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Viruses 2016, 8(2), 36; doi:10.3390/v8020036

Begomovirus-Associated Satellite DNA Diversity Captured Through Vector-Enabled Metagenomic (VEM) Surveys Using Whiteflies (Aleyrodidae)

1
College of Marine Science, University of South Florida, Saint Petersburg, FL 33701, USA
2
School of Biological Sciences and Biomolecular Interaction Centre, University of Canterbury, Ilam, Christchurch 8041, New Zealand
3
Department of Plant Pathology, University of Florida, Gainesville, FL 32611, USA
4
Structural Biology Research Unit, Department of Clinical Laboratory Sciences, University of Cape Town, Rondebosch, Cape Town 7701, South Africa
5
Instituto de Hortofruticultura Subtropical y Mediterránea ‘‘La Mayora’’ (IHSM-UMA-CSIC), Consejo Superior de Investigaciones Científicas, Estación Experimental ‘‘La Mayora’’, Algarrobo-Costa, Málaga 29750, Spain
*
Author to whom correspondence should be addressed.
Academic Editor: Thomas Hohn
Received: 8 December 2015 / Revised: 15 January 2016 / Accepted: 22 January 2016 / Published: 2 February 2016
(This article belongs to the Section Viruses of Plants, Fungi and Protozoa)
View Full-Text   |   Download PDF [1421 KB, uploaded 2 February 2016]   |  

Abstract

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. View Full-Text
Keywords: begomovirus; begomovirus-associated satellites; alphasatellites; betasatellites; gammasatellites; Ipomoea satellites; metagenomics; whitefly; vector; ssDNA begomovirus; begomovirus-associated satellites; alphasatellites; betasatellites; gammasatellites; Ipomoea satellites; metagenomics; whitefly; vector; ssDNA
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This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. (CC BY 4.0).

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MDPI and ACS Style

Rosario, K.; Marr, C.; Varsani, A.; Kraberger, S.; Stainton, D.; Moriones, E.; Polston, J.E.; Breitbart, M. Begomovirus-Associated Satellite DNA Diversity Captured Through Vector-Enabled Metagenomic (VEM) Surveys Using Whiteflies (Aleyrodidae). Viruses 2016, 8, 36.

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