Investigations into the Virome of Grasses Growing in the Environment of Sugarcane in Florida

Samples of 26 plant species and the aphid Melanaphis sorghi were collected in the Everglades Agricultural Area (South Florida) from 2017-2019 to investigate the virome of grasses growing in the environment of sugarcane. Leaf samples were obtained from cultivated as well as from wild species. Detection and identification of the viruses present in 388 plant and 11 aphid samples were performed using the virion-associated nucleic acid (VANA)-metagenomics approach. Twenty-four viruses were identified, and 12 plant species and the aphid were infected by at least one virus. Fourteen of these 24 viruses were known viruses whereas 10 were putatively new virus species, including an alphaendornavirus (family Endornaviridae), an alphanucleorhabdovirus (Rhabdoviridae), an amalgavirus (Amalgaviridae), a marafivirus (Tymoviridae), a mastrevirus (Geminiviridae), and a sobemovirus (Solemoviridae). The highest number of viruses was detected in Columbus grass and sorghum (10 and 11, respectively). Sugarcane mosaic virus (SCMV; Potyvirus sacchari, Potyviridae) and maize chlorotic dwarf virus (Waikavirus zeae, Secoviridae) were the most widespread viruses, occurring in nine and seven plant species, respectively, and were also detected in the aphid. In a phylogenetic tree constructed with partial genome sequences (4,000 nt) of SCMV obtained from GenBank and herein, virus isolates from eight plant species were distributed in three different lineages, thus suggesting significant diversity of this virus in Florida. Only two Saccharum-infecting viruses, SCMV and sugarcane yellow leaf virus (Polerovirus SCYLV, Solemoviridae) were detected in sorghum and other grasses. These plants may, therefore, serve as putative reservoirs for the causal agents of two sugarcane diseases in Florida.