Viromes of field-grown tomatoes and peppers in Tennessee revealed by RNA sequencing followed by bioinformatic analysis

The prevalent viruses in a population of 106 tomato and 53 pepper field-grown plants in Tennessee (TN) was investigated by RNA sequencing and analysis as two separate pools of ribosomal-depleted total RNA. Contigs of potato leafroll virus (PLRV), red clover vein mosaic virus, tomato spotted wilt virus and a novel rhabdovirus were detected only in tomato and those of bell pepper endornavirus (BPEV), and pepper cryptic virus 2 (PCV-2) only in pepper. Additionally, contigs of five other viruses (solanum nigrum ilarvirus 1; SNIV-1, southern tomato virus; STV, tobacco vein-clearing virus; ToVCV, tomato mosaic virus; ToMV and tomato ringspot virus; ToRSV) were detected in both tomatoes and peppers. Moreover, contigs were assembled of a potentially novel tobamovirus from both tomatoes and peppers. The presence of PLRV, STV, ToVCV, and the novel tobamovirus sequences in the original tomato samples and those of BPEV, PCV-2, ToMV, and ToRSV in the original pepper samples were confirmed by RT-PCR followed by Sanger sequencing. This study represents the first survey of viromes of field-grown tomatoes and peppers in TN. To the best of our knowledge, SNIV-1, STV and ToVCV have not been reported previously associated with peppers elsewhere in the world.