三种侧耳属真菌基因组密码子偏好性比较分析

Comparative analysis of codon preference pattern in three species of Pleurotus based on genome data

为了解3种侧耳属真菌基因组密码子的使用偏性及影响因素,本研究以糙皮侧耳、刺芹侧耳和白灵侧耳基因组CDS序列为研究对象,通过生物信息学方法对3种侧耳密码子使用偏性进行了分析。结果表明,3种侧耳基因组总碱基组成差异小,GC含量高。RSCU、RFSC分析表明糙皮侧耳G/C结尾的偏好密码子的比例最高(82.14%),并且有3个特有偏好密码子。3种侧耳共有偏好密码子25个,以G/C结尾的占80%;共有高频密码子3个,均以G/C结尾。密码子相似性分析表明3种侧耳密码子使用模式比较相似(相似性指数均小于0.001),其中刺芹侧耳与白灵侧耳的相似性最高(相似性指数为0.000259014);且3种侧耳密码子的使用频率与灰盖鬼伞和金针菇较为接近。PR2-plot、ENc-GC3和中性绘图分析表明3种侧耳密码子偏好性使用主要受自然选择影响,在一定程度上也受碱基突变压力和其他因素影响。上述结论为分析侧耳真菌的进化规律及选择最佳异源表达受体系统提供了依据。

To understand the codon usage bias pattern and its influencing factors for the whole genome in three species of the genus Pleurotus,bioinformatic software tools were employed to systematically analyze the CDS sequences of the three species.The results showed that at the genome level,the differences in the total base composition were small,and the G/C content was higher.RSCU and RFSC analysis showed that Pleurotus ostreatus has the highest proportion of G/C(82.14%)ending preferred codons,and three of the preferred codons were unique.There were 25 identical preferred codons in the three Pleurotus species,80%of which end with G/C;there were three common high-frequency codons,all of which end with G/C.Codon usage similarity analysis showed that the codon preference pattern in the three species was similar(similarity index0.001),in particular,Pleurotus eryngii and Pleurotus tuoliensis had the highest similarity(similarity index=0.000259014);the codon usage frequency of the three Pleurotus species were close to that of Coprinopsis cinerea and Flammulina filiformis.PR2-Plot,ENc-GC3,and neutrality plot analysis indicated that the codon usage variation was mainly influenced by natural selection,and also by base mutation pressure and other factors to a certain extent.The results provide important data for analyzing the evolutionary rule of Pleurotus and developing the efficient heterologous expression receptor system.