Illuminating the Plant Rhabdovirus Landscape through Metatranscriptomics Data
Rhabdoviruses infect a large number of plant species and cause significant crop diseases. They have a negative-sense, single-stranded unsegmented or bisegmented RNA genome. The number of plant-associated rhabdovirid sequences has grown in the last few years in concert with the extensive use of high-...
| Autores principales: | , , |
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| Formato: | Artículo |
| Lenguaje: | Inglés |
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MDPI
2021
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| Materias: | |
| Acceso en línea: | http://hdl.handle.net/20.500.12123/9760 https://www.mdpi.com/1999-4915/13/7/1304 https://doi.org/10.3390/v13071304 |
| _version_ | 1855484455995572224 |
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| author | Bejerman, Nicolas Esteban Dietzgen, Ralf Georg Debat, Humberto Julio |
| author_browse | Bejerman, Nicolas Esteban Debat, Humberto Julio Dietzgen, Ralf Georg |
| author_facet | Bejerman, Nicolas Esteban Dietzgen, Ralf Georg Debat, Humberto Julio |
| author_sort | Bejerman, Nicolas Esteban |
| collection | INTA Digital |
| description | Rhabdoviruses infect a large number of plant species and cause significant crop diseases. They have a negative-sense, single-stranded unsegmented or bisegmented RNA genome. The number of plant-associated rhabdovirid sequences has grown in the last few years in concert with the extensive use of high-throughput sequencing platforms. Here, we report the discovery of 27 novel rhabdovirus genomes associated with 25 different host plant species and one insect, which were hidden in public databases. These viral sequences were identified through homology searches in more than 3000 plant and insect transcriptomes from the National Center for Biotechnology Information (NCBI) Sequence Read Archive (SRA) using known plant rhabdovirus sequences as the query. The identification, assembly and curation of raw SRA reads resulted in sixteen viral genome sequences with full-length coding regions and ten partial genomes. Highlights of the obtained sequences include viruses with unique and novel genome organizations among known plant rhabdoviruses. Phylogenetic analysis showed that thirteen of the novel viruses were related to cytorhabdoviruses, one to alphanucleorhabdoviruses, five to betanucleorhabdoviruses, one to dichorhaviruses and seven to varicosaviruses. These findings resulted in the most complete phylogeny of plant rhabdoviruses to date and shed new light on the phylogenetic relationships and evolutionary landscape of this group of plant viruses. Furthermore, this study provided additional evidence for the complexity and diversity of plant rhabdovirus genomes and demonstrated that analyzing SRA public data provides an invaluable tool to accelerate virus discovery, gain evolutionary insights and refine virus taxonomy |
| format | Artículo |
| id | INTA9760 |
| institution | Instituto Nacional de Tecnología Agropecuaria (INTA -Argentina) |
| language | Inglés |
| publishDate | 2021 |
| publishDateRange | 2021 |
| publishDateSort | 2021 |
| publisher | MDPI |
| publisherStr | MDPI |
| record_format | dspace |
| spelling | INTA97602025-07-18T13:38:10Z Illuminating the Plant Rhabdovirus Landscape through Metatranscriptomics Data Bejerman, Nicolas Esteban Dietzgen, Ralf Georg Debat, Humberto Julio Plant Rhabdoviruses Taxonomía Cultivos Genomas Evolution Taxonomy Crops Genomes Rhabdovirus de las Plantas Metatranscriptomics Rhabdoviruses infect a large number of plant species and cause significant crop diseases. They have a negative-sense, single-stranded unsegmented or bisegmented RNA genome. The number of plant-associated rhabdovirid sequences has grown in the last few years in concert with the extensive use of high-throughput sequencing platforms. Here, we report the discovery of 27 novel rhabdovirus genomes associated with 25 different host plant species and one insect, which were hidden in public databases. These viral sequences were identified through homology searches in more than 3000 plant and insect transcriptomes from the National Center for Biotechnology Information (NCBI) Sequence Read Archive (SRA) using known plant rhabdovirus sequences as the query. The identification, assembly and curation of raw SRA reads resulted in sixteen viral genome sequences with full-length coding regions and ten partial genomes. Highlights of the obtained sequences include viruses with unique and novel genome organizations among known plant rhabdoviruses. Phylogenetic analysis showed that thirteen of the novel viruses were related to cytorhabdoviruses, one to alphanucleorhabdoviruses, five to betanucleorhabdoviruses, one to dichorhaviruses and seven to varicosaviruses. These findings resulted in the most complete phylogeny of plant rhabdoviruses to date and shed new light on the phylogenetic relationships and evolutionary landscape of this group of plant viruses. Furthermore, this study provided additional evidence for the complexity and diversity of plant rhabdovirus genomes and demonstrated that analyzing SRA public data provides an invaluable tool to accelerate virus discovery, gain evolutionary insights 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: Dietzgen, Ralf G. University of Queensland. Queensland Alliance for Agriculture and Food Innovation; Australia 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 2021-07-07T17:13:18Z 2021-07-07T17:13:18Z 2021-07-05 info:ar-repo/semantics/artículo info:eu-repo/semantics/article info:eu-repo/semantics/publishedVersion http://hdl.handle.net/20.500.12123/9760 https://www.mdpi.com/1999-4915/13/7/1304 1999-4915 (online) https://doi.org/10.3390/v13071304 eng info:eu-repo/semantics/openAccess http://creativecommons.org/licenses/by-nc-sa/4.0/ Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0) application/pdf MDPI Viruses 13 (7) : 1304 (2021) |
| spellingShingle | Plant Rhabdoviruses Taxonomía Cultivos Genomas Evolution Taxonomy Crops Genomes Rhabdovirus de las Plantas Metatranscriptomics Bejerman, Nicolas Esteban Dietzgen, Ralf Georg Debat, Humberto Julio Illuminating the Plant Rhabdovirus Landscape through Metatranscriptomics Data |
| title | Illuminating the Plant Rhabdovirus Landscape through Metatranscriptomics Data |
| title_full | Illuminating the Plant Rhabdovirus Landscape through Metatranscriptomics Data |
| title_fullStr | Illuminating the Plant Rhabdovirus Landscape through Metatranscriptomics Data |
| title_full_unstemmed | Illuminating the Plant Rhabdovirus Landscape through Metatranscriptomics Data |
| title_short | Illuminating the Plant Rhabdovirus Landscape through Metatranscriptomics Data |
| title_sort | illuminating the plant rhabdovirus landscape through metatranscriptomics data |
| topic | Plant Rhabdoviruses Taxonomía Cultivos Genomas Evolution Taxonomy Crops Genomes Rhabdovirus de las Plantas Metatranscriptomics |
| url | http://hdl.handle.net/20.500.12123/9760 https://www.mdpi.com/1999-4915/13/7/1304 https://doi.org/10.3390/v13071304 |
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