Unlocking the Hidden Genetic Diversity of Varicosaviruses, the Neglected Plant Rhabdoviruses
The genus Varicosavirus is one of six genera of plant-infecting rhabdoviruses. Varicosaviruses have non-enveloped, flexuous, rod-shaped virions and a negative-sense, single-stranded RNA genome. A distinguishing feature of varicosaviruses, which is shared with dichorhaviruses, is a bi-segmented genom...
| Authors: | ; ; |
|---|---|
| Format: | Article |
| Status: | Published version |
| Publication date: | 2022 |
| Country: | Argentina |
| Institution: | Instituto Nacional de Tecnología Agropecuaria |
| Repository: | INTA Digital (INTA) |
| Language: | English |
| OAI Identifier: | oai:localhost:20.500.12123/13476 |
| Online Access: | http://hdl.handle.net/20.500.12123/13476 https://www.mdpi.com/2076-0817/11/10/1127 https://doi.org/10.3390/pathogens11101127 |
| Access Level: | Open access |
| Keyword: | Plant Rhabdoviruses Taxonomía Rhabdovirus de las Plantas Taxonomy Varicosaviruses Genome Architecture Virus Taxonomy Metatranscriptomics Taxonomía de Virus |
| _version_ | 1878403354745372672 |
|---|---|
| author | Bejerman, Nicolas Esteban |
| author2 | Dietzgen, Ralf G. Debat, Humberto Julio |
| author2_role | author author |
| author_browse | Bejerman, Nicolas Esteban Debat, Humberto Julio Dietzgen, Ralf G. |
| author_facet | Bejerman, Nicolas Esteban Dietzgen, Ralf G. Debat, Humberto Julio |
| author_role | author |
| collection | INTA Digital (INTA) |
| description | The genus Varicosavirus is one of six genera of plant-infecting rhabdoviruses. Varicosaviruses have non-enveloped, flexuous, rod-shaped virions and a negative-sense, single-stranded RNA genome. A distinguishing feature of varicosaviruses, which is shared with dichorhaviruses, is a bi-segmented genome. Before 2017, a sole varicosavirus was known and characterized, and then two more varicosaviruses were identified through high-throughput sequencing in 2017 and 2018. More recently, the number of known varicosaviruses has substantially increased in concert with the extensive use of high-throughput sequencing platforms and data mining approaches. The novel varicosaviruses have revealed not only sequence diversity, but also plasticity in terms of genome architecture, including a virus with a tentatively unsegmented genome. Here, we report the discovery of 45 novel varicosavirus genomes which were identified in publicly available metatranscriptomic data. The identification, assembly, and curation of the raw Sequence Read Archive reads has resulted in 39 viral genome sequences with full-length coding regions and 6 with nearly complete coding regions. The highlights of the obtained sequences include eight varicosaviruses with unsegmented genomes, which are linked to a phylogenetic clade associated with gymnosperms. These findings have resulted in the most complete phylogeny of varicosaviruses to date and shed new light on the phylogenetic relationships and evolutionary landscape of this group of plant rhabdoviruses. Thus, the extensive use of sequence data mining for virus discovery has allowed us to unlock of the hidden genetic diversity of varicosaviruses, the largely neglected plant rhabdoviruses. |
| eu_rights_str_mv | openAccess |
| format | article |
| id | AR_6e997e6bb0d7c554f60d45d0033cab99 |
| identifier_str_mv | 2076-0817 |
| institution | Instituto Nacional de Tecnología Agropecuaria |
| instname_str | Instituto Nacional de Tecnología Agropecuaria |
| language | eng |
| network_acronym_str | AR |
| network_name_str | Argentina |
| oai_identifier_str | oai:localhost:20.500.12123/13476 |
| publishDate | 2022 |
| publishDateSort | 2022 |
| publisher | MDPI |
| publisherStr | MDPI |
| reponame_str | INTA Digital (INTA) |
| spelling | Unlocking the Hidden Genetic Diversity of Varicosaviruses, the Neglected Plant Rhabdoviruses Bejerman, Nicolas Esteban Dietzgen, Ralf G. Debat, Humberto Julio Plant Rhabdoviruses Taxonomía Rhabdovirus de las Plantas Taxonomy Varicosaviruses Genome Architecture Virus Taxonomy Metatranscriptomics Taxonomía de Virus The genus Varicosavirus is one of six genera of plant-infecting rhabdoviruses. Varicosaviruses have non-enveloped, flexuous, rod-shaped virions and a negative-sense, single-stranded RNA genome. A distinguishing feature of varicosaviruses, which is shared with dichorhaviruses, is a bi-segmented genome. Before 2017, a sole varicosavirus was known and characterized, and then two more varicosaviruses were identified through high-throughput sequencing in 2017 and 2018. More recently, the number of known varicosaviruses has substantially increased in concert with the extensive use of high-throughput sequencing platforms and data mining approaches. The novel varicosaviruses have revealed not only sequence diversity, but also plasticity in terms of genome architecture, including a virus with a tentatively unsegmented genome. Here, we report the discovery of 45 novel varicosavirus genomes which were identified in publicly available metatranscriptomic data. The identification, assembly, and curation of the raw Sequence Read Archive reads has resulted in 39 viral genome sequences with full-length coding regions and 6 with nearly complete coding regions. The highlights of the obtained sequences include eight varicosaviruses with unsegmented genomes, which are linked to a phylogenetic clade associated with gymnosperms. These findings have resulted in the most complete phylogeny of varicosaviruses to date and shed new light on the phylogenetic relationships and evolutionary landscape of this group of plant rhabdoviruses. Thus, the extensive use of sequence data mining for virus discovery has allowed us to unlock of the hidden genetic diversity of varicosaviruses, the largely neglected plant rhabdoviruses. 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 MDPI http://hdl.handle.net/20.500.12123/13476 https://www.mdpi.com/2076-0817/11/10/1127 2076-0817 https://doi.org/10.3390/pathogens11101127 |
| spellingShingle | Unlocking the Hidden Genetic Diversity of Varicosaviruses, the Neglected Plant Rhabdoviruses Bejerman, Nicolas Esteban Plant Rhabdoviruses Taxonomía Rhabdovirus de las Plantas Taxonomy Varicosaviruses Genome Architecture Virus Taxonomy Metatranscriptomics Taxonomía de Virus |
| status_str | publishedVersion |
| title | Unlocking the Hidden Genetic Diversity of Varicosaviruses, the Neglected Plant Rhabdoviruses |
| title_full | Unlocking the Hidden Genetic Diversity of Varicosaviruses, the Neglected Plant Rhabdoviruses |
| title_fullStr | Unlocking the Hidden Genetic Diversity of Varicosaviruses, the Neglected Plant Rhabdoviruses |
| title_full_unstemmed | Unlocking the Hidden Genetic Diversity of Varicosaviruses, the Neglected Plant Rhabdoviruses |
| title_short | Unlocking the Hidden Genetic Diversity of Varicosaviruses, the Neglected Plant Rhabdoviruses |
| title_sort | Unlocking the Hidden Genetic Diversity of Varicosaviruses, the Neglected Plant Rhabdoviruses |
| topic | Plant Rhabdoviruses Taxonomía Rhabdovirus de las Plantas Taxonomy Varicosaviruses Genome Architecture Virus Taxonomy Metatranscriptomics Taxonomía de Virus |
| topic_facet | Plant Rhabdoviruses Taxonomía Rhabdovirus de las Plantas Taxonomy Varicosaviruses Genome Architecture Virus Taxonomy Metatranscriptomics Taxonomía de Virus |
| url | http://hdl.handle.net/20.500.12123/13476 https://www.mdpi.com/2076-0817/11/10/1127 https://doi.org/10.3390/pathogens11101127 |