The analysis of the virome associated with Freesia refracta plants with necrotic disorder sheds new light on the phylogenetic relationships in the Konkoviridae and Yueviridae families

BACKGROUND: The necrotic disorder of freesia, first described in 1970 in Northern Europe, is still affecting freesia cultivation globally. Although several viruses have been listed as possible causal agents, the etiology of the disease is still not clear and is possibly linked to a combination of different factors. In this study, a high-throughput sequencing (HTS) virome analysis was performed on total RNA extracts derived from symptomatic freesia leaves. METHODS: Freesia leaves showing necrotic disorder symptoms were collected in the Liguria region (Northwestern Italy) in 2011, 2014 and 2022. Total RNA was extracted and sent to specialized companies for rRNA-depletion library construction and Illumina sequencing. Ad hoc bioinformatics and phylogenetic analyses were performed on HTS data in order to identify and characterize plant viral entities. The Serratus Project Database was used to explore publicly available metatranscriptomic datasets with the aim of expanding selected viral families. RESULTS: Freesia konkovirus 1, a novel virus putatively belonging to the recently ratified Konkoviridae family was identified and characterized. The family was further expanded through public metatranscriptomic data analyses; its phylogeny was investigated, and new genera were proposed. Moreover, a novel virus, putatively belonging to the Yueviridae family, was partially characterized, and its phylogenetic position was discussed. CONCLUSIONS: This is the first untargeted HTS virome analysis of freesia necrotic disorder. Through a combined wet-lab and in silico approach, we identified unknown novel viruses, increasing the current knowledge of the diversity of viral agents that infect freesia, expanding and clarifying the phylogenesis of the very recently ratified families of Konkoviridae and Yueviridae, and highlighting possibly new actors in the freesia necrotic disorder.