Metagenomics of Neotropical Single-Stranded DNA Viruses in Tomato Cultivars with and without theTy-1 Gene

A complex of begomoviruses (Geminiviridae) can cause severe tomato yield losses in the neotropics. Here, next-generation sequencing was employed for large-scale assessment of single-stranded (ss)DNA virus diversity in tomatoes either harboring or lacking the large-spectrum begomovirus toleranceTy-1 gene. Individual leaf samples exhibiting begomovirus-like symptoms (n= 107) were field-collected, circular DNA-enriched, subdivided into pools (with and withoutTy-1), and Illumina-sequenced. Virus-specific PCR and Sanger dideoxy sequencing validations confirmed 15 distinct ssDNA virus/subviral agents (occurring mainly in mixed infections), which highlight the potential drawbacks of employing virus-specific resistance in tomato breeding. More viruses (14 versus 6 species) were observed in tomatoes without theTy-1 gene. A gemycircularvirus (Genomoviridae), a new alpha-satellite, and two novelBegomovirusspecies were identified exclusively in samples without theTy-1 gene. A novel begomovirus was found only in theTy-1 pool, being the only species associated with severe symptoms inTy-1 plants in our survey. Our work is the first step towards the elucidation of the potential begomovirus adaptation toTy-1 and its specific filtering effects on a subset of ssDNA viral/subviral agents.