芝麻叶绿体基因组的密码子使用偏性及其影响因素

Codon Usage Bias and Its Influencing Factors in the Chloroplast Genome of Sesame

通过分析芝麻叶绿体基因组密码子的使用偏性,阐明其密码子的使用偏性特征,并探讨其影响因素。以芝麻叶绿体基因组的50个蛋白编码序列为研究对象,利用CodonW等软件对其密码子使用模式及影响因素进行了分析。结果发现,芝麻叶绿体基因的GC含量平均为38.48%,密码子3个位置的GC含量平均值分别为47.22%、39.88%和28.33%(即GC_(1)>GC_(2)>GC_(3));GC_(1)和GC_(2)相关性显著,但它们与GC_(3)相关性都不显著;ENC值的范围为36.59~57.73,平均值为47.20,都高于35;密码子使用偏性受多种因素的影响,其中自然选择是主要影响因素;对应性分析发现,前4个轴为主要影响因素,总共代表了近70%的变异来源,但不同轴与密码子其他相关指标的相关性并不相同;通过高频密码子和最优密码子分析,共获得了32个高频密码子,16个最优密码子,这些密码子第3位碱基也都偏向于使用A或T(U)。本研究表明芝麻叶绿体基因组的密码子使用偏性较弱,其主要受到自然选择的影响,并且密码子第3位碱基多以A或T(U)结尾。

This research was trying to clarify the characters of codon usage bias(CUB)and explore their influencing factors in the chloroplast genome of sesame(Sesamum indicum L.).In total of 50 CDS(coding DNA sequence)encoding different proteins of sesame chloroplast were used for the analysis by using the CodonW and related softwares.The results showed that the average GC content of the sesame chloroplast genes was 38.48% and the average GC content of three positions of the gene codons was 47.22%,39.88% and 28.33%,respectively(that is:GC_(1)>GC_(2)>GC_(3)).The GC_(1) and GC_(2) contents were significantly correlated,while both of them were not significantly correlated with the GC_(3) content.The effective number of codons(ENC),which was ranged from 36.59 to 57.73 with an average of 47.20,were all larger than 35.It also showed that the CUB was affected by many factors while mainly by natural selection.The correspondence analysis showed that the first four axes almost represented 70% of the total source of variance,but the correlations between different axes and other related indexes were different.In addition,in total of 32 high frequency codons and 16 optimal codons were obtained by the high frequency codon and optimal codon analyses,and the third base of these codons was also biased of A or T(U)bases.This research suggested that the overall CUB in the chloroplast genome of sesame was weaker and mainly influenced by natural selection,and the third base of the codons was bias to use A or T(U).