Genome-Wide Variation Profile of the Genus<em> Tobamovirus</em>

The genus Tobamovirus belongs to the family Virgaviridae, and the genome consists of monopartite, positive, single-strand RNA. Most species have four open reading frames encoding four essential proteins. Transmission occurs by mechanical contact between plants and sometimes by seed. Tobamovirus fructirugosum (Tomato brown rugose fruit virus, ToBRFV) is the most recent species in the genus, was first reported in 2015, broke genetic resistance that had been effective in tomato for sixty years, has caused devastating damage to tomato production worldwide, and highlights the importance of understanding genomic variation and evolution of tobamoviruses. In this study, we measured and characterized nucleotide variation for the entire genome and for all species in the genus Tobamovirus and measured the selection pressure acting on each open reading frame. Results showed that low nucleotide diversity and negative selection pressure are general features of tobamoviruses, with values that are approximately the same across open reading frames and without hypervariable areas. A comparison of nucleotide diversity between T. fructirugosum and its close relatives, T. tomatotessellati (Tomato mosaic virus, ToMV) and T. tabaci (Tobacco mosaic virus, TMV), showed low nucleotide diversity in the movement protein region harboring the resistance-breaking mutation. Furthermore, phylogenetic and diversity analyses showed that T. fructirugosum continues to evolve, and geographical distribution and host influence genomic diversity.