Conserve Nucleotide Motifs within Tobamovirus Genomic Promoters

The Relationship between Viruses and Plant Cells in Natural Ecosystems and Some Approaches to Their Regulation

“…Synonymous codon usage in the genes of the dwarf soybean virus and the potato X virus varies widely depending on the gene; amino acid and codon; gene overlapping; first two nucleotides in codons; mononucleotide context, located upstream and downstream of the codon; GC-content in virus-encoded genes and in the third codon positions [19,22]. The overlapping of genes has an influence on the decrease in total nucleotide substitutions by 2.5-fold, in the number of synonymous substitutions in the third codon positions -by 2.8-4.3fold, in dicodon content of genes -by 1.4-1.6-fold.…”

“…It was shown that the frequency of nucleotide substitutions in viral genes depends on the nucleotide and strain pairs, the length and localization of gene regions as well as the substitution types and their codon positions [22]. The highest correlation of substitution frequency was shown for different nucleotide pairs (u→c/c→g, 1240), codon positions (third/second, 17,3) and substitution types (transitions/transversions, 5,8), the least -for forward and back substitutions in the same nucleotide pairs (1,03-1,6).…”