菠萝蜜叶绿体基因组密码子偏好性分析

Codon bias analysis of chloroplast genome of Artocarpus heterophyllus

从菠萝蜜叶绿体基因组中筛选出51条蛋白编码序列,并使用CodonW和CUSP在线程序对其密码子使用偏好性及其影响因素进行了探究。结果表明,菠萝蜜叶绿体基因组中的密码子各碱基的GC含量从首位到末位呈递减趋势,偏好以A/U结尾。有效密码子数在[35.64,53.19]区间内,且68.63%的基因有效密码子数大于45,表明密码子偏好性较弱。相关性分析显示,密码子的偏好性与碱基第3位的组成和基因长度有关,而碱基第1位的GC含量则影响基因的表达水平。菠萝蜜叶绿体基因组密码子的中性绘图、奇偶偏好性以及有效密码子绘图分析结果显示,内部突变和自然选择都会影响密码子的使用模式。最优密码子分析结果显示,有16个密码子满足筛选条件,进一步验证了密码子偏好以A/U结尾。对各基因的有效密码子相对使用度进行聚类分析的结果显示,基因的偏好与基因功能之间的进化模式相互独立。

A total of 51 coding sequences of Artocarpus heterophyllus chloroplast genome were analyzed for codon usage preference and influencing factor by CodonW and CUSP online programs.The results showed that the GC content of each base of A.heterophyllus chloroplast codon decreased successively from the first base to the last one,and the codon preferred to end with A/U.The effective number of codons(ENC)ranged from 35.64 to 53.19,and 68.63%of genes had ENC values greater than 45,indicating weak codon preference.Correlation analysis showed that its codon preference was related to the composition of the last base and gene length,and GC content of the first base affected gene expression level.The results of neutral mapping,parity preference,and effective codon mapping of A.heterophyllus chloroplast genome showed that internal mutation and natural selection may affect codon usage patterns.Optimal codon analysis showed that 16 codons met the screening requirements,and further verified that the codon preferred to end with A/U.RSCU cluster analysis of each gene showed that the patterns of evolution between gene preference and gene function were independent from each other.