红藻rbcL基因密码子偏爱性分析

红藻是我们日常生活中一类非常重要的海洋生物资源。为探究红藻rbcL基因密码子的偏爱性,确定该类基因的最优密码子,本研究通过使用CodonW 1.4.4、CUSP和SPSS 20.0软件对20条红藻rbcL基因进行了多元统计和密码子偏爱性分析,最终获得了红藻rbcL基因三个位置的GC碱基含量、ENC值和RSCU值。结果显示,红藻rbcL基因AT碱基含量高于GC碱基,ENC值为41.89,说明红藻rbcL基因密码子偏爱于A/T碱基结尾。ENC绘图分析,PR2-plot分析和中性绘图分析表明自然选择是影响rbcL基因密码子偏爱性的主要因素。通过与拟南芥等五个物种的密码子使用频率比较,发现红藻rbcL基因和它们均有较大的差异性。最后筛选得到了UUU、UUA、AUU等18个最优密码子,均偏向于以A/U碱基结尾。研究结果对红藻资源的开发利用和rbcL基因的表达研究具有重要意义。

The Codon Usage Analysis in rbcL Gene within Rhodophyta

Rhodophyta is a very important marine resource in our daily life.To explore the codon bias of the rbcL gene within rhodophyta and to identify the optimal codon,codon preference and multivariate statistical analysis of 20 rbcL genes within rhodophyta were performed by using CodonW 1.4.4,CUSP,and SPSS 20.0 software,getting the content of GC at three positions of codons,ENC values and RSCU values.The results showed that the content of AT is higher than that of GC of rbcL genes within rhodophyta,and the ENC value is 41.89,which indicate that the codons of rbcL gene within rhodophyta prefer the end of A or T.According to the ENC-plot analysis,PR2-plot analysis and neutral drawing analysis,codon bias of rbcL gene is mainly affected by natural selection.By compared with the codon usage frequency of five species such as Arabidopsis thaliana,we find that there is a great difference between the rbcL gene and them.Finally,18 optimal codons are identified such as UUU,UUA,AUU,which prefer the end of A or U.The results are of great significance to the exploitation and utilization of rhodophyta and the study of rbcl gene expression.