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

José M Irazoqui,Ceferino R Flores,Verónica A Bornancini,Ariel F Amadio,Carlos G Vaghi Medina,Paola M López Lambertini

doi:10.3390/v12020202

Abstract

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.

Highlights

Begomovirus, the largest genus within the family Geminiviridae, comprises viruses with circular ssDNA genome that infect both dicotyledon and monocotyledon plants and are transmitted by the whitefly Bemisia tabaci Gennadius (Hemiptera: Aleyrodidae) [1]
Begomovirus infections were detected by multiplex-PCR in 51.48% of the pepper samples collected in Northwestern Argentina (NWA)
Since the nucleotide identity was below 91%, the corresponding threshold for species demarcation [53], we proposed this as a new begomovirus species, with the name pepper blistering leaf virus (PepBLV), according to symptoms observed in pepper field plant (Figure 1a)

Summary

Introduction

Begomovirus, the largest genus within the family Geminiviridae, comprises viruses with circular ssDNA genome that infect both dicotyledon and monocotyledon plants and are transmitted by the whitefly Bemisia tabaci Gennadius (Hemiptera: Aleyrodidae) [1]. Most of the new world (NW) native begomoviruses have bipartite genomes, known as DNA-A and DNA-B Northwestern Argentina (NWA) is one of the major horticultural production areas where begomoviruses cause economic losses. In this region, sweet pepper (Capsicum annuum L.) is an important crop mostly grown under greenhouse conditions with a production area of about 6662 ha [4]. In the Americas, the genetic diversity of begomoviruses identified in pepper is less than that reported in tomato [5]. There is no information about begomoviruses infecting pepper in Argentina. The first records of begomoviruses affecting pepper crops were reported for the United States and Mexico in Viruses 2020, 12, 202; doi:10.3390/v12020202 www.mdpi.com/journal/viruses

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Results

Conclusion