桃基因密码子使用模式及其偏好性分析

Analysis of Codon Usage Patterns and Codon Usage Bias in Peach(Prunus persica)

为深入研究桃密码子使用特征,本研究基于桃(Prunus persica)基因组26873个注释基因编码序列的GC含量特征、有效密码子数(ENC)和同义密码子相对使用频率(RSCU)等参数的计算,统计分析了桃基因组密码子的偏好性及其密码子使用模式。分析结果表明桃密码子使用具有偏好性,61个密码子中存在4个密码子TCA,ACA,GCA,GAA为桃最优密码子,它们均以A结尾。进一步统计桃与其它9种近缘蔷薇科植物的密码子使用频率,发现近缘种属的密码子使用规律具有一定相似性。研究同时发现桃基因组tRNA基因拷贝数与氨基酸及特定密码子的出现频率呈正相关。这些结果揭示了桃基因组密码子的使用模式,为相关密码子使用机制研究及基因工程改良提供了重要的参考。

To dissect the codon usage characteristic,our study analyzed codon usage biases and codon usage patterns of peach(Prunus persica)genome,based on the statistical calculations of related GC content,effective number of codons(ENC)and relative synonymous codons(RSCU)from 26873 coding sequences.The analyses showed that there were obvious biases in codon usage,and 4 out of 61 codons(UCA,ACA,GCA and GAA)were defined as the optimal codons,all of which end with Adenine at the third codon position.Further analyses of codon usage frequency among peach and other 9 relative species in Rosaceae found that the codon usage patterns in the relative genus were similar.Our results also suggested that there was a positive correlation between the copy number of tR NA genes and the occurrence frequency of corresponding amino acids(Specific codons)in the peach genome.These results revealed codon usage patterns in peach and provide an important reference for the relevant studies on codon usage mechanism and the genetic engineering.