Biological characterization and complete genome analysis of Tobamovirus fructirugosum from Türkiye

Tomato brown rugose fruit virus ( Tobamovirus fructirugosum, ToBRFV), a member of the Tobamovirus genus, represents a significant threat to economically important Solanaceous crops. This study investigated ToBRFV in tomato and pepper, encompassing the following: molecular detection and identification of the virus; symptom development in susceptible hosts; screening of varieties for the presence of the Tm-2 2 gene, a known Tobamovirus resistance gene; and complete genome sequencing and analysis for comprehensive genetic characterization of ToBRFV isolates. In 2024, tomato and pepper varieties were mechanically inoculated with ToBRFV, and disease severity was assessed. The symptom development was both rapid and severe, with certain varieties demonstrating a high degree of susceptibility, while others exhibited sensitivity, and a single variety demonstrated tolerance. Tetra-primer Amplification Refractory Mutation System (ARMS) co-dominant markers were used to investigate the Tm-2 2 resistance gene. Surprisingly, some varieties carrying resistance genes still developed viral infections. Double-stranded RNA (dsRNA) was extracted from infected plants and subjected to high-throughput sequencing (HTS) for complete genome analysis. For the validation of HTS results, primer pairs targeting overlapping regions spanning the complete ToBRFV genome, were designed and employed in reverse transcription polymerase chain reaction (RT-PCR) analysis, followed by Sanger sequencing. The ToBRFV RNA-dependent RNA polymerase (RdRp) gene of selected isolates was partially analyzed. Furthermore, phylogenetic and recombination analyses were conducted. The results confirm the highly stable and contagious nature of ToBRFV. These findings contribute to a better understanding of ToBRFV diversity and resistance, providing valuable information for the development of virus management strategies.