球孢白僵菌基因组密码子使用模式及其影响因素分析

球孢白僵菌Beauveria bassiana是一类成功用于全球生物防治的重要病原真菌,这是由于其宿主范围广及毒力多样化特性决定的.利用球孢白僵菌已公布全基因组数据,开展密码子使用偏好分析,以理解其基因组特征和宿主适应性.尽管通过密码子指数CAI,CBI,ENc的计算,认为球孢白僵菌密码子使用偏性较弱.但根据RSCU值鉴定最优密码子,发现球孢白僵菌基因组强烈偏好使用第三位碱基G/C的密码子,尤其是C结尾的密码子.对密码子第三位碱基进行PR2分析,发现球孢白僵菌密码子偏好性还表现在倾向于使用嘧啶结尾密码子,即U使用频率高于A,C使用频率高于G.该偏好模式通过相关性分析,认为核苷酸组成是影响球孢白僵菌密码子偏好性的一个重要因素.而ENc图和对应分析则表明除核苷酸组成外,球孢白僵菌密码子使用偏好还受到基因功能及其他多种因素的影响.中性绘图分析认为,球孢白僵菌密码子使用偏好受到外界选择下的定向突变压力作用,并推测该选择来自于其宿主.而该定向突变压力也是加快球孢白僵菌自身基因组进化和毒力多样化的一种动力,使其能适应在700多种昆虫宿主中寄生.

Codon Usage Bias (CUB) Pattern and Its Influencing Factors for the Whole Genome of Beauveria bassiana

An extremely wide host range of Beauveria bassiana makes this fungus one of the most successful commercial fungal entomopathogens for worldwide biological pest control. In a study reported herein, the codon usage bias (CUB) for the whole genome of B. bassiana was analyzed based on the data available so as to understand its genomic features and host adaptation. Although the presence of a weak CUB of B. bassiana genome was revealed based on an analysis of codon indices (CAI, CBI and ENc), nearly all of the optimal and the preferred codons in B. bassiana genome were found of G/C at the third codon position, especially C. Parity Rule 2 (PR2) plot analysis of the third codon position of the codon showed that pyrimidines (U and C) were used more frequently than purines (A and G). Correlation analysis of this CUB pattern indicated that nucleotide composition and gene function were two main factors accounting for B. bassiana CUB, and the ENc-plot and the correspondence analysis suggested that in addition to nucleotide composition, B. bassiana CUB was influenced by gene function and a variety of other factors as well. Neutrality analysis revealed that the directed mutational pressure under natural selection rather than the non-directed mutational pressure under random genetic drift played a more active role in the B. bassiana genome, suggesting that it might be a key motivation of adapting to over 700 species of insect hosts for B. bassiana.