Polymorphism and structural variation of rps16 group-II intron in the Solanum species

Nucleotide sequences of the self-splicing group-II intron of rps16 have first been determined in nine species of the Solanum genus. It was found that the observed variations in the intron length (855–864 bp) was associated with indels of 1 to 9 bp. Altogether, five indels and 50 nucleotide substitutions were detected, which were used to identify six Solanum haplotypes. Although the intron sequence was in general fairly well conserved, the distribution of the described mutations among its structural elements corresponding to six pre-RNA domains was qualitatively and quantitatively nonuniform. The highest polymorphism levels were observed in domains I, II, and IV. The sequence of domain V was absolutely invariable, which is in agreement with its functional significance. The chloroplast rpS16 intron sequences have been characterized in nine Solanum species. The intron length ranged from 855 bp to 864 bp, which is associated with 1–9-nucleotide indels. In total five indels and 50 nucleotide substitutions have been detected and six Solanum haplotypes have been revealed. Solanum rpS16 introns has been characterized by mutation rate heterogeneity between structure regions of all six domains its pre-RNA. Intron domains I, II, IV are shown to be more variable. Sequences of the domain V are invariant, that agrees with its functional significance.