Variability of the N-protein and the intergenic region of the S RNA of tomato spotted wilt tospovirus (TSWV)

The genetic heterogeneity of the N protein gene and the intergenic region ( IGR) of the S RNA from tomato spotted wilt virus (TSWV) isolates, collected in Bulgaria. were compared with isolates from other parts of the world. Th e results substantiated the highly conserved nature of the N protein. Twent y six independent sequences revealed only seven variable amino acid positio ns, common to all isolates. The type of amino acids present in these positi ons seems to be independent of the geographical origin. In contrast to the structural N protein, comparisons of the related IGR-seq uences led to clusters correlated with the geographical origin of the isola tes. Although the overall sequence homology in the IGRs was much lower than for the N proteins, three conserved parts within this region were identifi ed. The outstanding part was a central area of 31 nucleotides with a signif icantly increased GC-content. This was located in both viral- and viral-com plement RNA at structures with similar foldings, which led to the assumptio n that this stabilised structure, rather than a sequence motive, might serv e as a transcription terminator during the synthesis of the two mRNAs from the ambisense segments.