Fig. 1

Examples of different symptomatology observed on the leaves of alfalfa (Medicago sativa L) plants infected with Snake River alfalfa virus (SRAV-WA1) in Washington State, USA. Sample 1 contained 7,016 reads of SRAV and 11,797 covered bases; sample 2 contained 10,684 reads mapped to the virus and 11,699 covered bases; sample 3 contained 47,175 reads mapped to the virus and 11,838 covered bases; sample 4 contained 71,267 viral reads and 11,811 covered bases; sample 5 contained 8,079 reads and 11,872 covered bases (100% vs. reference genome); and sample 6 contained 19,539 viral reads and covered 11,795 bases. Multiple viral, fungal and bacterial pathogens were also identified in samples in which SRAV was found. These included alfalfa mosaic virus, bean leaf roll virus, pea streak virus, partitiviruses, amalgavirus, lucerne transient streak virus, Alternaria alternata, Alternaria arborescens, Bipolaris spp., Stemphylium lycopersici, Fusarium spp., Pseudomonas spp., Erwinia spp., etc. thus emphasizing the importance of pathobiome in signs and symptoms of disease