栀子叶绿体基因组密码子偏好性分析

Codon usage bias in the chloroplast genome of Gardenia jasminoides

分析栀子叶绿体基因组密码子的偏好性并探讨其主要影响因素,为栀子叶绿体基因组研究及其遗传改良提供参考依据。利用Codon W1.4.2、CUSP和SPSS 20.0软件统计和计算密码子的碱基含量,分析密码子使用模式。结果表明:栀子叶绿体基因组密码子第3位GC含量(GC3)为28.44%,低于第1(GC1)、2位GC含量(GC2),GC1和GC2分别为47.33%、39.56%;有效密码子数(ENC)为36.78~56.95,平均值为47.42;ENC与GC1、GC2之间的相关性均不显著,与GC3之间呈极显著正相关,相关系数为0.356;GC1和GC2的平均值(GC12)与GC3之间的相关性不显著,相关系数为0.102;45.45%基因的ENC比值频数为0.0~0.1;结合高频及高表达密码子分析结果,最终确定UUU、UUA、UUG等19个密码子为栀子叶绿体基因组的最优密码子。综合分析显示,栀子叶绿体基因组密码子末位碱基偏好以A或U结尾,偏好性弱,其密码子偏好性主要受自然环境选择和突变因素的影响,是多因素共同作用的结果。

Codon usage bias of Gardenia jasminoides Ellis chloroplast genome and its main influencing factors were analyzed to pro⁃vide a basis for the study of G.jasminoides chloroplast genome and its genetic improvement.Base content and usage pattern of chloro⁃plast genome codon were analyzed by Codon W1.4.2,CUSP and SPSS 20.0 software.The results showed that GC content of the 3rd base(GC3,28.44%)of the G.jasminoides chloroplast genome codon was lower than that of the 1st base(GC1,47.33%)and the 2nd base(GC2,39.56%).The effective number of codon(ENC)ranged from 36.78 to 56.95,with an average of 47.42.ENC had no significant correlation with GC1 and GC2,but had extremely significant positive correlation with GC3(correlation coefficient,0.356).There was no significant correlation between the mean value of GC1 and GC2(GC12)and GC3(correlation coefficient,0.102).Up to 45.45%of the genes studied had ENC ratio of 0.0-0.1.A total of 19 codons such as UUU,UUA and UUG were de⁃termined as the optimal codons of G.jasminoides chloroplast genome by the analysis of high frequency codon and high expression co⁃don.Comprehensive analysis revealed that G.jasminoides chloroplast genome codons prefered to end with A or U with weak bias,and its codon usage bias was affected by multiple factors,mainly by natural environment selection and mutation.