Jiang Wei, Lv Beibei, Wu Xiao, Wang Jinbin, Wu Guogan, Shi Chunhui, Tang Xueming
Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, People's Republic of China.
Shanghai Key Laboratory of Agricultural Genetics and Breeding, Shanghai, People's Republic of China.
Biotechnol Appl Biochem. 2017 Mar;64(2):218-224. doi: 10.1002/bab.1538. Epub 2016 Dec 15.
In this study, trends in synonymous codons usage of Volvariella volvecea have been first examined by analysis of complete coding sequences and gene chip data. The results showed that GC content at three codon positions are obviously different and there were several factors shaping the codon usage of V. volvacea genes, including base composition. The comparison of codon usage among four edible fungi such as V. volvacea, Agaricus bisporus, Coprinopsis cinerea, and Pleurotus ostreatus indicated that the similar codon usage pattern was used among V. volvacea, A. bisporus and P. ostreatus, but there was significantly different codon usage pattern of C. cinerea. Two arrays of optimal codons were determined by effective number of codons (ENC) values and gene chip database separately, resulting that most of the ENC-predicted optimal codons were included in the array of gene chip resulted optimal codons. This study can provide useful information for codon usage pattern analysis and gene transformation of V. volvacea.
在本研究中，首次通过对完整编码序列和基因芯片数据的分析，研究了草菇同义密码子的使用趋势。结果表明，三个密码子位置的GC含量明显不同，有几个因素影响草菇基因的密码子使用，包括碱基组成。对草菇、双孢蘑菇、灰盖鬼伞和平菇这四种食用菌的密码子使用情况进行比较，结果表明草菇、双孢蘑菇和平菇之间使用的密码子模式相似，但灰盖鬼伞的密码子使用模式有显著差异。分别通过有效密码子数（ENC）值和基因芯片数据库确定了两组最优密码子，结果显示，ENC预测的最优密码子大多包含在基因芯片结果的最优密码子组中。本研究可为草菇的密码子使用模式分析和基因转化提供有用信息。
