title: [Codon bias and nucleotide substitutions in soybean dwarf virus].
abstract: Computational analysis of codon usage bias and spontaneous nucleotide substitutions in six strains of soybean dwarf virus was performed. It was shown that synonymous codon usage in the virus genes varies widely depending on the gene, gene overlapping, codon, codon's two first nucleotides, mononucleotide context located upstream and downstream of the codon, GC-content in virus-encoded genes and in the third codon position. Overlapping of genes causes a 2.5-fold decrease of the total number of nucleotide substitutions, 2.8-4.3-fold decrease of the number of synonymous substitutions in the third codon position, 1.4-1.6-fold decrease of the dicodon content in genes. At the same time there is a significant increase of nonsynonymous substitutions in the second codon position as well as a high codon bias (Fop = 0.94-1.0) and correlation between the nucleotide content in genes and in the third codon positions (r = 0.73-0.74). The results obtained evidence for selection of dicodons in the viral genes.
authors: A M
authors: AM
authors: Kyrychenko
authors: O I
authors: OI
authors: Hordeĭchik
authors: I S
authors: IS
authors: Shcherbatenko
mesh_terms: D001482:Base Composition / Q000235:genetics; D001483:Base Sequence; D003062:Codon / Q000235:genetics*; D019295:Computational Biology; D030541:Databases, Genetic; D019143:Evolution, Molecular; D005814:Genes, Viral; D017793:Luteovirus / Q000145:classification / Q000235:genetics*; D008969:Molecular Sequence Data; D009154:Mutation / Q000235:genetics*; D009711:Nucleotides / Q000235:genetics*; D012641:Selection, Genetic; D013025:Glycine max / Q000821:virology
chemical_list: D003062:Codon; D009711:Nucleotides