Begomovirus-Associated Satellite DNA Diversity Captured Through Vector-Enabled Metagenomic (VEM) Surveys Using Whiteflies (Aleyrodidae)
Monopartite begomoviruses (Geminiviridae), which are whitefly-transmitted single-stranded DNA viruses known for causing devastating crop diseases, are often associated with satellite DNAs. Since begomovirus acquisition or exchange of satellite DNAs may lead to adaptation to new plant hosts and emerg...
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| Format: | Article |
| Language: | English |
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MDPI AG
2016-02-01
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| Series: | Viruses |
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| Online Access: | http://www.mdpi.com/1999-4915/8/2/36 |
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| author | Karyna Rosario Christian Marr Arvind Varsani Simona Kraberger Daisy Stainton Enrique Moriones Jane E. Polston Mya Breitbart |
| author_facet | Karyna Rosario Christian Marr Arvind Varsani Simona Kraberger Daisy Stainton Enrique Moriones Jane E. Polston Mya Breitbart |
| author_sort | Karyna Rosario |
| collection | DOAJ |
| description | Monopartite begomoviruses (Geminiviridae), which are whitefly-transmitted single-stranded DNA viruses known for causing devastating crop diseases, are often associated with satellite DNAs. Since begomovirus acquisition or exchange of satellite DNAs may lead to adaptation to new plant hosts and emergence of new disease complexes, it is important to investigate the diversity and distribution of these molecules. This study reports begomovirus-associated satellite DNAs identified during a vector-enabled metagenomic (VEM) survey of begomoviruses using whiteflies collected in various locations (California (USA), Guatemala, Israel, Puerto Rico, and Spain). Protein-encoding satellite DNAs, including alphasatellites and betasatellites, were identified in Israel, Puerto Rico, and Guatemala. Novel alphasatellites were detected in samples from Guatemala and Puerto Rico, resulting in the description of a phylogenetic clade (DNA-3-type alphasatellites) dominated by New World sequences. In addition, a diversity of small (~640–750 nucleotides) satellite DNAs similar to satellites associated with begomoviruses infecting Ipomoea spp. were detected in Puerto Rico and Spain. A third class of satellite molecules, named gammasatellites, is proposed to encompass the increasing number of reported small (<1 kilobase), non-coding begomovirus-associated satellite DNAs. This VEM-based survey indicates that, although recently recovered begomovirus genomes are variations of known genetic themes, satellite DNAs hold unexplored genetic diversity. |
| first_indexed | 2024-12-12T08:28:55Z |
| format | Article |
| id | doaj.art-d1c4f87d714a41a4acaa8505f1d21218 |
| institution | Directory Open Access Journal |
| issn | 1999-4915 |
| language | English |
| last_indexed | 2024-12-12T08:28:55Z |
| publishDate | 2016-02-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Viruses |
| spelling | doaj.art-d1c4f87d714a41a4acaa8505f1d212182022-12-22T00:31:10ZengMDPI AGViruses1999-49152016-02-01823610.3390/v8020036v8020036Begomovirus-Associated Satellite DNA Diversity Captured Through Vector-Enabled Metagenomic (VEM) Surveys Using Whiteflies (Aleyrodidae)Karyna Rosario0Christian Marr1Arvind Varsani2Simona Kraberger3Daisy Stainton4Enrique Moriones5Jane E. Polston6Mya Breitbart7College of Marine Science, University of South Florida, Saint Petersburg, FL 33701, USACollege of Marine Science, University of South Florida, Saint Petersburg, FL 33701, USASchool of Biological Sciences and Biomolecular Interaction Centre, University of Canterbury, Ilam, Christchurch 8041, New ZealandSchool of Biological Sciences and Biomolecular Interaction Centre, University of Canterbury, Ilam, Christchurch 8041, New ZealandSchool of Biological Sciences and Biomolecular Interaction Centre, University of Canterbury, Ilam, Christchurch 8041, New ZealandInstituto de Hortofruticultura Subtropical y Mediterránea ‘‘La Mayora’’ (IHSM-UMA-CSIC), Consejo Superior de Investigaciones Científicas, Estación Experimental ‘‘La Mayora’’, Algarrobo-Costa, Málaga 29750, SpainDepartment of Plant Pathology, University of Florida, Gainesville, FL 32611, USACollege of Marine Science, University of South Florida, Saint Petersburg, FL 33701, USAMonopartite begomoviruses (Geminiviridae), which are whitefly-transmitted single-stranded DNA viruses known for causing devastating crop diseases, are often associated with satellite DNAs. Since begomovirus acquisition or exchange of satellite DNAs may lead to adaptation to new plant hosts and emergence of new disease complexes, it is important to investigate the diversity and distribution of these molecules. This study reports begomovirus-associated satellite DNAs identified during a vector-enabled metagenomic (VEM) survey of begomoviruses using whiteflies collected in various locations (California (USA), Guatemala, Israel, Puerto Rico, and Spain). Protein-encoding satellite DNAs, including alphasatellites and betasatellites, were identified in Israel, Puerto Rico, and Guatemala. Novel alphasatellites were detected in samples from Guatemala and Puerto Rico, resulting in the description of a phylogenetic clade (DNA-3-type alphasatellites) dominated by New World sequences. In addition, a diversity of small (~640–750 nucleotides) satellite DNAs similar to satellites associated with begomoviruses infecting Ipomoea spp. were detected in Puerto Rico and Spain. A third class of satellite molecules, named gammasatellites, is proposed to encompass the increasing number of reported small (<1 kilobase), non-coding begomovirus-associated satellite DNAs. This VEM-based survey indicates that, although recently recovered begomovirus genomes are variations of known genetic themes, satellite DNAs hold unexplored genetic diversity.http://www.mdpi.com/1999-4915/8/2/36begomovirusbegomovirus-associated satellitesalphasatellitesbetasatellitesgammasatellitesIpomoea satellitesmetagenomicswhiteflyvectorssDNA |
| spellingShingle | Karyna Rosario Christian Marr Arvind Varsani Simona Kraberger Daisy Stainton Enrique Moriones Jane E. Polston Mya Breitbart Begomovirus-Associated Satellite DNA Diversity Captured Through Vector-Enabled Metagenomic (VEM) Surveys Using Whiteflies (Aleyrodidae) Viruses begomovirus begomovirus-associated satellites alphasatellites betasatellites gammasatellites Ipomoea satellites metagenomics whitefly vector ssDNA |
| title | Begomovirus-Associated Satellite DNA Diversity Captured Through Vector-Enabled Metagenomic (VEM) Surveys Using Whiteflies (Aleyrodidae) |
| title_full | Begomovirus-Associated Satellite DNA Diversity Captured Through Vector-Enabled Metagenomic (VEM) Surveys Using Whiteflies (Aleyrodidae) |
| title_fullStr | Begomovirus-Associated Satellite DNA Diversity Captured Through Vector-Enabled Metagenomic (VEM) Surveys Using Whiteflies (Aleyrodidae) |
| title_full_unstemmed | Begomovirus-Associated Satellite DNA Diversity Captured Through Vector-Enabled Metagenomic (VEM) Surveys Using Whiteflies (Aleyrodidae) |
| title_short | Begomovirus-Associated Satellite DNA Diversity Captured Through Vector-Enabled Metagenomic (VEM) Surveys Using Whiteflies (Aleyrodidae) |
| title_sort | begomovirus associated satellite dna diversity captured through vector enabled metagenomic vem surveys using whiteflies aleyrodidae |
| topic | begomovirus begomovirus-associated satellites alphasatellites betasatellites gammasatellites Ipomoea satellites metagenomics whitefly vector ssDNA |
| url | http://www.mdpi.com/1999-4915/8/2/36 |
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