茄腐镰孢(Fusarium solani)线粒体基因组密码子偏好性分析

Analysis of Codon Usage Bias in Mitochondria Genome of Fusarium solani

密码子使用偏好性作为功能基因组重要的进化特征而被广泛报道,但是有关真菌线粒体基因组密码子使用偏好性的研究相对较少。本试验以茄腐镰孢线粒体基因组为研究对象,运用Codon W软件及RSCU在线软件对所筛选到的22条编码基因密码子3个位置上的GC含量、有效密码子数、同义密码子使用频率和最优密码子进行了分析。同时,确定了茄腐镰孢线粒体基因组的最优密码子,并探讨了影响密码子偏性形成的相关因素。分析结果表明,茄腐镰孢线粒体密码子3位的GC含量为GC1(32.7%)>GC2(28.0%)>GC3(19.7%),第3位GC含量明显小于第1、2位,表现出对以A或者T结尾的密码子发生较强烈的偏向使用;且确定的21个最优密码子中有20个以A或者T结尾。通过中性绘图及ENC分析得出茄腐镰孢线粒体基因组密码子的使用偏好受到选择作用和突变压力的共同影响,选择作用为主要影响因素。

It is widely reporte d codon usage bias as an important evolution feature in genome, but little is known about codon usage bias in fungal mitochondrial genome. In this study, we analyzed the content of GC at 3codon positions(GC1, GC2, GC3), effective number of codon(ENC) and relative synonymous codon usage(RSCU)in F. solani mitochondria genome using Codon W software and RSCU online software. Further, the optimal codons of F. solani mitochondria genome mitochondrial genome were determined, and the reason of codon usage bias was cleared. GC content results showed that the content of GC1(32.7%) is more than that of GC2(28.0%) and GC3(19.7%), indicating AT content in genes was higher than GC content and genes favored A or T at the third position. The optimal codons results showed that the third position exclusively used A or T. Neutrality plots and ENC-plot results showed that both selection and mutation contributed to codon usage bias in F. solani mitochondria genome, but selection bias was the major influence on codon usage.