High-throughput sequencing-based virome analysis reveals genomic diversity and recombination of tomato-infecting viruses in Korea

Tomatoes are one of the most economically valuable vegetable crops globally, yet viral diseases significantly hinder their production. Tomatoes are associated with the highest reported number of virus and viroid species, totaling approximately 312, but limited information exists on their diversity and prevalence in specific regions such as Korea. This study aimed to characterize the tomato virome in the Gyeongsang and Jeolla regions of Korea using high-throughput sequencing of 122 samples. Seven viruses were detected, including five previously reported-tomato yellow leaf curl virus (TYLCV), tomato chlorosis virus (ToCV), tomato spotted wilt orthotospovirus, Southern tomato virus, and pepper mild mottle virus-and two viruses previously unreported in Korea: olive latent virus 1 and tobacco necrosis virus A. TYLCV and ToCV were the most prevalent, detected in nearly all samples. Genome analysis revealed the ongoing spread of a ToCV isolate in Korea, the introduction of an overseas mild strain of TYLCV (TYLCV-Mld), and a putative lineage of TYLCV isolates resulting from interspecies recombination among begomoviruses. These findings provide critical insights into the diversity and dynamics of tomato viromes in Korea and have significant implications for disease management, underscoring the need for continued surveillance against emerging viral threats.