on a set of 96 plant samples. These two metagenomics approaches were further used on a total of 740 plant samples of the 6 targeted crops. Following demultiplexing, reads were either mapped against viral references or assembled into contigs and annotated using Blast analyses, leading to the identification and molecular characterization of 5 new viral species in garlic, 10 in yams, 7 in sugarcane, and 3 in vanilla. Sequences hinting at the possible presence of additional novel agents were also identified. In addition, a systematic search was performed on publicly available EST resources for the 6 targeted crops in order to identify yet uncharacterized viral agents. For all newly identified viruses, corresponding EST sequences were downloaded, assembled in contigs and taxonomic relationships were established. Sequences assembled from NGS reads and EST datamining were used to design specific primers for the detection of the novel viral species, allowing studies of their prevalence and diversity in germplasm collections conserved in European outermost regions and providing insights into transmission modes of some of these novel viruses. The potential of metagenomics for plant virus discovery and diagnostics will be discussed, together with the risk of complicating the exchange of plant materiel following the discovery of new virus species in conserved plant germplasm. conference_item info:eu-repo/semantics/conferenceObject Conference info:eu-repo/semantics/publishedVersion http://agritrop.cirad.fr/575812/1/document_575812.pdf application/pdf Cirad license info:eu-repo/semantics/openAccess https://agritrop.cirad.fr/mention_legale.html |
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H20 - Maladies des plantes H20 - Maladies des plantes Teycheney, Pierre-Yves Bandou, Eric Gomez, Rose-Marie Lange, David Pavis, Claudie Umber, Marie Acina Manbole, Isabelle Nina Bonheur, Lydiane Daugrois, Jean-Heinrich Fernandez, Emmanuel Filloux, Denis Julian, Charlotte Roumagnac, Philippe Grisoni, Michel Pierret, Alycia Rubington, Margot Candresse, Thierry Contreras, Sandy Faure, Chantal Marais, Armelle Theil, Sébastien Da Câmara Machado, Artur Mendonça, Duarte Pinheiro de Carvalho, Miguel A.A. Silva, Emanuel Viral treasure hunt in European outermost territories: how metagenomics boosts the discovery of novel viral species in tropical and sub-tropical crops germplasm. [O.18] |
description |
A comparative assay of 8 viral metagenomic protocols based on next generation sequencing (NGS) was performed on 6 tropical and subtropical crops (banana, garlic, sugarcane, sweet potato, vanilla and yam) originating from the Azores, Guadeloupe, Madeira and Réunion. Roche 454-based sequencing of purified dsRNA and virion-associated nucleic acids (VANA) proved the best strategies for recovering plant virus sequences following a first screening performed on a set of 96 plant samples. These two metagenomics approaches were further used on a total of 740 plant samples of the 6 targeted crops. Following demultiplexing, reads were either mapped against viral references or assembled into contigs and annotated using Blast analyses, leading to the identification and molecular characterization of 5 new viral species in garlic, 10 in yams, 7 in sugarcane, and 3 in vanilla. Sequences hinting at the possible presence of additional novel agents were also identified. In addition, a systematic search was performed on publicly available EST resources for the 6 targeted crops in order to identify yet uncharacterized viral agents. For all newly identified viruses, corresponding EST sequences were downloaded, assembled in contigs and taxonomic relationships were established. Sequences assembled from NGS reads and EST datamining were used to design specific primers for the detection of the novel viral species, allowing studies of their prevalence and diversity in germplasm collections conserved in European outermost regions and providing insights into transmission modes of some of these novel viruses. The potential of metagenomics for plant virus discovery and diagnostics will be discussed, together with the risk of complicating the exchange of plant materiel following the discovery of new virus species in conserved plant germplasm. |
format |
conference_item |
topic_facet |
H20 - Maladies des plantes |
author |
Teycheney, Pierre-Yves Bandou, Eric Gomez, Rose-Marie Lange, David Pavis, Claudie Umber, Marie Acina Manbole, Isabelle Nina Bonheur, Lydiane Daugrois, Jean-Heinrich Fernandez, Emmanuel Filloux, Denis Julian, Charlotte Roumagnac, Philippe Grisoni, Michel Pierret, Alycia Rubington, Margot Candresse, Thierry Contreras, Sandy Faure, Chantal Marais, Armelle Theil, Sébastien Da Câmara Machado, Artur Mendonça, Duarte Pinheiro de Carvalho, Miguel A.A. Silva, Emanuel |
author_facet |
Teycheney, Pierre-Yves Bandou, Eric Gomez, Rose-Marie Lange, David Pavis, Claudie Umber, Marie Acina Manbole, Isabelle Nina Bonheur, Lydiane Daugrois, Jean-Heinrich Fernandez, Emmanuel Filloux, Denis Julian, Charlotte Roumagnac, Philippe Grisoni, Michel Pierret, Alycia Rubington, Margot Candresse, Thierry Contreras, Sandy Faure, Chantal Marais, Armelle Theil, Sébastien Da Câmara Machado, Artur Mendonça, Duarte Pinheiro de Carvalho, Miguel A.A. Silva, Emanuel |
author_sort |
Teycheney, Pierre-Yves |
title |
Viral treasure hunt in European outermost territories: how metagenomics boosts the discovery of novel viral species in tropical and sub-tropical crops germplasm. [O.18] |
title_short |
Viral treasure hunt in European outermost territories: how metagenomics boosts the discovery of novel viral species in tropical and sub-tropical crops germplasm. [O.18] |
title_full |
Viral treasure hunt in European outermost territories: how metagenomics boosts the discovery of novel viral species in tropical and sub-tropical crops germplasm. [O.18] |
title_fullStr |
Viral treasure hunt in European outermost territories: how metagenomics boosts the discovery of novel viral species in tropical and sub-tropical crops germplasm. [O.18] |
title_full_unstemmed |
Viral treasure hunt in European outermost territories: how metagenomics boosts the discovery of novel viral species in tropical and sub-tropical crops germplasm. [O.18] |
title_sort |
viral treasure hunt in european outermost territories: how metagenomics boosts the discovery of novel viral species in tropical and sub-tropical crops germplasm. [o.18] |
publisher |
s.n. |
url |
http://agritrop.cirad.fr/575812/ http://agritrop.cirad.fr/575812/1/document_575812.pdf |
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