Unveiling the Petunia hybrida Virome: Metatranscriptomic Profiling from the Bulgarian Market and In Vitro Cultures

RNA sequencing is a high-throughput sequencing method essential for unbiased detection and characterization of known and emerging plant viruses. Its high sensitivity makes it particularly well-suited for identifying low-abundance viral sequences, even in asymptomatic plants or those affected by complex, mixed infections. Here, we conducted a metatranscriptomic survey of <i>Petunia hybrida</i> plants from the Bulgarian market, both symptomatic and asymptomatic, and their corresponding in vitro plantlets. Viruses were detected in all tested samples demonstrating that visual symptoms are not a reliable indicator of infection. The viromes were dominated by petunia vein clearing virus (PVCV, <i>Petuvirus venapetuniae</i>), cucumber mosaic virus (CMV, <i>Cucumovirus CMV</i>), and tomato aspermy virus (TAV, <i>Cucumovirus TAV</i>), along with bacteriophages and fungus-associated viruses. However, the PVCV and CMV abundance was elevated in in vitro samples, possibly due to cutting-induced activation and/or prolonged cultivation. Phylogenetic analysis of the Bulgarian CMV, TAV, and PVCV isolates highlights their genetic links to strains from a wide geographic range and diverse hosts, emphasizing the potential for virus movement and genetic exchange among plant viruses across regions and species. It also suggests that petunias may contribute to the transmission dynamics of viruses within ornamental trade networks. These findings also emphasize the phytosanitary risks to horticulture and establish a basis for further investigation into plant virus ecology.