紫花苜蓿叶绿体基因组密码子偏好性分析

Analysis of codon usage bias in the chloroplast genome of alfalfa(Medicago sativa)

关键词:  紫花苜蓿, 叶绿体基因组, 密码子偏好性, 最优密码子

Key words:  Medicago sativa, chloroplast genome, codon usage bias, optimal codons

摘要:

为分析紫花苜蓿叶绿体基因组密码子偏好性的使用模式,该文以紫花苜蓿叶绿体基因组中筛选到的49条蛋白质编码序列为研究对象,利用CodonW、CUSP、CHIPS、SPSS等软件对其密码子的使用模式和偏好性进行研究。结果表明:(1)紫花苜蓿叶绿体基因的第3位密码子的平均GC含量为26.44%,有效密码子数(ENC)在40.6～51.41之间,多数密码子的偏好性较弱。(2)相对同义密码子使用度(RSCU)分析发现,RSCU>1 的密码子数目有30个,以A、U结尾的有29个,说明了紫花苜蓿叶绿体基因组A或U出现的频率较高。(3)中性分析发现,GC3与 GC12的相关性不显著,表明密码子偏性主要受自然选择的影响; ENC-plot 分析发现一部分基因落在曲线的下方及周围,表明突变也影响了部分密码子偏性的形成。此外,有17个密码子被鉴定为紫花苜蓿叶绿体基因组的最优密码子。紫花苜蓿叶绿体基因组的密码子偏好性可能受自然选择和突变的共同作用。该研究将为紫花苜蓿叶绿体基因工程的开展和目标性状的遗传改良奠定基础。

Abstract:

To character the codon usage patterns of chloroplast genome in alfalfa, forty-nine coding DNA sequences were analyzed using CodonW, CUSP, CHIPS and SPSS softwares. The results were as follows:(1)The average GC content at the 3rd codon position was 26.44% in the alfalfa chloroplast genome. The effective codon number(ENC)ranged from 40.6 to 51.41, indicating that codon bias was weak in the alfalfa chloroplast genome.(2)Thirty codons showed relative synonymous codon usage(RSCU)value greater than 1, including 29 codons ending with A and U, which suggested that the third codon position preferred A or U.(3)Neutrality analysis showed no significant correlation was observed between GC3 and GC12, suggesting natural selection mainly contributed to the codon usage bias. ENC-plot analysis showed that there were some genes with low ENC values lying below or near the expected curve, which indicated that mutation also affected the formation of codon usage bias. In addition, 17 codons were identified as optimal codons in alfalfa. We concluded that the codon usage bias of alfalfa is formed under effect of natural selection and mutational bias. This study will lay a good foundation for development of chloroplast genetic engineering and molecular breeding of alfalfa.