蒺藜苜蓿叶绿体密码子偏好性分析

doi:10.11686/cyxb2015016

草业学报 ›› 2015, Vol. 24 ›› Issue (12): 171-179.DOI: 10.11686/cyxb2015016

蒺藜苜蓿叶绿体密码子偏好性分析

杨国锋^1，2，*，苏昆龙^1，2，赵怡然¹，宋智斌^1，2，孙娟¹

1.青岛农业大学经济草本植物应用研究所,山东青岛 266109；
2.青岛农业大学生命科学学院,山东省高校植物生物技术重点实验室,山东青岛266109

收稿日期:2015-01-12 出版日期:2015-12-20 发布日期:2015-12-20
通讯作者: yanggf@qau.edu.cn
作者简介:杨国锋(1977-),男,山东青岛人,在读博士。yanggf@qau.edu.cn
基金资助:
现代农业产业技术体系(CARS-35),公益性行业项目(200903060)和国家自然科学基金青年科学基金项目(31200906)资助

Analysis of codon usage in the chloroplast genome of Medicago truncatula

YANG Guo-Feng^{1, 2, *}, SU Kun-Long^{1, 2}, ZHAO Yi-Ran¹, SONG Zhi-Bin^{1, 2}, SUN Juan¹

1.Institute of Economic Herb Plants, Qingdao Agricultural University, Qingdao 266109, China;
2.College of Life Sciences, Qingdao Agricultural University, Key Lab of Plant Biotechnology in Universities of Shandong Province, Qingdao 266109, China

Received:2015-01-12 Online:2015-12-20 Published:2015-12-20

摘要/Abstract

摘要： 本文对蒺藜苜蓿叶绿体基因组全序列密码子进行分析,筛选出50条CDS(coding DNA sequence)利用CodonW软件进行分析其密码子使用模式。结果显示,蒺藜苜蓿叶绿体基因组密码子第3位碱基GC含量为26.9%,即第3位密码子富含A和U,ENC值在37.11~51.91之间密码子偏好性较弱。相对同义密码子使用度分析显示RSCU值大于1的密码子有23个,其中以A和U为结尾20个。中性绘图分析显示GC₁₂与GC₃的相关系数为0.341,相关性不显著,回归系数为0.4843;单基因ENC比值多分布在-0.05~0.05,即大部分基因ENC值离ENC期望值较近;对应性分析,第一轴显示了12.50%的差异为主要影响因素,第一轴与ENC和GC₃的相关系数分别为0.091和-0.092,均相关不显著。综合这几项分析发现蒺藜苜蓿叶绿体基因组密码子偏好性主要受到突变的影响,但是并不是唯一的影响因素,其他因素对密码子偏好性也可能有一定的影响。最终通过高表达优越密码子方法确定得出UUA、UUG、CCU等23个密码子为最优密码子,为之后对外源基因进行改造,提高其在叶绿体中的表达效率奠定了基础。

Abstract: The complete nucleotide sequence of the chloroplast genome of Medicago truncatula was investigated. Fifty CDS (coding DNA sequences) selected from the chloroplast genome sequence of M. truncatula, were analyzed using CodonW software. The results show that the third codon position was rich in A and U. ENC ranged from 37.1 to 51.9 meaning that the codon bias was weak. There were 23 codons with relative synonymous codon usage greater than 1 and 20 codons ending with A and T. ENC-plot analysis showed that GC₃ was not correlated with GC₁₂; ENC ratio’s of most genes ranged from -0.05 to 0.05. In the correspondence analysis of the first group of four axes, the first axis showed 10.3% variation. The correlation coefficients for axis 1 between ENC and GC₃ were 0.091 and -0.092 respectively (not significant). Synonymous codon usage bias was found, mainly due to the effect of mutation pressure, but there were other factors. In addition, analysis of the high expression codons enabled 23 to be affirmed as the “optimal codons” as UAA, UUG, CCU. The results provide evidence for molecular modification of exogenous genes to increase the expression efficiency in M. truncatula chloroplasts.

杨国锋，苏昆龙，赵怡然，宋智斌，孙娟. 蒺藜苜蓿叶绿体密码子偏好性分析[J]. 草业学报, 2015, 24(12): 171-179.

YANG Guo-Feng, SU Kun-Long, ZHAO Yi-Ran, SONG Zhi-Bin, SUN Juan. Analysis of codon usage in the chloroplast genome of Medicago truncatula[J]. Acta Prataculturae Sinica, 2015, 24(12): 171-179.

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蒺藜苜蓿叶绿体密码子偏好性分析

Analysis of codon usage in the chloroplast genome of Medicago truncatula

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