Use of NGS for discovery of viruses in the soybean aphid
Soybean aphid (Aphis glycines) is one of the most economically important pest insects of soybean. In the US, soybean aphid represents the first insect pest of soybean to consistently cause significant yield losses over wide areas, with yield decreases as high as 40%. To develop a biological control method, it is critical to have information on pathogens of soybean aphid. We sought to identify viruses that infect soybean aphid using Next Generation (Illumina) Sequencing of partially purified viruses from soybean aphids collected in Iowa (IA), Michigan (MI), Ohio (OH), and China. For the data analysis, de novo assembly of sequences was conducted using CLC Genomics Workbench. Deep sequencing analysis indicated that the soybean aphid viruses vary among the regions, but they are all positive stranded ssRNA viruses. Sequences corresponding to many viruses in the order Picornavirales were found. For example, aphid lethal paralysis-like dicistroviruses were found in all four regions. We also sequenced the near-complete genome of a new virus related to Big Sioux River Virus, a virus associated with honeybees. Sequences of a tetra-like virus, Aphis glycines virus 1 (AGV1, S. Liu and B. Bonning, unpublished) were abundant in all US samples, but partially sequence in the sample from China. Plant viral sequences were also found, including sequences with 93% identity to cotton leafroll dwarf polerovirus were found in the sample from China. A novel virus distantly related to the cileviruses of plant and insects was present in the OH samples. Sequences These results reveal the first viruses identified in soybean aphid and new plant viruses that may be vectored by soybean aphid.