Composition of plant-associated RNA virus communities in two Brazilian regions with different levels of human intervention

Recent high-throughput sequencing (HTS)-based studies of transcriptomes and metatranscriptomes have expanded our understanding of the global RNA virome with a vast number of novel RNA viruses revealed in diverse host organisms. Nevertheless, ecosystem-level understanding of plant virus dynamics is hampered by the paucity of information from wild communities, as most plant viral dynamics monitoring has been performed on cropping systems. It has been proposed that the emergence of viral diseases in cultivated plants is linked to ecological disturbances caused by human intervention in natural ecosystems, and that the interface areas between natural and agricultural ecosystems are hotspots of emergence of new viruses. Here, we employed a geometagenomics approach to characterize virus communities in two ecosystems with different levels of human interference, including interface areas, in the state of Minas Gerais, in the Southeast region of Brazil. dsRNA was extracted from collected plants and sequenced with an Oxford Nanopore MinION device. Several tools were used to identify and classify the viruses present in the samples, including BLAST, PalmScan, profile HMMs, and geNomad. Our results indicate a greater diversity of plants and viruses, and a much greater proportion of unclassified viruses, in the ecosystem with a lower degree of human intervention.