Exploring the Diversity of Plant-Associated Viruses and Related Viruses in Riverine Freshwater Samples Collected in Berlin, Germany
Plant-infecting RNA viruses from 30 families and floating genera, as well as a great number of uncultured as yet-unclassified plant-associated viruses have been described. Even so, the plant RNA virosphere is still underexplored. RNA extracted from enriched virus particles of 50 L water samples from...
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| Format: | Article |
| Language: | English |
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MDPI AG
2023-12-01
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| Series: | Pathogens |
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| Online Access: | https://www.mdpi.com/2076-0817/12/12/1458 |
| _version_ | 1797379719170097152 |
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| author | Roland Zell Marco Groth Lukas Selinka Hans-Christoph Selinka |
| author_facet | Roland Zell Marco Groth Lukas Selinka Hans-Christoph Selinka |
| author_sort | Roland Zell |
| collection | DOAJ |
| description | Plant-infecting RNA viruses from 30 families and floating genera, as well as a great number of uncultured as yet-unclassified plant-associated viruses have been described. Even so, the plant RNA virosphere is still underexplored. RNA extracted from enriched virus particles of 50 L water samples from the Teltow Canal and the Havel River in Berlin, Germany, was sequenced using Illumina next-generation sequencing. Sequences were searched for plant viruses with BLAST and DIAMOND. Phylogenetic analyses were conducted with IQ-TREE 2. Altogether, 647 virus sequences greater than 1 kb were detected and further analyzed. These data revealed the presence of accepted and novel viruses related to <i>Albetovirus</i>, <i>Alphaflexiviridae</i>, <i>Aspiviridae</i>, <i>Bromoviridae</i>, <i>Endornaviridae</i>, <i>Partitiviridae</i>, <i>Potyviridae</i>, <i>Solemoviridae</i>, <i>Tombusviridae</i> and <i>Virgaviridae</i>. The vast majority of the sequences were novel and could not be taxonomically assigned. Several tombus- and endorna-like viruses make use of alternative translation tables that suggest unicellular green algae, ciliates, or diplomonades as their hosts. The identification of 27 albeto-like satellite viruses increases available sequence data five-fold. Sixteen new poty-like viruses align with other poty-like viruses in a link that combines the <i>Astroviridae</i> and <i>Potyviridae</i> families. Further, the identification of viruses with peptidase A6-like and peptidase A21-like capsid proteins suggests horizontal gene transfer in the evolution of these viruses. |
| first_indexed | 2024-03-08T20:27:02Z |
| format | Article |
| id | doaj.art-7f1171cd10ef4907a96981011f5dbcf0 |
| institution | Directory Open Access Journal |
| issn | 2076-0817 |
| language | English |
| last_indexed | 2024-03-08T20:27:02Z |
| publishDate | 2023-12-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Pathogens |
| spelling | doaj.art-7f1171cd10ef4907a96981011f5dbcf02023-12-22T14:31:04ZengMDPI AGPathogens2076-08172023-12-011212145810.3390/pathogens12121458Exploring the Diversity of Plant-Associated Viruses and Related Viruses in Riverine Freshwater Samples Collected in Berlin, GermanyRoland Zell0Marco Groth1Lukas Selinka2Hans-Christoph Selinka3Section of Experimental Virology, Institute for Medical Microbiology, Jena University Hospital, Friedrich Schiller University, 07745 Jena, GermanyCF Next Generation Sequencing, Leibniz Institute on Aging-Fritz Lipmann Institute, 07745 Jena, GermanySection of Experimental Virology, Institute for Medical Microbiology, Jena University Hospital, Friedrich Schiller University, 07745 Jena, GermanySection II 1.4 Microbiological Risks, Department of Environmental Hygiene, German Environment Agency, 14195 Berlin, GermanyPlant-infecting RNA viruses from 30 families and floating genera, as well as a great number of uncultured as yet-unclassified plant-associated viruses have been described. Even so, the plant RNA virosphere is still underexplored. RNA extracted from enriched virus particles of 50 L water samples from the Teltow Canal and the Havel River in Berlin, Germany, was sequenced using Illumina next-generation sequencing. Sequences were searched for plant viruses with BLAST and DIAMOND. Phylogenetic analyses were conducted with IQ-TREE 2. Altogether, 647 virus sequences greater than 1 kb were detected and further analyzed. These data revealed the presence of accepted and novel viruses related to <i>Albetovirus</i>, <i>Alphaflexiviridae</i>, <i>Aspiviridae</i>, <i>Bromoviridae</i>, <i>Endornaviridae</i>, <i>Partitiviridae</i>, <i>Potyviridae</i>, <i>Solemoviridae</i>, <i>Tombusviridae</i> and <i>Virgaviridae</i>. The vast majority of the sequences were novel and could not be taxonomically assigned. Several tombus- and endorna-like viruses make use of alternative translation tables that suggest unicellular green algae, ciliates, or diplomonades as their hosts. The identification of 27 albeto-like satellite viruses increases available sequence data five-fold. Sixteen new poty-like viruses align with other poty-like viruses in a link that combines the <i>Astroviridae</i> and <i>Potyviridae</i> families. Further, the identification of viruses with peptidase A6-like and peptidase A21-like capsid proteins suggests horizontal gene transfer in the evolution of these viruses.https://www.mdpi.com/2076-0817/12/12/1458riverine ecosystemsviromesphylogenetic analysismetagenomicRNA virusesplant viruses |
| spellingShingle | Roland Zell Marco Groth Lukas Selinka Hans-Christoph Selinka Exploring the Diversity of Plant-Associated Viruses and Related Viruses in Riverine Freshwater Samples Collected in Berlin, Germany Pathogens riverine ecosystems viromes phylogenetic analysis metagenomic RNA viruses plant viruses |
| title | Exploring the Diversity of Plant-Associated Viruses and Related Viruses in Riverine Freshwater Samples Collected in Berlin, Germany |
| title_full | Exploring the Diversity of Plant-Associated Viruses and Related Viruses in Riverine Freshwater Samples Collected in Berlin, Germany |
| title_fullStr | Exploring the Diversity of Plant-Associated Viruses and Related Viruses in Riverine Freshwater Samples Collected in Berlin, Germany |
| title_full_unstemmed | Exploring the Diversity of Plant-Associated Viruses and Related Viruses in Riverine Freshwater Samples Collected in Berlin, Germany |
| title_short | Exploring the Diversity of Plant-Associated Viruses and Related Viruses in Riverine Freshwater Samples Collected in Berlin, Germany |
| title_sort | exploring the diversity of plant associated viruses and related viruses in riverine freshwater samples collected in berlin germany |
| topic | riverine ecosystems viromes phylogenetic analysis metagenomic RNA viruses plant viruses |
| url | https://www.mdpi.com/2076-0817/12/12/1458 |
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