RNA Viral Communities Are Structured by Host Plant Phylogeny in Oak and Conifer Leaves

Abstract

Wild plants can suffer devastating diseases, experience asymptomatic persistent infections, and serve as reservoirs for viruses of agricultural crops; however, we have a limited understanding of the natural plant virosphere. To access representatives of locally and globally distinct wild plants and investigate their viral diversity, we extracted and sequenced double-stranded RNA from leaves from 16 healthy oak and conifer trees in the University of California–Davis Arboretum (Davis, CA, U.S.A.). From de novo assemblies, we recovered 389 RNA-dependent RNA polymerase gene sequences from 384 putative viral species, and identified 580 putative viral contigs via virus prediction software followed by manual confirmation of virus annotation. Based on similarity to known viruses, most recovered viruses were predicted to infect plants or fungi, with the highest diversity and abundance observed in the Totiviridae and Mitoviridae families. Phyllosphere viral community composition differed significantly by host plant phylogeny, suggesting the potential for host-specific viromes. The phyllosphere viral community of one oak tree differed substantially from other oak viral communities and contained a greater proportion of putative mycoviral sequences, potentially due to the tree’s more advanced senescence at the time of sampling. These results suggest that oak and conifer trees harbor a vast diversity of viruses with as-yet-unknown roles in plant health and phyllosphere microbial ecology.