双孢蘑菇基因组密码子的偏好性分析

Codon usage bias analysis of the genome-wide genes encoded in Agaricus bisporus

双孢蘑菇Agaricus bisporus是世界上最广泛栽培的食用菌之一。本研究通过分析双孢蘑菇基因组密码子使用偏性,探讨密码子偏性的影响因素及其对基因表达的影响。以双孢蘑菇基因组和转录组数据为依据,分析了双孢蘑菇基因组基因、高表达基因(high expression gene,HEG)和低表达基因(low expression gene,LEG)的密码子使用性。发现双孢蘑菇基因组编码基因平均GC含量为49.08%,T3s值(35.59%)最高,平均ENC值偏高,多数基因表达潜力较低。共鉴定出14个最优密码子,均以C或T结尾,并且遵循密码子中嘌呤和嘧啶使用的均衡性原则。高表达基因具有更强的密码子偏性,进化过程中受到基因突变和自然选择等多种因素影响。基因表达与G/C碱基含量和CAI值呈极显著正相关。高表达基因编码了多种与真菌生长发育相关的蛋白和酶类。研究结果明确了双孢蘑菇基因密码子的使用偏性,为双孢蘑菇转基因育种和品质改良提供了参考。

Agaricus bisporus is an important species of edible mushrooms.To understand the influencing factors of codon bias and their relationship with gene expression,the codon usage bias of A.bisporus genome was analyzed.Based on the genome and transcriptome data,the codon usage of genomic genes,high expression genes(HEG)and low expression genes(LEG)in A.bisporus were analyzed.The results showed that the average GC content of coding genes was 49.08%in A.bisporus;the T3 s value(35.59%)was the highest,and the average ENC(effective number of codons)value was high,while the expression potential of most A.bisporus genes was low.A total of fourteen optimal codons was identified,and all ended with the nucleotide C or T.The optimal codons adhered to the equilibrium of purine and pyrimidine.Comparatively,high expression genes have stronger codon bias and are affected by many factors,such as gene mutation,natural selection and so on.Gene expression was positively correlated with G/C content and codon adaptation index value.The highly expressed genes encode a variety of proteins and enzymes related to the growth and development of fungi.The results revealed the characteristics of the codon usage bias of A.bisporus genes,providing a reference for transgenic breeding and quality improvement of A.bisporus.