Benyvirus genomes consist of two to five molecules of linear positive-sense single-stranded RNAs (ssRNAs) which terminate in a 3' poly(A) tail. In naturally infected sugar beets, the BNYVV genome consists of four and in some isolates five RNAs of c. 6.7,4.6,1.8,1.4, and 1.3 kb (Figure 2). Complete or partial nucleotide sequences have been determined for several isolates. After repeated mechanical transfers to local lesion hosts, BNYVV isolates often contain only partially deleted forms of their RNAs 3,4, and/or 5, or they lose these small RNAs altogether. RNA1 and RNA2 contain all the genetic information necessary to enable multiplication, encapsidation, and cell-to-cell movement on local lesion hosts (see below); the additional presence of RNA3 and RNA4, however, is essential for vector-mediated transmission and disease development in sugar beet roots. RNA5 which is found only in limited areas increases the virulence of the virus.
Four genomic RNA species have also been identified for BSBMV and RSNV, but only two for BdMV. The BdMV isolate might possibly have lost additional small RNAs after prolonged cultivation on C. quinoa as do isolates of BNYVV. The complete sequence has been published for all four RNAs of an isolate of BSBMV. The complete sequences of RNA1 (c. 7.0 kb) and RNA2 (c. 4.3 kb) of BdMV and a partial sequence of RSNV RNA1 (2239 nt) have also been determined but not yet released.
Available data indicate that the genome organization is similar for all four viruses. Highest nucleotide sequence identities are found in the RNA1-encoded replication-associated proteins (c. 84% for the pair BNYVV/BSBMV) and the RNA2-encoded second triple gene block (TGB) proteins (c. 82% for the pair BNYVV/BSBMV; c. 50% for the pair BNYVV/BdMV), but the lowest ones in the RNA2-encoded cysteine-rich proteins, which are presumably RNA-silencing suppressors (c. 38% for the pair BNYVV/BSBMV; c. 20% for the pair BNYVV/BdMV).
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