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[摘要]
目的 分析刺五加功能基因密码子的使用方式及其影响因素。方法 以刺五加的17条功能基因为材料,利用CodonW和SPSS软件进行多元统计分析和对应性分析。结果 刺五加功能基因密码子3个位置的GC量依次为51.03%、41.23%和40.04%,三者均与整个编码区的GC量显著相关(P<0.05),GC12与GC3的相关系数为0.262,未达到显著水平。同义密码子的相对使用频率大于1的密码子共27个,其中22个以A或T碱基结尾。对应性分析的结果表明,第1轴显示了22.78%的差异,与GC3、密码子适应指数和密码子偏好指数均极显著相关(P<0.01),相关系数分别为0.786、0.686和0.617,与有效密码子数的相关性未达显著水平。第2轴显示了19.28%的差异,且仅与有效密码子数极显著相关(r=0.635)。确定了刺五加功能基因的17个最优密码子。结论 刺五加的功能基因偏好使用以A或T碱基结尾的密码子,其使用模式受选择和突变的共同影响。
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[Abstract]
Objective To analyze the codon usage of functional genes in Eleutherococcus senticosus and their influencing factors. Methods The multivariate statistical analysis and correspondence analysis were carried out using CodonW and SPSS software with codon of 17 genes selected from the functional genes of E. senticosus. Results GC contents at the three positions of functional gene codons in E. senticosus was 51.03%, 41.23%, and 40.04%, all of which had a significant correlation coefficient (P < 0.05). The correlation coefficients with GC12 and GC3 were 0.262, and both were insignificant. The relative synonymous codon usage of 27 codons was greater than 1, among which 22 codons ended with A or T base. In the corresponding analysis, the first axis showed the variation of 22.78%, and there were significant correlation coefficients in codon adaptation, codon bias index, and GC3 (P < 0.01). The correlation coefficients were 0.686, 0.617, and 0.786, respectively, but they were insignificantly related with the effective number of codons (ENC). The second axis showed the variation of 19.28% and it was only significantly related with ENC (r = 0.635). Seventeen optimized codons in functional genes of E. senticosus were defined. Conclusion All codons of functional genes in E. senticosus prefer to ending with A or T base. The codon usage bias is formed under the effects of mutation and selection.
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[基金项目]
国家自然科学基金资助项目(30701086);河北省自然科学基金项目(C2009001252);河北省自然科学基金-石药集团医药联合研究基金项目(H2012401006)