Exploring the tymovirales landscape through metatranscriptomics data

Autores
Bejerman, Nicolas Esteban; Debat, Humberto Julio
Año de publicación
2022
Idioma
inglés
Tipo de recurso
artículo
Estado
versión publicada
Descripción
Tymovirales is an order of viruses with positive-sense RNA genomes that mostly infect plants, but also fungi and insects. The number of genome sequences of viruses that could fit this taxon has been growing in the last few years with the extensive use of high-throughput sequencing. Here, we report the discovery of 31 novel viral genome sequences associated with 27 different host plant species, which were hidden in public databases. These viral sequences were identified through homology searches in more than 3,000 plant transcriptomes from the NCBI Sequence Read Archive (SRA) using known tymovirales sequences as queries. Identification, assembly, and curation of raw SRA reads resulted in 29 viral genome sequences with complete coding regions, and two representing partial genomes. Some of the obtained sequences highlight novel genome organizations for members of the order. Phylogenetic analysis showed that six of the novel viruses are related to alphaflexiviruses, 17 to betaflexiviruses, two to deltaflexiviruses, and six to tymovirids. These findings shed new light on the phylogenetic relationships and evolutionary landscape of this group of viruses. Furthermore, this study illustrates the complexity and genome diversity among members of the order and demonstrates that analyzing public SRA data provides an invaluable tool to accelerate virus discovery and refine virus taxonomy.
Instituto de Patología Vegetal
Fil: Bejerman, Nicolas Esteban. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Patología Vegetal; Argentina
Fil: Bejerman, Nicolas Esteban. Consejo Nacional de Investigaciones Científicas y Técnicas. Unidad de Fitopatología y Modelización Agrícola (UFyMA); 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
Fuente
Archives of Virology (Published: 16 June 2022)
Materia
Tymovirales
RNA Viruses
Genomes
Tymoviridae
Taxonomy of Viruses
Deltaflexiviridae
Alphaflexiviruses
Taxonomía de Virus
Nivel de accesibilidad
acceso restringido
Condiciones de uso
Repositorio
INTA Digital (INTA)
Institución
Instituto Nacional de Tecnología Agropecuaria
OAI Identificador
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spelling Exploring the tymovirales landscape through metatranscriptomics dataBejerman, Nicolas EstebanDebat, Humberto JulioTymoviralesRNA VirusesGenomesTymoviridaeTaxonomy of VirusesDeltaflexiviridaeAlphaflexivirusesTaxonomía de VirusTymovirales is an order of viruses with positive-sense RNA genomes that mostly infect plants, but also fungi and insects. The number of genome sequences of viruses that could fit this taxon has been growing in the last few years with the extensive use of high-throughput sequencing. Here, we report the discovery of 31 novel viral genome sequences associated with 27 different host plant species, which were hidden in public databases. These viral sequences were identified through homology searches in more than 3,000 plant transcriptomes from the NCBI Sequence Read Archive (SRA) using known tymovirales sequences as queries. Identification, assembly, and curation of raw SRA reads resulted in 29 viral genome sequences with complete coding regions, and two representing partial genomes. Some of the obtained sequences highlight novel genome organizations for members of the order. Phylogenetic analysis showed that six of the novel viruses are related to alphaflexiviruses, 17 to betaflexiviruses, two to deltaflexiviruses, and six to tymovirids. These findings shed new light on the phylogenetic relationships and evolutionary landscape of this group of viruses. Furthermore, this study illustrates the complexity and genome diversity among members of the order and demonstrates that analyzing public SRA data provides an invaluable tool to accelerate virus discovery and refine virus taxonomy.Instituto de Patología VegetalFil: Bejerman, Nicolas Esteban. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Patología Vegetal; ArgentinaFil: Bejerman, Nicolas Esteban. Consejo Nacional de Investigaciones Científicas y Técnicas. Unidad de Fitopatología y Modelización Agrícola (UFyMA); 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); ArgentinaSpringer2022-06-30T10:56:28Z2022-06-30T10:56:28Z2022-06-16info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfhttp://hdl.handle.net/20.500.12123/12197https://link.springer.com/article/10.1007/s00705-022-05493-90304-86081432-8798 ( online)https://doi.org/10.1007/s00705-022-05493-9Archives of Virology (Published: 16 June 2022)reponame:INTA Digital (INTA)instname:Instituto Nacional de Tecnología Agropecuariaenginfo:eu-repo/semantics/restrictedAccess2025-11-13T08:47:14Zoai:localhost:20.500.12123/12197instacron:INTAInstitucionalhttp://repositorio.inta.gob.ar/Organismo científico-tecnológicoNo correspondehttp://repositorio.inta.gob.ar/oai/requesttripaldi.nicolas@inta.gob.arArgentinaNo correspondeNo correspondeNo correspondeopendoar:l2025-11-13 08:47:14.447INTA Digital (INTA) - Instituto Nacional de Tecnología Agropecuariafalse
dc.title.none.fl_str_mv Exploring the tymovirales landscape through metatranscriptomics data
title Exploring the tymovirales landscape through metatranscriptomics data
spellingShingle Exploring the tymovirales landscape through metatranscriptomics data
Bejerman, Nicolas Esteban
Tymovirales
RNA Viruses
Genomes
Tymoviridae
Taxonomy of Viruses
Deltaflexiviridae
Alphaflexiviruses
Taxonomía de Virus
title_short Exploring the tymovirales landscape through metatranscriptomics data
title_full Exploring the tymovirales landscape through metatranscriptomics data
title_fullStr Exploring the tymovirales landscape through metatranscriptomics data
title_full_unstemmed Exploring the tymovirales landscape through metatranscriptomics data
title_sort Exploring the tymovirales landscape through metatranscriptomics data
dc.creator.none.fl_str_mv Bejerman, Nicolas Esteban
Debat, Humberto Julio
author Bejerman, Nicolas Esteban
author_facet Bejerman, Nicolas Esteban
Debat, Humberto Julio
author_role author
author2 Debat, Humberto Julio
author2_role author
dc.subject.none.fl_str_mv Tymovirales
RNA Viruses
Genomes
Tymoviridae
Taxonomy of Viruses
Deltaflexiviridae
Alphaflexiviruses
Taxonomía de Virus
topic Tymovirales
RNA Viruses
Genomes
Tymoviridae
Taxonomy of Viruses
Deltaflexiviridae
Alphaflexiviruses
Taxonomía de Virus
dc.description.none.fl_txt_mv Tymovirales is an order of viruses with positive-sense RNA genomes that mostly infect plants, but also fungi and insects. The number of genome sequences of viruses that could fit this taxon has been growing in the last few years with the extensive use of high-throughput sequencing. Here, we report the discovery of 31 novel viral genome sequences associated with 27 different host plant species, which were hidden in public databases. These viral sequences were identified through homology searches in more than 3,000 plant transcriptomes from the NCBI Sequence Read Archive (SRA) using known tymovirales sequences as queries. Identification, assembly, and curation of raw SRA reads resulted in 29 viral genome sequences with complete coding regions, and two representing partial genomes. Some of the obtained sequences highlight novel genome organizations for members of the order. Phylogenetic analysis showed that six of the novel viruses are related to alphaflexiviruses, 17 to betaflexiviruses, two to deltaflexiviruses, and six to tymovirids. These findings shed new light on the phylogenetic relationships and evolutionary landscape of this group of viruses. Furthermore, this study illustrates the complexity and genome diversity among members of the order and demonstrates that analyzing public SRA data provides an invaluable tool to accelerate virus discovery and refine virus taxonomy.
Instituto de Patología Vegetal
Fil: Bejerman, Nicolas Esteban. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Patología Vegetal; Argentina
Fil: Bejerman, Nicolas Esteban. Consejo Nacional de Investigaciones Científicas y Técnicas. Unidad de Fitopatología y Modelización Agrícola (UFyMA); 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
description Tymovirales is an order of viruses with positive-sense RNA genomes that mostly infect plants, but also fungi and insects. The number of genome sequences of viruses that could fit this taxon has been growing in the last few years with the extensive use of high-throughput sequencing. Here, we report the discovery of 31 novel viral genome sequences associated with 27 different host plant species, which were hidden in public databases. These viral sequences were identified through homology searches in more than 3,000 plant transcriptomes from the NCBI Sequence Read Archive (SRA) using known tymovirales sequences as queries. Identification, assembly, and curation of raw SRA reads resulted in 29 viral genome sequences with complete coding regions, and two representing partial genomes. Some of the obtained sequences highlight novel genome organizations for members of the order. Phylogenetic analysis showed that six of the novel viruses are related to alphaflexiviruses, 17 to betaflexiviruses, two to deltaflexiviruses, and six to tymovirids. These findings shed new light on the phylogenetic relationships and evolutionary landscape of this group of viruses. Furthermore, this study illustrates the complexity and genome diversity among members of the order and demonstrates that analyzing public SRA data provides an invaluable tool to accelerate virus discovery and refine virus taxonomy.
publishDate 2022
dc.date.none.fl_str_mv 2022-06-30T10:56:28Z
2022-06-30T10:56:28Z
2022-06-16
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/20.500.12123/12197
https://link.springer.com/article/10.1007/s00705-022-05493-9
0304-8608
1432-8798 ( online)
https://doi.org/10.1007/s00705-022-05493-9
url http://hdl.handle.net/20.500.12123/12197
https://link.springer.com/article/10.1007/s00705-022-05493-9
https://doi.org/10.1007/s00705-022-05493-9
identifier_str_mv 0304-8608
1432-8798 ( online)
dc.language.none.fl_str_mv eng
language eng
dc.rights.none.fl_str_mv info:eu-repo/semantics/restrictedAccess
eu_rights_str_mv restrictedAccess
dc.format.none.fl_str_mv application/pdf
dc.publisher.none.fl_str_mv Springer
publisher.none.fl_str_mv Springer
dc.source.none.fl_str_mv Archives of Virology (Published: 16 June 2022)
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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score 12.738264

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