DOI: 10.5061/dryad.b1pg3
title: Data from: Seed transmission of soybean vein necrosis virus: the first Tospovirus implicated in seed transmission

description: Soybean vein necrosis virus (SVNV; genus Tospovirus; Family Bunyaviridae)
 is a negative-sense single-stranded RNA virus that has been detected
 across the United States and in Ontario, Canada. In 2013, a seed lot of a
 commercial soybean variety (Glycine max) with a high percentage of
 discolored, deformed and undersized seed was obtained. A random sample of
 this seed was planted in a growth room under standard conditions.
 Germination was greater than 90% and the resulting seedlings looked
 normal. Four composite samples of six plants each were tested by reverse
 transcription polymerase chain reaction (RT-PCR) using published primers
 complimentary to the S genomic segment of SVNV. Two composite leaflet
 samples retrieved from seedlings yielded amplicons with a size and
 sequence predictive of SVNV. Additional testing of twelve arbitrarily
 selected individual plants resulted in the identification of two SVNV
 positive plants. Experiments were repeated by growing seedlings from the
 same seed lot in an isolated room inside a thrips-proof cage to further
 eliminate any external source of infection. Also, increased care was taken
 to reduce any possible PCR contamination. Three positive plants out of
 forty-eight were found using these measures. Published and newly designed
 primers for the L and M RNAs of SVNV were also used to test the extracted
 RNA and strengthen the diagnosis of viral infection. In experiments, by
 three scientists, in two different labs all three genomic RNAs of SVNV
 were amplified in these plant materials. RNA-seq analysis was also
 conducted using RNA extracted from a composite seedling sample found to be
 SVNV-positive and a symptomatic sample collected from the field. This
 analysis revealed both sense and anti-sense reads from all three gene
 segments in both samples. We have shown that SVNV can be transmitted in
 seed to seedlings from an infected seed lot at a rate of 6%. To our
 knowledge this is the first report of seed-transmission of a Tospovirus.
description: Seed Quality Raw data
 and Analysis codeSeed quality raw data
 with SAS statistical analysis codeSequence Raw
 DataRaw Sequences for PCR
 products resulting from PCR reactions using primers in Table 1 of the
 manuscriptSequences_PlosOne.docxSequences of nested PCR products-SVNV-06302015Sequences of typical Nested PCR ProductsAlignment-BAST-SVNVAlignment of Typical sequences from nested PCR against known SVNV sequences150701J2_07E_2-27-2M-1Raw Sequencing Trace File of a SVNV-positive seed sample.R10_Root_SVNV-seqRaw sequence from soybean root extractionRaw Gene Counts for RNAseq AnalysisUnique Gene Read counts for SVNV genes for bulk and field samples.Raw Gene Count Data_RNAseq.xlsxBulk Sample Mapped Counts for RNA seqTotal Mapped Counts for the RNA seq analysis of the bulked sample.Bulk_MappedCounts.pdfBulk Sample Mapped Counts Unique RNA seqUnique Mapped Counts for the RNA seq analysis of the bulked sample.Bulk_MappedCounts_Unique.pdfField sample Mapped counts RNA seqTotal Mapped Counts for the RNA seq analysis of the symptomatic field sample.Field_Fig2A_MappedCounts.pdfField Sample Mapped Counts Unique RNA seqUnique Mapped Counts for the RNA seq analysis of the symptomatic field sample.Field_Fig2B_MappedCounts_Unique.pdf