Characterization of genetically divergent tomato-associated geminivirus 1 isolates from table beet ( Beta vulgaris ) and tomato ( Solanum lycopersicum )

Metagenomic approaches in conjunction with high-throughput sequencing (HTS) have been employed for the discovery of novel plant-associated viral species, including members of the Geminiviridae family. In the present work, the HTS strategy allowed for the identification of genetically divergent tomato-associated geminivirus 1 (TaGV1) isolates from tomato and table beet in Brasilia-DF, Brazil. The complete genomes of these novel isolates displayed 2573 nucleotides in length (recovered by Sanger sequencing) with 83% identity to previously reported TaGV1 isolates and ≈ 63% identity with a range of capulaviruses. Phylogenetic analyses of all the available TaGV1 isolates, using either their complete genomes or Rep gene (C1:C2) sequences, indicated the genus Capulavirus as the closest group, whereas the CP (V1) gene information indicated the closest relationship with members of the genus Topocuvirus. Southern hybridization confirmed the TaGV1 association with one out of five and two out of 15 original field-collected table beet and tomato leaf samples, respectively. Leaf curling and overall size reduction were observed in two out of seven Nicotiana benthamiana plants in biolistic inoculation assays with an infectious TaGV1 clone (obtained from one novel isolate from tomato). However, no systemic infection was detected in the inoculated tomato and table beet seedlings. Additional infectivity assays with a new set of table beet and tomato accessions as well as a large number of indicator plants are needed to establish the host range of these new TaGV1 isolates.