摘要
基因组密码子使用受多种因素的影响 ,本试验通过对应分析探讨了若干重要因子对粳稻品种“日本晴”叶绿体全基因组序列密码子用法的效应。结果指出 ,在影响最大的第一条向量轴上 ,基因的位置坐标与该基因的表达水平(CAI)和GC3s极显著相关 (r =0 785 和 - 0 80 4 ) ,而CAI与GC3s高度负相关 (r =- 0 917 ) ;说明基因表达水平的高低是影响密码子使用的主要因素 ,并且高表达的基因强烈偏好使用以T或A结尾的密码子。基因编码区碱基组成的影响力远不及基因的表达水平 ,G +C含量与ENC、CAI以及第一条向量轴上基因位置坐标的相关系数分别为0 344 、- 0 4 2 2 和 - 0 4 2 1 ;相关性测验和方差分析均表明基因长度对密码子的使用影响不大 ,估计与那些编码未知功能的ORFs的存在有关 ;复制转录对密码子的使用没有明显的选择。将高表达优越密码子分析法和高频密码子分析法相结合 ,确定了TGT和GAA等 12个密码子为叶绿体基因组的主要偏爱密码子。
The codon usage in the genome is usually influenced by many factors A correspondence analysis was performed for exploring the effects of several important factors on codon usage in the complete chloroplast genome sequences of Nipponbare The results showed that there were significant correlations ( r =0 785 ** and -0 804 ** ) between the gene position on first axis and gene expression level, with both the assessments (Codon Adaptation Index,CAI and GC3s values ), whereas a strongly negative correlation ( r = -0 917 ** ) between CAI and GC3s values, indicating that the natural selection on gene expression level was the major factor affecting the codon usage of Nipponbare, and that highly expressed genes had a stronger preference for codons with T or A at the third nucleotide position From a lower positive correlation between GC content and ENC ( r =0 344 ** ), and lower negative correlations between GC content and CAI, axis 1 coordinates ( r = -0 422 ** and -0 421 ** , respectively), we could conclude that the GC content in coding region gave a less contribution to codon usage bias than that to gene expression level The results of correlation analysis and variance analysis showed that gene lengths did not significantly affected genomic codon usage bias, which was probably related to those ORFs with unidentified function The replication transcription selection had a far less influence on the codon usage of a gene Through an analysis of both the high expression codon and high frequency codon, we defined 12 codons from 12 amino acids as the major preference codons in cv Nipponbare
出处
《作物学报》
CAS
CSCD
北大核心
2004年第12期1220-1224,共5页
Acta Agronomica Sinica
基金
国家自然科学基金 (3 9870 42 1)
浙江省重点科研项目 (2 0 0 3C2 2 0 0 7)资助。
