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Blueberry red ringspot virus genomes from Florida inferred through analysis of blueberry root transcriptomes
A growing number of metagenomics-based approaches have been used for the discovery of viruses in insects, cultivated plants, and water in agricultural production systems. In this study, sixteen blueberry root transcriptomes from eight clonally propagated blueberry plants of cultivar ‘Emerald’ (inter...
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| Published in: | Scientific reports 2020-07, Vol.10 (1), p.12043-12043, Article 12043 |
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| creator | Saad, N. Alcalá-Briseño, R. I. Polston, J. E. Olmstead, J. W. Varsani, A. Harmon, P. F. |
| description | A growing number of metagenomics-based approaches have been used for the discovery of viruses in insects, cultivated plants, and water in agricultural production systems. In this study, sixteen blueberry root transcriptomes from eight clonally propagated blueberry plants of cultivar ‘Emerald’ (interspecific hybrid of
Vaccinium corymbosum
and
V. darrowi
) generated as part of a separate study on varietal tolerance to soil salinity were analyzed for plant viral sequences
.
The objective was to determine if the asymptomatic plants harbored the latent blueberry red ringspot virus (BRRV) in their roots. The only currently known mechanism of transmission of BRRV is through vegetative propagation; however, the virus can remain latent for years with some plants of ‘Emerald’ never developing red ringspot symptoms. Bioinformatic analyses of ‘Emerald’ transcriptomes using de novo assembly and reference-based mapping approaches yielded eight complete viral genomes of BRRV (genus
Soymovirus
, family
Caulimoviridae
). Validation in vitro by PCR confirmed the presence of BRRV in 100% of the ‘Emerald’ root samples. Sequence and phylogenetic analyses showed 94% to 97% nucleotide identity between BRRV genomes from Florida and sequences from Czech Republic, Japan, Poland, Slovenia, and the United States. Taken together, this study documented the first detection of a complete BRRV genome from roots of asymptomatic blueberry plants and in Florida through in silico analysis of plant transcriptomes. |
| doi_str_mv | 10.1038/s41598-020-68654-3 |
| format | article |
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Vaccinium corymbosum
and
V. darrowi
) generated as part of a separate study on varietal tolerance to soil salinity were analyzed for plant viral sequences
.
The objective was to determine if the asymptomatic plants harbored the latent blueberry red ringspot virus (BRRV) in their roots. The only currently known mechanism of transmission of BRRV is through vegetative propagation; however, the virus can remain latent for years with some plants of ‘Emerald’ never developing red ringspot symptoms. Bioinformatic analyses of ‘Emerald’ transcriptomes using de novo assembly and reference-based mapping approaches yielded eight complete viral genomes of BRRV (genus
Soymovirus
, family
Caulimoviridae
). Validation in vitro by PCR confirmed the presence of BRRV in 100% of the ‘Emerald’ root samples. Sequence and phylogenetic analyses showed 94% to 97% nucleotide identity between BRRV genomes from Florida and sequences from Czech Republic, Japan, Poland, Slovenia, and the United States. Taken together, this study documented the first detection of a complete BRRV genome from roots of asymptomatic blueberry plants and in Florida through in silico analysis of plant transcriptomes.</description><identifier>ISSN: 2045-2322</identifier><identifier>EISSN: 2045-2322</identifier><identifier>DOI: 10.1038/s41598-020-68654-3</identifier><identifier>PMID: 32694553</identifier><language>eng</language><publisher>London: Nature Publishing Group UK</publisher><subject>631/114 ; 631/449 ; Agricultural production ; Blueberry Plants - genetics ; Blueberry Plants - virology ; Caulimoviridae ; Cultivars ; Cultivated plants ; Evolution, Molecular ; Flowers & plants ; Fruits ; Gene Expression Profiling ; Gene mapping ; Genome, Viral - genetics ; Genomes ; Host-Pathogen Interactions ; Humanities and Social Sciences ; Interspecific ; Metagenomics ; multidisciplinary ; Phylogeny ; Plant Diseases - genetics ; Plant Diseases - virology ; Plant propagation ; Plant Roots - genetics ; Plant Roots - virology ; Plant Viruses - classification ; Plant Viruses - genetics ; Propagation ; Roots ; Science ; Science (multidisciplinary) ; Soil salinity ; Transcriptome ; Vaccinium corymbosum ; Vaccinium darrowii ; Viruses</subject><ispartof>Scientific reports, 2020-07, Vol.10 (1), p.12043-12043, Article 12043</ispartof><rights>The Author(s) 2020</rights><rights>The Author(s) 2020. This work is published under http://creativecommons.org/licenses/by/4.0/ (the “License”). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c511t-d42fd4fc8f4511667579da36bbaa819bb249422454f48d09b2e480e9253789d03</citedby><cites>FETCH-LOGICAL-c511t-d42fd4fc8f4511667579da36bbaa819bb249422454f48d09b2e480e9253789d03</cites><orcidid>0000-0003-4111-2415 ; 0000-0002-7031-2195</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.proquest.com/docview/2425720064/fulltextPDF?pq-origsite=primo$$EPDF$$P50$$Gproquest$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.proquest.com/docview/2425720064?pq-origsite=primo$$EHTML$$P50$$Gproquest$$Hfree_for_read</linktohtml><link.rule.ids>230,314,727,780,784,885,25753,27924,27925,37012,37013,44590,53791,53793,75126</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/32694553$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Saad, N.</creatorcontrib><creatorcontrib>Alcalá-Briseño, R. I.</creatorcontrib><creatorcontrib>Polston, J. E.</creatorcontrib><creatorcontrib>Olmstead, J. W.</creatorcontrib><creatorcontrib>Varsani, A.</creatorcontrib><creatorcontrib>Harmon, P. F.</creatorcontrib><title>Blueberry red ringspot virus genomes from Florida inferred through analysis of blueberry root transcriptomes</title><title>Scientific reports</title><addtitle>Sci Rep</addtitle><addtitle>Sci Rep</addtitle><description>A growing number of metagenomics-based approaches have been used for the discovery of viruses in insects, cultivated plants, and water in agricultural production systems. In this study, sixteen blueberry root transcriptomes from eight clonally propagated blueberry plants of cultivar ‘Emerald’ (interspecific hybrid of
Vaccinium corymbosum
and
V. darrowi
) generated as part of a separate study on varietal tolerance to soil salinity were analyzed for plant viral sequences
.
The objective was to determine if the asymptomatic plants harbored the latent blueberry red ringspot virus (BRRV) in their roots. The only currently known mechanism of transmission of BRRV is through vegetative propagation; however, the virus can remain latent for years with some plants of ‘Emerald’ never developing red ringspot symptoms. Bioinformatic analyses of ‘Emerald’ transcriptomes using de novo assembly and reference-based mapping approaches yielded eight complete viral genomes of BRRV (genus
Soymovirus
, family
Caulimoviridae
). Validation in vitro by PCR confirmed the presence of BRRV in 100% of the ‘Emerald’ root samples. Sequence and phylogenetic analyses showed 94% to 97% nucleotide identity between BRRV genomes from Florida and sequences from Czech Republic, Japan, Poland, Slovenia, and the United States. Taken together, this study documented the first detection of a complete BRRV genome from roots of asymptomatic blueberry plants and in Florida through in silico analysis of plant transcriptomes.</description><subject>631/114</subject><subject>631/449</subject><subject>Agricultural production</subject><subject>Blueberry Plants - genetics</subject><subject>Blueberry Plants - virology</subject><subject>Caulimoviridae</subject><subject>Cultivars</subject><subject>Cultivated plants</subject><subject>Evolution, Molecular</subject><subject>Flowers & plants</subject><subject>Fruits</subject><subject>Gene Expression Profiling</subject><subject>Gene mapping</subject><subject>Genome, Viral - genetics</subject><subject>Genomes</subject><subject>Host-Pathogen Interactions</subject><subject>Humanities and Social Sciences</subject><subject>Interspecific</subject><subject>Metagenomics</subject><subject>multidisciplinary</subject><subject>Phylogeny</subject><subject>Plant Diseases - genetics</subject><subject>Plant Diseases - virology</subject><subject>Plant propagation</subject><subject>Plant Roots - genetics</subject><subject>Plant Roots - virology</subject><subject>Plant Viruses - classification</subject><subject>Plant Viruses - genetics</subject><subject>Propagation</subject><subject>Roots</subject><subject>Science</subject><subject>Science (multidisciplinary)</subject><subject>Soil salinity</subject><subject>Transcriptome</subject><subject>Vaccinium corymbosum</subject><subject>Vaccinium darrowii</subject><subject>Viruses</subject><issn>2045-2322</issn><issn>2045-2322</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2020</creationdate><recordtype>article</recordtype><sourceid>PIMPY</sourceid><recordid>eNp9kcFuFSEUhonR2KbtC3RhSNy4GYXDgRk2JtpYNWnSjV0TZgbupZkZRphpct--3N7aVheyAcJ3Pg78hJxz9pEz0XzKyKVuKgasUo2SWIlX5BgYygoEwOsX6yNylvMtK0OCRq7fkiMBSqOU4pgMX4fVtS6lHU2upylMmzzHhd6FtGa6cVMcXaY-xZFeDjGF3tIw-cIXeNmmuG621E522OWQafS0fdbFolmSnXKXwrzsPafkjbdDdmeP8wm5ufz26-JHdXX9_efFl6uqk5wvVY_ge_Rd47HslaplrXsrVNta23DdtoAaAVCix6ZnugWHDXMapKgb3TNxQj4fvPPajq7v3FT6GMycwmjTzkQbzN8nU9iaTbwztaiRK10EHx4FKf5eXV7MGHLnhsFOLq7ZAILida04L-j7f9DbuKbyIw-UrIExhYWCA9WlmHNy_qkZzsw-T3PI05Q8zUOeRpSidy-f8VTyJ70CiAOQ531wLj3f_R_tPYYsrVk</recordid><startdate>20200721</startdate><enddate>20200721</enddate><creator>Saad, N.</creator><creator>Alcalá-Briseño, R. 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I.</au><au>Polston, J. E.</au><au>Olmstead, J. W.</au><au>Varsani, A.</au><au>Harmon, P. F.</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Blueberry red ringspot virus genomes from Florida inferred through analysis of blueberry root transcriptomes</atitle><jtitle>Scientific reports</jtitle><stitle>Sci Rep</stitle><addtitle>Sci Rep</addtitle><date>2020-07-21</date><risdate>2020</risdate><volume>10</volume><issue>1</issue><spage>12043</spage><epage>12043</epage><pages>12043-12043</pages><artnum>12043</artnum><issn>2045-2322</issn><eissn>2045-2322</eissn><abstract>A growing number of metagenomics-based approaches have been used for the discovery of viruses in insects, cultivated plants, and water in agricultural production systems. In this study, sixteen blueberry root transcriptomes from eight clonally propagated blueberry plants of cultivar ‘Emerald’ (interspecific hybrid of
Vaccinium corymbosum
and
V. darrowi
) generated as part of a separate study on varietal tolerance to soil salinity were analyzed for plant viral sequences
.
The objective was to determine if the asymptomatic plants harbored the latent blueberry red ringspot virus (BRRV) in their roots. The only currently known mechanism of transmission of BRRV is through vegetative propagation; however, the virus can remain latent for years with some plants of ‘Emerald’ never developing red ringspot symptoms. Bioinformatic analyses of ‘Emerald’ transcriptomes using de novo assembly and reference-based mapping approaches yielded eight complete viral genomes of BRRV (genus
Soymovirus
, family
Caulimoviridae
). Validation in vitro by PCR confirmed the presence of BRRV in 100% of the ‘Emerald’ root samples. Sequence and phylogenetic analyses showed 94% to 97% nucleotide identity between BRRV genomes from Florida and sequences from Czech Republic, Japan, Poland, Slovenia, and the United States. Taken together, this study documented the first detection of a complete BRRV genome from roots of asymptomatic blueberry plants and in Florida through in silico analysis of plant transcriptomes.</abstract><cop>London</cop><pub>Nature Publishing Group UK</pub><pmid>32694553</pmid><doi>10.1038/s41598-020-68654-3</doi><tpages>1</tpages><orcidid>https://orcid.org/0000-0003-4111-2415</orcidid><orcidid>https://orcid.org/0000-0002-7031-2195</orcidid><oa>free_for_read</oa></addata></record> |
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| language | eng |
| recordid | cdi_pubmedcentral_primary_oai_pubmedcentral_nih_gov_7374169 |
| source | Publicly Available Content Database; PubMed Central; Free Full-Text Journals in Chemistry; Springer Nature - nature.com Journals - Fully Open Access |
| subjects | 631/114 631/449 Agricultural production Blueberry Plants - genetics Blueberry Plants - virology Caulimoviridae Cultivars Cultivated plants Evolution, Molecular Flowers & plants Fruits Gene Expression Profiling Gene mapping Genome, Viral - genetics Genomes Host-Pathogen Interactions Humanities and Social Sciences Interspecific Metagenomics multidisciplinary Phylogeny Plant Diseases - genetics Plant Diseases - virology Plant propagation Plant Roots - genetics Plant Roots - virology Plant Viruses - classification Plant Viruses - genetics Propagation Roots Science Science (multidisciplinary) Soil salinity Transcriptome Vaccinium corymbosum Vaccinium darrowii Viruses |
| title | Blueberry red ringspot virus genomes from Florida inferred through analysis of blueberry root transcriptomes |
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