三种块菌(松露)全基因组密码子使用偏性及其影响因素

块菌又称松露,为珍稀野生药食兼用的大型真菌,具有极高的营养保健价值。密码子使用偏性分析可为块菌的遗传进化与资源开发提供理论依据。基于黑孢块菌(Tuber melanosporum)、白块菌(T. magnatum)和波氏块菌(T. borchii)的基因组数据,利用CodonW 1.4.2、Mega X软件和EMBOSS在线网站,系统分析3种块菌基因组密码子使用特征及其影响因素。结果显示,3种块菌基因组密码子使用模式高度相似,密码子第3位偏好鸟嘌呤或胞嘧啶(G/C),有效密码子数值较高,其中,黑孢块菌与波氏块菌密码子使用性相似度最高,白块菌鸟嘌呤或胞嘧啶碱基相关参数均较高。3种块菌最优密码子中G/C结尾的分别占81.8%、78.9%和61.9%,三者共有的高频密码子24个,共有的最优密码子14个,均偏好鸟嘌呤或胞嘧啶或胸腺嘧啶结尾的密码子,但总体偏好性不强。奇偶偏性、ENC-GC3s关联、中性绘图和对应性分析显示,3种块菌密码子使用偏性形成受选择压力等多种因素影响,其中黑孢块菌主要受翻译选择压力影响,白块菌主要受翻译选择外的其他因素影响,波氏块菌受选择压力影响相对较弱。研究表明,3种块菌基因组密码子使用模式相似,偏性较弱,表达潜力较低,受多种因素影响,研究结果可为块菌的物种演化研究和遗传育种提供理论基础。

Codon usage bias and its influencing factors in the whole genome of three truffles

Truffle is a rare wild macrofungi for both medicine and food, it has high value in nutrition and health care. Codon bias analysis can provide a theoretical basis for genetic evolution and resource development of truffles. Based on the genomic data of Tuber melanosporum, T. magnatum and T. borchii, CodonW 1.4 2, Mega X software, and EMBOSS online website were used to systematically analyze the codon usage bias and influencing factors of the genomes of three truffles. The results showed that the codon usage patterns of the three truffles were highly similar, with a tendency to use the guanine or cytosine ending codons, and the effective number of codons showed high values. Among them, the similarity of codon usage between T. melanosporum and T. borchii was the highest. The guanine or cytosine (G/C) base related parameters of T. magnatum were higher than other two species. Among the optimal codons of the three truffles, the G/C ending codons accounted for 81.8%, 78.9% and 61.9% respectively. 24 high-frequency codons and 14 optimal codons were common in the three truffles. All of them prefer the guanine or cytosine or thymineas ending codons, but the preference was not strong as a whole. The results of Parity Rule 2 plot, ENC-plot, neutrality plot and correspondence analysis showed that the formation of codon bias of the three truffles were mainly affected by multiple factors such as selection pressure. Among them, T. melanosporum was mainly affected by translational selection pressure, and T. magnatum was mainly affected by other factors other than translational selection, and T. borchii was relatively less affected by selection pressure. The results showed that the codon use patterns of the three truffles were similar, and the codon usage bias was weak with low expression potential. The codon bias was mainly affected by multiple factors. The results provided a theoretical basis for species evolution and genetic breeding of truffles.