Viromes of ten alfalfa plants in Australia reveal diverse known viruses and a novel RNA virus

Autores
Samarfard, Samira; McTaggart, Alistair R.; Sharman, Murray; Bejerman, Nicolas; Dietzgen, Ralf G.
Año de publicación
2020
Idioma
inglés
Tipo de recurso
artículo
Estado
versión publicada
Descripción
Alfalfa plants in the field can display a range of virus-like symptoms, especially when grown over many years for seed production. Most known alfalfa viruses have RNA genomes, some of which can be detected using diagnostic assays, but many viruses of alfalfa are not well characterized. This study aims to identify the RNA and DNA virus complexes associated with alfalfa plants in Australia. To maximize the detection of RNA viruses, we purified double-stranded RNA (dsRNA) for high throughput sequencing and characterized the viromes of ten alfalfa samples that showed diverse virus-like symptoms. Using Illumina sequencing of tagged cDNA libraries from immune-captured dsRNA, we identified sequences of the single-stranded RNA viruses, alfalfa mosaic virus (AMV), bean leafroll virus, a new emaravirus tentatively named alfalfa ringspot-associated virus, and persistent dsRNA viruses belonging to the families Amalgaviridae and Partitiviridae. Furthermore, rolling circle amplification and restriction enzyme digestion revealed the complete genome of chickpea chlorosis Australia virus, a mastrevirus (family Geminiviridae) previously reported only from chickpea and French bean that was 97% identical to the chickpea isolate. The sequence data also enabled the assembly of the first complete genome (RNAs 1–3) of an Australian AMV isolate from alfalfa.
Fil: Samarfard, Samira. The University of Queensland; Australia
Fil: McTaggart, Alistair R.. The University of Queensland; Australia
Fil: Sharman, Murray. The University of Queensland; Australia
Fil: Bejerman, Nicolas. Instituto Nacional de Tecnología Agropecuaria. Centro de Investigaciones Agropecuarias. Unidad de Fitopatología y Modelización Agrícola - Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Unidad de Fitopatología y Modelización Agrícola; Argentina
Fil: Dietzgen, Ralf G.. The University of Queensland; Australia
Materia
alfalfa
virome
australia
high-throughput sequencing
Nivel de accesibilidad
acceso abierto
Condiciones de uso
https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
Repositorio
CONICET Digital (CONICET)
Institución
Consejo Nacional de Investigaciones Científicas y Técnicas
OAI Identificador
oai:ri.conicet.gov.ar:11336/135332
Acceder
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oai_identifier_str oai:ri.conicet.gov.ar:11336/135332
network_acronym_str CONICETDig
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network_name_str CONICET Digital (CONICET)
spelling Viromes of ten alfalfa plants in Australia reveal diverse known viruses and a novel RNA virusSamarfard, SamiraMcTaggart, Alistair R.Sharman, MurrayBejerman, NicolasDietzgen, Ralf G.alfalfaviromeaustraliahigh-throughput sequencinghttps://purl.org/becyt/ford/1.6https://purl.org/becyt/ford/1Alfalfa plants in the field can display a range of virus-like symptoms, especially when grown over many years for seed production. Most known alfalfa viruses have RNA genomes, some of which can be detected using diagnostic assays, but many viruses of alfalfa are not well characterized. This study aims to identify the RNA and DNA virus complexes associated with alfalfa plants in Australia. To maximize the detection of RNA viruses, we purified double-stranded RNA (dsRNA) for high throughput sequencing and characterized the viromes of ten alfalfa samples that showed diverse virus-like symptoms. Using Illumina sequencing of tagged cDNA libraries from immune-captured dsRNA, we identified sequences of the single-stranded RNA viruses, alfalfa mosaic virus (AMV), bean leafroll virus, a new emaravirus tentatively named alfalfa ringspot-associated virus, and persistent dsRNA viruses belonging to the families Amalgaviridae and Partitiviridae. Furthermore, rolling circle amplification and restriction enzyme digestion revealed the complete genome of chickpea chlorosis Australia virus, a mastrevirus (family Geminiviridae) previously reported only from chickpea and French bean that was 97% identical to the chickpea isolate. The sequence data also enabled the assembly of the first complete genome (RNAs 1–3) of an Australian AMV isolate from alfalfa.Fil: Samarfard, Samira. The University of Queensland; AustraliaFil: McTaggart, Alistair R.. The University of Queensland; AustraliaFil: Sharman, Murray. The University of Queensland; AustraliaFil: Bejerman, Nicolas. Instituto Nacional de Tecnología Agropecuaria. Centro de Investigaciones Agropecuarias. Unidad de Fitopatología y Modelización Agrícola - Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Unidad de Fitopatología y Modelización Agrícola; ArgentinaFil: Dietzgen, Ralf G.. The University of Queensland; AustraliaMDPI AG2020-03info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfapplication/pdfhttp://hdl.handle.net/11336/135332Samarfard, Samira; McTaggart, Alistair R.; Sharman, Murray; Bejerman, Nicolas; Dietzgen, Ralf G.; Viromes of ten alfalfa plants in Australia reveal diverse known viruses and a novel RNA virus; MDPI AG; Pathogens; 9; 3; 3-2020; 1-242076-0817CONICET DigitalCONICETenginfo:eu-repo/semantics/altIdentifier/url/https://www.mdpi.com/2076-0817/9/3/214info:eu-repo/semantics/altIdentifier/doi/10.3390/pathogens9030214info:eu-repo/semantics/openAccesshttps://creativecommons.org/licenses/by-nc-sa/2.5/ar/reponame:CONICET Digital (CONICET)instname:Consejo Nacional de Investigaciones Científicas y Técnicas2025-09-03T09:57:13Zoai:ri.conicet.gov.ar:11336/135332instacron:CONICETInstitucionalhttp://ri.conicet.gov.ar/Organismo científico-tecnológicoNo correspondehttp://ri.conicet.gov.ar/oai/requestdasensio@conicet.gov.ar; lcarlino@conicet.gov.arArgentinaNo correspondeNo correspondeNo correspondeopendoar:34982025-09-03 09:57:13.383CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicasfalse
dc.title.none.fl_str_mv Viromes of ten alfalfa plants in Australia reveal diverse known viruses and a novel RNA virus
title Viromes of ten alfalfa plants in Australia reveal diverse known viruses and a novel RNA virus
spellingShingle Viromes of ten alfalfa plants in Australia reveal diverse known viruses and a novel RNA virus
Samarfard, Samira
alfalfa
virome
australia
high-throughput sequencing
title_short Viromes of ten alfalfa plants in Australia reveal diverse known viruses and a novel RNA virus
title_full Viromes of ten alfalfa plants in Australia reveal diverse known viruses and a novel RNA virus
title_fullStr Viromes of ten alfalfa plants in Australia reveal diverse known viruses and a novel RNA virus
title_full_unstemmed Viromes of ten alfalfa plants in Australia reveal diverse known viruses and a novel RNA virus
title_sort Viromes of ten alfalfa plants in Australia reveal diverse known viruses and a novel RNA virus
dc.creator.none.fl_str_mv Samarfard, Samira
McTaggart, Alistair R.
Sharman, Murray
Bejerman, Nicolas
Dietzgen, Ralf G.
author Samarfard, Samira
author_facet Samarfard, Samira
McTaggart, Alistair R.
Sharman, Murray
Bejerman, Nicolas
Dietzgen, Ralf G.
author_role author
author2 McTaggart, Alistair R.
Sharman, Murray
Bejerman, Nicolas
Dietzgen, Ralf G.
author2_role author
author
author
author
dc.subject.none.fl_str_mv alfalfa
virome
australia
high-throughput sequencing
topic alfalfa
virome
australia
high-throughput sequencing
purl_subject.fl_str_mv https://purl.org/becyt/ford/1.6
https://purl.org/becyt/ford/1
dc.description.none.fl_txt_mv Alfalfa plants in the field can display a range of virus-like symptoms, especially when grown over many years for seed production. Most known alfalfa viruses have RNA genomes, some of which can be detected using diagnostic assays, but many viruses of alfalfa are not well characterized. This study aims to identify the RNA and DNA virus complexes associated with alfalfa plants in Australia. To maximize the detection of RNA viruses, we purified double-stranded RNA (dsRNA) for high throughput sequencing and characterized the viromes of ten alfalfa samples that showed diverse virus-like symptoms. Using Illumina sequencing of tagged cDNA libraries from immune-captured dsRNA, we identified sequences of the single-stranded RNA viruses, alfalfa mosaic virus (AMV), bean leafroll virus, a new emaravirus tentatively named alfalfa ringspot-associated virus, and persistent dsRNA viruses belonging to the families Amalgaviridae and Partitiviridae. Furthermore, rolling circle amplification and restriction enzyme digestion revealed the complete genome of chickpea chlorosis Australia virus, a mastrevirus (family Geminiviridae) previously reported only from chickpea and French bean that was 97% identical to the chickpea isolate. The sequence data also enabled the assembly of the first complete genome (RNAs 1–3) of an Australian AMV isolate from alfalfa.
Fil: Samarfard, Samira. The University of Queensland; Australia
Fil: McTaggart, Alistair R.. The University of Queensland; Australia
Fil: Sharman, Murray. The University of Queensland; Australia
Fil: Bejerman, Nicolas. Instituto Nacional de Tecnología Agropecuaria. Centro de Investigaciones Agropecuarias. Unidad de Fitopatología y Modelización Agrícola - Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Unidad de Fitopatología y Modelización Agrícola; Argentina
Fil: Dietzgen, Ralf G.. The University of Queensland; Australia
description Alfalfa plants in the field can display a range of virus-like symptoms, especially when grown over many years for seed production. Most known alfalfa viruses have RNA genomes, some of which can be detected using diagnostic assays, but many viruses of alfalfa are not well characterized. This study aims to identify the RNA and DNA virus complexes associated with alfalfa plants in Australia. To maximize the detection of RNA viruses, we purified double-stranded RNA (dsRNA) for high throughput sequencing and characterized the viromes of ten alfalfa samples that showed diverse virus-like symptoms. Using Illumina sequencing of tagged cDNA libraries from immune-captured dsRNA, we identified sequences of the single-stranded RNA viruses, alfalfa mosaic virus (AMV), bean leafroll virus, a new emaravirus tentatively named alfalfa ringspot-associated virus, and persistent dsRNA viruses belonging to the families Amalgaviridae and Partitiviridae. Furthermore, rolling circle amplification and restriction enzyme digestion revealed the complete genome of chickpea chlorosis Australia virus, a mastrevirus (family Geminiviridae) previously reported only from chickpea and French bean that was 97% identical to the chickpea isolate. The sequence data also enabled the assembly of the first complete genome (RNAs 1–3) of an Australian AMV isolate from alfalfa.
publishDate 2020
dc.date.none.fl_str_mv 2020-03
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/11336/135332
Samarfard, Samira; McTaggart, Alistair R.; Sharman, Murray; Bejerman, Nicolas; Dietzgen, Ralf G.; Viromes of ten alfalfa plants in Australia reveal diverse known viruses and a novel RNA virus; MDPI AG; Pathogens; 9; 3; 3-2020; 1-24
2076-0817
CONICET Digital
CONICET
url http://hdl.handle.net/11336/135332
identifier_str_mv Samarfard, Samira; McTaggart, Alistair R.; Sharman, Murray; Bejerman, Nicolas; Dietzgen, Ralf G.; Viromes of ten alfalfa plants in Australia reveal diverse known viruses and a novel RNA virus; MDPI AG; Pathogens; 9; 3; 3-2020; 1-24
2076-0817
CONICET Digital
CONICET
dc.language.none.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv info:eu-repo/semantics/altIdentifier/url/https://www.mdpi.com/2076-0817/9/3/214
info:eu-repo/semantics/altIdentifier/doi/10.3390/pathogens9030214
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
eu_rights_str_mv openAccess
rights_invalid_str_mv https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
dc.format.none.fl_str_mv application/pdf
application/pdf
dc.publisher.none.fl_str_mv MDPI AG
publisher.none.fl_str_mv MDPI AG
dc.source.none.fl_str_mv reponame:CONICET Digital (CONICET)
instname:Consejo Nacional de Investigaciones Científicas y Técnicas
reponame_str CONICET Digital (CONICET)
collection CONICET Digital (CONICET)
instname_str Consejo Nacional de Investigaciones Científicas y Técnicas
repository.name.fl_str_mv CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicas
repository.mail.fl_str_mv dasensio@conicet.gov.ar; lcarlino@conicet.gov.ar
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score 13.13397

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