观赏植物DFR基因的密码子使用模式比较

Codon Usage Patterns Analysis for DFR Genes in Ornamental Plants

二氢黄酮醇4-还原酶(dihydroflavonol 4-reductase, DFR)是植物类黄酮代谢途径的关键酶之一,在植物花色修饰起重要作用。本研究以观赏植物的21个DFR基因为研究对象,利用CodonW和MEGA 5.05等软件分析其密码子使用模式,探讨影响密码子使用偏性的主要因素。结果表明:观赏植物DFR基因密码子使用偏性较弱;DFR基因在单/双子叶观赏植物之间的密码子使用偏好性存在差异;单子叶观赏植物偏好以G/C结尾,而双子叶观赏植物偏好使用A/T结尾。有效密码子数分析显示,大部分观赏植物DFR基因(占供试材料76.19%)分布于期望曲线下方;奇偶偏好分析发现,嘌呤(A和G)和嘧啶(T和C)的使用频率存在不均衡使用。由此可推测观赏植物DFR基因的密码子偏性使用模式受到突变压力和选择作用等因素的共同影响。此外,还确定了ATT等倾向以A/T结尾的15个最优密码子。本研究结果为观赏植物花色转基因研究中的密码子改造及优化提供了理论参考。

Dihydroflavonol-4-reductase(DFR) gene plays an important role in genetic modification of colors and it is a key enzyme in flavonoid biosynthesis. Codon of 21 DFR homologous genes which were selected from ornamental plants were studied. By CodonW and MEGA 5.05 softwares were used to evaluate different parameter of codon usage bias. The results showed that codon usage bias of DFR genes from ornamental plants was weak.There are obvious difference in the synonymous codon bias of DFR genes between monocotyledon and dicotyledon,monocotyledons was biased toward synonymous codons with G or C codon in GC3 s value, dicotyledons preferred to use the end of the A or T. ENC-plot analysis showed that most DFR genes(accounting for 76.19% of all DFR genes) were distributed below the ENC expected value curve. The parity rule 2(PR2-plot) analysis showed that there was imbalance use problem between the AG and TC contents. It can be concluded that the codon usage pattern of 21 DFR homologous genes from ornamental plants was affected by not only mutation pressure and but also selection effect. Meanwhile, we defined 15 optimal codons, which all ended with A or T. The paper can be a theoretical reference for codon optimized and synthesized in genetic engineering of flower color of ornamental plants.