Vector-Enabled Metagenomic (VEM) Surveys Using Whiteflies (Aleyrodidae) Reveal Novel Begomovirus Species in the New and OldWorlds

Abstract

Whitefly-transmitted viruses belonging to the genus Begomovirus (family Geminiviridae) represent a substantial threat to agricultural food production. The rapid evolutionary potential of these single-stranded DNA viruses combined with the polyphagous feeding behavior of their whitefly vector (Bemisia tabaci) can lead to the emergence of damaging viral strains. Therefore, it is crucial to characterize begomoviruses circulating in different regions and crops globally. This study utilized vector-enabled metagenomics (VEM) coupled with high-throughput sequencing to survey begomoviruses directly from whiteflies collected in various locations (California (USA), Guatemala, Israel, Puerto Rico, and Spain). Begomoviruses were detected in all locations, with the highest diversity identified in Guatemala where up to seven different species were identified in a single field. Both bipartite and monopartite viruses were detected, including seven new begomovirus species from Guatemala, Puerto Rico, and Spain. This begomovirus survey extends the known diversity of these highly damaging plant viruses. However, the new genomes described here and in the recent literature appear to reflect the outcome of interactions between closely-related species, often resulting from recombination, instead of unique, highly divergent species.

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

“…This study analyzes data from a recent VEM study investigating begomovirus diversity using whiteflies; thus, detailed methods have been previously published [ 37 ]. Briefly, adult whiteflies were collected from various crop fields and uncultivated native vegetation from geographically distant locations (Guatemala, Israel, Puerto Rico, Spain, and United States) using battery-operated vacuums and manual aspirators ( Table 1 ).…”

“…This study surveyed begomoviruses and associated satellite DNAs present in whiteflies collected from multiple crops and native vegetation in several countries through vector-enabled metagenomics (VEM; where virus particles are purified and sequenced directly from insect vectors [ 34 , 35 , 36 ]). The VEM approach led to the detection of begomoviruses, including novel species, in all the locations [ 37 ]. Here we discuss the satellite DNAs identified through the VEM survey, which include several novel alphasatellites in the NW.…”

Erratum to: Discovery of two small circular ssDNA viruses associated with the whitefly Bemisia tabaci

“…Due to their highly polyphagous behaviour, these insects are consequently exposed to different pathosystems, possibly accumulating a wide range of viruses, including potential novel plant-and insectinfecting species. This premise was confirmed by Rosario et al [7], who used next generation sequencing (NGS) for assessing viral diversity present in B. tabaci whiteflies, an approach commonly termed vector-enabled metagenomics (VEM).…”

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

“…Circomics, the combination of RCA-restriction fragment length polymorphism (RCA-RFLP) and pyro-sequencing, has shed light on begomovirus species identification [26,27]. Another similar methodology is vector-enabled metagenomic (VEM), which surveys begomovirus using whiteflies [28][29][30]. VEM involves the purification of virus particles obtained from the insect vector and metagenomic sequencing.…”