Cloning of SOD Gene Segments and SNP Analysis in Evodia rutaecarpa

Two pairs of degenerate primers were designed according to the two conserved regions on the amino acid sequences of Cu/Zn-SOD gene and Mn/Fe-SOD gene from kinds of plants reported in GenBank in order to clone the core fragments of these two genes in ten Evodia rutaecarpa's plants.The length of Cu/Zn-SOD gene and Mn/Fe-SOD gene were 375 bp and 429 bp respectively.Every nucleotide sequence of Cu/Zn-SOD gene and Mn/Fe-SOD gene encoded 125 amino acids and 143 amino acids respectively.The biology softwares of DAMBE and DNA Star5.0 were used to analyze these sequences.The nucleotide similarity with other plants was above 74% and the amino acid similarity was above 79% at ten Cu/Zn-SOD gene fragments than other plants.The nucleotide similarity was above 78% and the amino acid similarity was above 81% in ten Mn/Fe-SOD gene fragments.Twenty-one sites of single nucleotides were discovered in the ten Cu/Zn-SOD gene fragments.Six amino acids sites transformed because of twenty-one single nucleotides variation.Seventeen variation sites of single nucleotides were discovered in the ten Mn / Fe-SOD gene fragments.Three amino acid sites transformed because of the variation of seventeen single nucleotides.Accoring to the calculation result,the polymorphism frequences in Cu / Zn-SOD gene and Mn / Fe-SOD gene were 1SNP /17.9 bp and 1SNP /25.2 bp,the nucleotide degrees of variation were 5.6% and 4.0%,the amino acid degrees of variation were 4.8% and 2.1%,respectively.Genetic diversity of cloned ten Cu / Zn-SOD gene fragments was analyzed by using the clustering procedure of Neighbor-Joining.