籼稻品种93-11同义密码子的使用偏性

Synonymous Codon Usage Bias in the Rice Cultivar 93-11 (Oryza sativa L.ssp.indica)

利用籼稻品种 93 11的全基因组序列及相应的EST数据 ,对影响同义密码子用法的若干因子进行了详细分析。指出 93 11基因的表达水平 (mRNA丰度 )与 3个同义密码子偏性指标CAI、CPP和ENC相关极显著 (r =0 2 2 7 ,0 14 5 和 - 0 14 7 ) ,表明高表达的基因其同义密码子非随机使用的程度越大 ;基因长度与CAI和CPP极显著负相关 (r=- 0 4 13 和 - 0 4 80 ) ,与ENC极显著正相关 (r=0 2 10 ) ,暗示较短的基因具有更高的转录活性 ;编码区G +C含量对其同义密码子偏性的贡献率远高于mRNA丰度和基因长度 ,G +C含量与CAI、CPP和ENC相关系数分别高达 0 877 ,0 832 和 - 0 74 0 ;起始编码区内A、T、C、G 4种碱基呈明显的 3周期振荡 ,尤以ATG下游第一个密码子所在的 3个位点 (+4、+5和 +6 )偏置最强烈 ,由此认为在这 3个特殊位点有较高的自然选择压存在 ;93 11中 2 5个最优密码子的首次确定将对水稻转基因具有指导意义。

By using the whole genome sequences and EST data from the indica rice cultivar 93 11,a detailed relative analysis is made of the effect of some impact factors on synonymous codon usage.The results showed that the gene expression level assessed by mRNA abundance is positive relative to the 'codon adaptation index' (CAI,0 227 ),and 'codon preference parameter' (CPP,0 145 ),but negative relative to 'effective number of codons' (ENC,-0 147 ),indicating that genes with higher expression showed more significant variation in codon usage.There are significant negative correlations between gene length and CAI,CPP ( r =-0 413 and -0 480 respectively),but a positive correlation between gene length and ENC ( r =0 210 ),which suggested a tendency of shorter genes to higher expression of the transcriptional activity in 93 11.From the results that a higher negative correlation between GC content and ENC ( r =-0 740 ),but higher positive correlations between GC content and CAI,CPP ( r =0 877 and 0 832 ,respectively),we can concluded that the GC content in coding region gave far more contribution to codon usage bias than that mRNA abundance and gene length.Four kinds of bases showed a three period distribution in the translation initiation region,the bias at the first codon sites,which located +4,+5 and +6,in the downstream of ATG being the largest.That suggested that there was a strong action of natural selection on these specific positions in the 93 11 genome.In this paper twenty five codons defined firstly as 'optimal codons' in 93 11 may provide some more useful information for rice gene transformation.