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Open AccessArticle

Reconstruction and Characterization of Full-Length Begomovirus and Alphasatellite Genomes Infecting Pepper through Metagenomics

1
Instituto de Patología Vegetal, IPAVE-CIAP-INTA, 5000 Córdoba, Argentina
2
Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Argentina
3
Estación Experimental Agropecuaria Rafaela-INTA, 2300 Rafaela, Santa Fe, Argentina
4
Estación Experimental Agropecuaria Yuto-INTA, 4518 Yuto, Argentina
*
Author to whom correspondence should be addressed.
Viruses 2020, 12(2), 202; https://doi.org/10.3390/v12020202
Received: 8 December 2019 / Revised: 10 January 2020 / Accepted: 16 January 2020 / Published: 11 February 2020
(This article belongs to the Section Viruses of Plants, Fungi and Protozoa)
In northwestern Argentina (NWA), pepper crops are threatened by the emergence of begomoviruses due to the spread of its vector, Bemisia tabaci (Gennadius). The genus Begomovirus includes pathogens that can have a monopartite or bipartite genome and are occasionally associated with sub-viral particles called satellites. This study characterized the diversity of begomovirus and alphasatellite species infecting pepper in NWA using a metagenomic approach. Using RCA-NGS (rolling circle amplification-next generation sequencing), 19 full-length begomovirus genomes (DNA-A and DNA-B) and one alphasatellite were assembled. This ecogenomic approach revealed six begomoviruses in single infections: soybean blistering mosaic virus (SbBMV), tomato yellow spot virus (ToYSV), tomato yellow vein streak virus (ToYVSV), tomato dwarf leaf virus (ToDfLV), sida golden mosaic Brazil virus (SiGMBRV), and a new proposed species, named pepper blistering leaf virus (PepBLV). SbBMV was the most frequently detected species, followed by ToYSV. Moreover, a new alphasatellite associated with ToYSV, named tomato yellow spot alphasatellite 2 (ToYSA-2), was reported for the first time in Argentina. For the Americas, this was the first report of an alphasatellite found in a crop (pepper) and in a weed (Leonurus japonicus). We also detected intra-species and inter-species recombination. View Full-Text
Keywords: Geminiviridae; Geminialphasatellitinae; RCA-NGS; pepper; recombination Geminiviridae; Geminialphasatellitinae; RCA-NGS; pepper; recombination
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MDPI and ACS Style

Bornancini, V.A.; Irazoqui, J.M.; Flores, C.R.; Vaghi Medina, C.G.; Amadio, A.F.; López Lambertini, P.M. Reconstruction and Characterization of Full-Length Begomovirus and Alphasatellite Genomes Infecting Pepper through Metagenomics. Viruses 2020, 12, 202.

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