Codon usage bias analysis of the genome-wide genes encoded in Agaricus bisporus [双孢蘑菇基因组密码子的偏好性分析]

作者：Han L.-H.; Dai D.-Q.; Zhao M.-Y.; Liu C.^*

来源：Mycosystema, 2021, 40(3): 603-615.

DOI：10.13346/j.mycosystema.200268

• Agaricus bisporus
• codon usage bias
• gene expression
• genome
• optimal codon

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 T3s 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.