落叶松-杨栅锈菌基因组密码子使用偏好分析

Codon usage bias analyses of the rust fungus Melampsora larici-populina genome

为了解落叶松-杨栅锈菌密码子使用模式,并探究影响其密码子偏好形成的因素,本研究利用CondonW对落叶松-杨栅锈菌标准菌株98AG31基因组中14650个基因进行分析,计算基因的有效密码子数,及64个密码子的相对使用度等偏好性参数。结果表明,落叶松-杨栅锈菌全基因组水平的密码子偏好程度较低,只有少数基因呈现出高偏好性。落叶松-杨栅锈菌的高频密码子多以A或T结尾,而最优密码子则倾向以G或C结尾。PR2-plot分析及ENC-plot曲线与中性绘图分析显示,落叶松-杨栅锈菌基因密码子使用模式受到选择压力和突变压力等多重因素的影响,相较于选择压力,落叶松-杨栅锈菌基因密码子的偏好更多地受到突变压力的影响。相关性分析表明,密码子碱基组成会对密码子偏好性产生影响,其他因素如序列长度等均不会影响密码子偏好性。

Based on 14650 genes encoded in the genome of the rust fungus Melampsora larici-populina,the effective condon number,relative synonymous condon usage and the factors contributing to the codon usage bias were investigated using the program CondonW.The results indicate that the codon usage bias of M.larici-populina is relatively low,and only a few genes are high biased.High frequent codons end with an A or T while optimal codons end with a G or C.The results of PR2-plot analysis,ENC plot analysis and neutrality analysis show that both natural selection and mutation play roles in shaping codon usage of this fungal species.However,mutational pressure may play a more important role in shaping codon usage bias than natural selection.A correlation analysis shows that base composition of condons is involved in shaping the codon usage pattern of M.larici-populina.