Molecular characterization of novel soybean-associated viruses identified by high-throughput sequencing

High-throughput sequencing of mRNA from soybean leaf samples collected from North Dakota and Illinois soybean fields revealed the presence of two novel soybean-associated viruses. The first virus has a single-stranded positive-sense RNA genome consisting of 8,693 nt that contains two large open reading frames (ORFs). The predicted amino acid sequence of the first ORF showed similarity to structural proteins, of members of the invertebrate-infecting Dicistroviridae and the sequence of the second ORF which is a nonstructural proteins lack affinity to other virus sequences available in GenBank. The presence of separate ORFs for the structural and nonstructural proteins was similar to members of the family Dicistroviridae, but the order of the two ORFs in the new virus was opposite to that of the family Dicistroviridae. Because of the virus' unique genome organization and the lack of strong phylogenetic association with previously described virus families, the soybean-associated virus may represent a novel virus family. The second virus also has a single stranded positive sense RNA genome, but has two genomic segments. The larger segment (RNA1), which is 8,208 nt long, encodes the replication-related proteins while the smaller segment (RNA2), which is 5,806 nt long, encodes the structural and movement proteins. Both the segments have a very long 3' untranslated regions with lengths of more than 1,550 nt. The predicted amino acid sequences for both the segments were closely related to members of subgroup C of the genus Nepovirus