Enhanced viral detection in grapevine via exome depletion and next-generation sequencing (NGS)

Autores
Cuello, Raul Andres; Zavallo, Diego; Vera, Pablo Alfredo; Sattler, Agustín; Puebla, Andrea Fabiana; Debat, Humberto Julio; Gomez Talquenca, Gonzalo; Asurmendi, Sebastian
Año de publicación
2026
Idioma
inglés
Tipo de recurso
artículo
Estado
versión publicada
Descripción
Grapevine (Vitis vinifera L.) is highly prone to viral infections that pose a significant threat to global viticulture sustainability. Traditional detection methods, such as PCR and ELISA, are limited to well-known pathogens, highlighting the need for more comprehensive and unbiased approaches. Here, we present the development of a cost-effective viral enrichment system adapted to next-generation sequencing (NGS) for the detection and characterization of grapevine viruses. Our strategy leverages hybridization-based capture using biotin-labelled cDNA probes hereafter named “Chloro-Zero” designed to selectively deplete highly abundant host transcripts, particularly plastid and ribosomal RNAs while preserving viral RNA. Probe design was informed by transcriptomic analysis of V. vinifera. We evaluated different subtractor-to-target RNA ratios, observing a consistent reduction of host RNA and a moderate enrichment of viral sequences. NGS analysis revealed improved recovery of low-abundance viral transcripts, with coverage levels comparable, to a certain extent, to those obtained using previously available commercial kits, but at a significantly lower cost. Although variability in depletion efficiency was observed, the results demonstrate the potential of this scalable and locally adaptable protocol for virome profiling in grapevines. By addressing key limitations of current depletion methods, our approach facilitates the detection of emerging viral threats and supports the development of more effective certification programs and sustainable management practices. Ongoing improvements in probe design and bioinformatic workflows are expected to enhance performance, providing a robust platform for broader applications in plant virology.
Instituto de Biotecnología
Fil: Cuello, Raul Andres. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Agrobiotecnología y Biología Molecular (IABIMO); Argentina
Fil: Cuello, Raul Andres. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Fil: Zavallo, Diego. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Agrobiotecnología y Biología Molecular (IABIMO); Argentina
Fil: Zavallo, Diego. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Fil: Vera, Pablo Alfredo. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Agrobiotecnología y Biología Molecular (IABIMO); Argentina
Fil: Vera, Pablo Alfredo. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Fil: Sattler, Agustín. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Mendoza; Argentina
Fil: Puebla, Andrea Fabiana. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Agrobiotecnología y Biología Molecular (IABIMO); Argentina
Fil: Puebla, Andrea Fabiana. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Fil: Debat, Humberto Julio. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Patología Vegetal; Argentina
Fil: Debat, Humberto Julio. Consejo Nacional de Investigaciones Científicas y Técnicas. Unidad de Fitopatología y Modelización Agrícola (UFyMA); Argentina
Fil: Gomez Talquenca, Gonzalo. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Mendoza; Argentina
Fil: Asurmendi, Sebastian. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Agrobiotecnología y Biología Molecular (IABIMO); Argentina
Fil: Asurmendi, Sebastian. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Fuente
Annals of Applied Biology (First published: 29 April 2026)
Materia
Hybridization
High-throughput Sequencing
Grapevines
Vitis vinifera
Viruses
Hibridación
Secuenciación de Alto Rendimiento
Vid
Virus
Nivel de accesibilidad
acceso restringido
Condiciones de uso
http://creativecommons.org/licenses/by-nc-sa/4.0/
Repositorio
INTA Digital (INTA)
Institución
Instituto Nacional de Tecnología Agropecuaria
OAI Identificador
oai:localhost:20.500.12123/26146
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network_name_str INTA Digital (INTA)
spelling Enhanced viral detection in grapevine via exome depletion and next-generation sequencing (NGS)Cuello, Raul AndresZavallo, DiegoVera, Pablo AlfredoSattler, AgustínPuebla, Andrea FabianaDebat, Humberto JulioGomez Talquenca, GonzaloAsurmendi, SebastianHybridizationHigh-throughput SequencingGrapevinesVitis viniferaVirusesHibridaciónSecuenciación de Alto RendimientoVidVirusGrapevine (Vitis vinifera L.) is highly prone to viral infections that pose a significant threat to global viticulture sustainability. Traditional detection methods, such as PCR and ELISA, are limited to well-known pathogens, highlighting the need for more comprehensive and unbiased approaches. Here, we present the development of a cost-effective viral enrichment system adapted to next-generation sequencing (NGS) for the detection and characterization of grapevine viruses. Our strategy leverages hybridization-based capture using biotin-labelled cDNA probes hereafter named “Chloro-Zero” designed to selectively deplete highly abundant host transcripts, particularly plastid and ribosomal RNAs while preserving viral RNA. Probe design was informed by transcriptomic analysis of V. vinifera. We evaluated different subtractor-to-target RNA ratios, observing a consistent reduction of host RNA and a moderate enrichment of viral sequences. NGS analysis revealed improved recovery of low-abundance viral transcripts, with coverage levels comparable, to a certain extent, to those obtained using previously available commercial kits, but at a significantly lower cost. Although variability in depletion efficiency was observed, the results demonstrate the potential of this scalable and locally adaptable protocol for virome profiling in grapevines. By addressing key limitations of current depletion methods, our approach facilitates the detection of emerging viral threats and supports the development of more effective certification programs and sustainable management practices. Ongoing improvements in probe design and bioinformatic workflows are expected to enhance performance, providing a robust platform for broader applications in plant virology.Instituto de BiotecnologíaFil: Cuello, Raul Andres. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Agrobiotecnología y Biología Molecular (IABIMO); ArgentinaFil: Cuello, Raul Andres. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Zavallo, Diego. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Agrobiotecnología y Biología Molecular (IABIMO); ArgentinaFil: Zavallo, Diego. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Vera, Pablo Alfredo. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Agrobiotecnología y Biología Molecular (IABIMO); ArgentinaFil: Vera, Pablo Alfredo. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Sattler, Agustín. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Mendoza; ArgentinaFil: Puebla, Andrea Fabiana. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Agrobiotecnología y Biología Molecular (IABIMO); ArgentinaFil: Puebla, Andrea Fabiana. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Debat, Humberto Julio. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Patología Vegetal; ArgentinaFil: Debat, Humberto Julio. Consejo Nacional de Investigaciones Científicas y Técnicas. Unidad de Fitopatología y Modelización Agrícola (UFyMA); ArgentinaFil: Gomez Talquenca, Gonzalo. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Mendoza; ArgentinaFil: Asurmendi, Sebastian. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Agrobiotecnología y Biología Molecular (IABIMO); ArgentinaFil: Asurmendi, Sebastian. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaWiley2026-05-12T09:57:57Z2026-05-12T09:57:57Z2026-04info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfhttp://hdl.handle.net/20.500.12123/26146https://onlinelibrary.wiley.com/doi/10.1111/aab.701311744-73480003-4746https://doi.org/10.1111/aab.70131Annals of Applied Biology (First published: 29 April 2026)reponame:INTA Digital (INTA)instname:Instituto Nacional de Tecnología Agropecuariaenginfo:eu-repograntAgreement/INTA/2023-PD-L01-I083, Determinación de los mecanismos moleculares que rigen las interacciones entre plantas y patógenos y desarrollo de herramientas para contribuir al control de enfermedadesinfo:eu-repo/semantics/restrictedAccesshttp://creativecommons.org/licenses/by-nc-sa/4.0/Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)2026-06-11T09:54:43Zoai:localhost:20.500.12123/26146instacron:INTAInstitucionalhttp://repositorio.inta.gob.ar/Organismo científico-tecnológicoNo correspondehttp://repositorio.inta.gob.ar/oai/requesttripaldi.nicolas@inta.gob.arArgentinaNo correspondeNo correspondeNo correspondeopendoar:l2026-06-11 09:54:44.203INTA Digital (INTA) - Instituto Nacional de Tecnología Agropecuariafalse
dc.title.none.fl_str_mv Enhanced viral detection in grapevine via exome depletion and next-generation sequencing (NGS)
title Enhanced viral detection in grapevine via exome depletion and next-generation sequencing (NGS)
spellingShingle Enhanced viral detection in grapevine via exome depletion and next-generation sequencing (NGS)
Cuello, Raul Andres
Hybridization
High-throughput Sequencing
Grapevines
Vitis vinifera
Viruses
Hibridación
Secuenciación de Alto Rendimiento
Vid
Virus
title_short Enhanced viral detection in grapevine via exome depletion and next-generation sequencing (NGS)
title_full Enhanced viral detection in grapevine via exome depletion and next-generation sequencing (NGS)
title_fullStr Enhanced viral detection in grapevine via exome depletion and next-generation sequencing (NGS)
title_full_unstemmed Enhanced viral detection in grapevine via exome depletion and next-generation sequencing (NGS)
title_sort Enhanced viral detection in grapevine via exome depletion and next-generation sequencing (NGS)
dc.creator.none.fl_str_mv Cuello, Raul Andres
Zavallo, Diego
Vera, Pablo Alfredo
Sattler, Agustín
Puebla, Andrea Fabiana
Debat, Humberto Julio
Gomez Talquenca, Gonzalo
Asurmendi, Sebastian
author Cuello, Raul Andres
author_facet Cuello, Raul Andres
Zavallo, Diego
Vera, Pablo Alfredo
Sattler, Agustín
Puebla, Andrea Fabiana
Debat, Humberto Julio
Gomez Talquenca, Gonzalo
Asurmendi, Sebastian
author_role author
author2 Zavallo, Diego
Vera, Pablo Alfredo
Sattler, Agustín
Puebla, Andrea Fabiana
Debat, Humberto Julio
Gomez Talquenca, Gonzalo
Asurmendi, Sebastian
author2_role author
author
author
author
author
author
author
dc.subject.none.fl_str_mv Hybridization
High-throughput Sequencing
Grapevines
Vitis vinifera
Viruses
Hibridación
Secuenciación de Alto Rendimiento
Vid
Virus
topic Hybridization
High-throughput Sequencing
Grapevines
Vitis vinifera
Viruses
Hibridación
Secuenciación de Alto Rendimiento
Vid
Virus
dc.description.none.fl_txt_mv Grapevine (Vitis vinifera L.) is highly prone to viral infections that pose a significant threat to global viticulture sustainability. Traditional detection methods, such as PCR and ELISA, are limited to well-known pathogens, highlighting the need for more comprehensive and unbiased approaches. Here, we present the development of a cost-effective viral enrichment system adapted to next-generation sequencing (NGS) for the detection and characterization of grapevine viruses. Our strategy leverages hybridization-based capture using biotin-labelled cDNA probes hereafter named “Chloro-Zero” designed to selectively deplete highly abundant host transcripts, particularly plastid and ribosomal RNAs while preserving viral RNA. Probe design was informed by transcriptomic analysis of V. vinifera. We evaluated different subtractor-to-target RNA ratios, observing a consistent reduction of host RNA and a moderate enrichment of viral sequences. NGS analysis revealed improved recovery of low-abundance viral transcripts, with coverage levels comparable, to a certain extent, to those obtained using previously available commercial kits, but at a significantly lower cost. Although variability in depletion efficiency was observed, the results demonstrate the potential of this scalable and locally adaptable protocol for virome profiling in grapevines. By addressing key limitations of current depletion methods, our approach facilitates the detection of emerging viral threats and supports the development of more effective certification programs and sustainable management practices. Ongoing improvements in probe design and bioinformatic workflows are expected to enhance performance, providing a robust platform for broader applications in plant virology.
Instituto de Biotecnología
Fil: Cuello, Raul Andres. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Agrobiotecnología y Biología Molecular (IABIMO); Argentina
Fil: Cuello, Raul Andres. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Fil: Zavallo, Diego. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Agrobiotecnología y Biología Molecular (IABIMO); Argentina
Fil: Zavallo, Diego. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Fil: Vera, Pablo Alfredo. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Agrobiotecnología y Biología Molecular (IABIMO); Argentina
Fil: Vera, Pablo Alfredo. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Fil: Sattler, Agustín. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Mendoza; Argentina
Fil: Puebla, Andrea Fabiana. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Agrobiotecnología y Biología Molecular (IABIMO); Argentina
Fil: Puebla, Andrea Fabiana. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Fil: Debat, Humberto Julio. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Patología Vegetal; Argentina
Fil: Debat, Humberto Julio. Consejo Nacional de Investigaciones Científicas y Técnicas. Unidad de Fitopatología y Modelización Agrícola (UFyMA); Argentina
Fil: Gomez Talquenca, Gonzalo. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Mendoza; Argentina
Fil: Asurmendi, Sebastian. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Agrobiotecnología y Biología Molecular (IABIMO); Argentina
Fil: Asurmendi, Sebastian. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
description Grapevine (Vitis vinifera L.) is highly prone to viral infections that pose a significant threat to global viticulture sustainability. Traditional detection methods, such as PCR and ELISA, are limited to well-known pathogens, highlighting the need for more comprehensive and unbiased approaches. Here, we present the development of a cost-effective viral enrichment system adapted to next-generation sequencing (NGS) for the detection and characterization of grapevine viruses. Our strategy leverages hybridization-based capture using biotin-labelled cDNA probes hereafter named “Chloro-Zero” designed to selectively deplete highly abundant host transcripts, particularly plastid and ribosomal RNAs while preserving viral RNA. Probe design was informed by transcriptomic analysis of V. vinifera. We evaluated different subtractor-to-target RNA ratios, observing a consistent reduction of host RNA and a moderate enrichment of viral sequences. NGS analysis revealed improved recovery of low-abundance viral transcripts, with coverage levels comparable, to a certain extent, to those obtained using previously available commercial kits, but at a significantly lower cost. Although variability in depletion efficiency was observed, the results demonstrate the potential of this scalable and locally adaptable protocol for virome profiling in grapevines. By addressing key limitations of current depletion methods, our approach facilitates the detection of emerging viral threats and supports the development of more effective certification programs and sustainable management practices. Ongoing improvements in probe design and bioinformatic workflows are expected to enhance performance, providing a robust platform for broader applications in plant virology.
publishDate 2026
dc.date.none.fl_str_mv 2026-05-12T09:57:57Z
2026-05-12T09:57:57Z
2026-04
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
http://purl.org/coar/resource_type/c_6501
info:ar-repo/semantics/articulo
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/20.500.12123/26146
https://onlinelibrary.wiley.com/doi/10.1111/aab.70131
1744-7348
0003-4746
https://doi.org/10.1111/aab.70131
url http://hdl.handle.net/20.500.12123/26146
https://onlinelibrary.wiley.com/doi/10.1111/aab.70131
https://doi.org/10.1111/aab.70131
identifier_str_mv 1744-7348
0003-4746
dc.language.none.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv info:eu-repograntAgreement/INTA/2023-PD-L01-I083, Determinación de los mecanismos moleculares que rigen las interacciones entre plantas y patógenos y desarrollo de herramientas para contribuir al control de enfermedades
dc.rights.none.fl_str_mv info:eu-repo/semantics/restrictedAccess
http://creativecommons.org/licenses/by-nc-sa/4.0/
Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)
eu_rights_str_mv restrictedAccess
rights_invalid_str_mv http://creativecommons.org/licenses/by-nc-sa/4.0/
Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)
dc.format.none.fl_str_mv application/pdf
dc.publisher.none.fl_str_mv Wiley
publisher.none.fl_str_mv Wiley
dc.source.none.fl_str_mv Annals of Applied Biology (First published: 29 April 2026)
reponame:INTA Digital (INTA)
instname:Instituto Nacional de Tecnología Agropecuaria
reponame_str INTA Digital (INTA)
collection INTA Digital (INTA)
instname_str Instituto Nacional de Tecnología Agropecuaria
repository.name.fl_str_mv INTA Digital (INTA) - Instituto Nacional de Tecnología Agropecuaria
repository.mail.fl_str_mv tripaldi.nicolas@inta.gob.ar
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