甘肃内生真菌基因组密码子使用的偏好性分析

doi:10.11686/cyxb2019335

草业学报 ›› 2020, Vol. 29 ›› Issue (5): 67-77.DOI: 10.11686/cyxb2019335

甘肃内生真菌基因组密码子使用的偏好性分析

李秀璋^1,2, 宋辉³, 张宗豪¹, 徐海峰¹, 刘欣¹, 李玉玲¹, 李春杰^2,*

1.青海大学畜牧兽医科学院,青海省畜牧兽医科学院,青海西宁 810016;
2.兰州大学草地农业生态系统国家重点实验室,兰州大学农业农村部草牧业创新重点实验室,兰州大学草地农业教育部工程研究中心,兰州大学甘肃省西部草业技术创新中心,兰州大学草地农业科技学院,甘肃兰州 730020;
3.青岛农业大学动物科技学院,山东青岛 266109

收稿日期:2019-07-22 出版日期:2020-05-20 发布日期:2020-05-20
通讯作者: * E-mail: chunjie@lzu.edu.cn
作者简介:李秀璋(1987-),男,甘肃庆阳人,助理研究员,博士。E-mail: xiuzhang11@163.com
基金资助:
国家重点基础研究发展规划(“973”计划)(2014CB138702),国家自然科学基金(30070546),111引智基地(B12002)和青海省自然基金青年项目(2017-ZJ-918Q)资助

Analysis of codon usage bias in the genome of Epichloё gansuensis

LI Xiu-zhang^1,2, SONG Hui³, ZHANG Zong-hao¹, XU Hai-feng¹, LIU Xin¹, LI Yu-ling¹, LI Chun-jie^2,*

1.Academy of Animal and Veterinary Sciences, Qinghai University, Qinghai Academy of Animal and Veterinary Sciences, Xining 810016, China;
2.State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China;
3.College of Animal Science and Technology, Qingdao Agricultural University, Qingdao 266109, China

Received:2019-07-22 Online:2020-05-20 Published:2020-05-20
Contact: * E-mail: chunjie@lzu.edu.cn

摘要/Abstract

摘要： 在翻译过程中,三联体密码子指导氨基酸肽链的合成。长期进化过程中,有些氨基酸对应多个三联体密码子,形成了密码子兼并性。不同物种的基因组中,一些氨基酸偏好使用某种密码子,形成密码子使用的偏好性。突变和自然选择压力是影响密码子使用偏好性的两个主要因素。甘肃内生真菌是一种重要的禾草内生真菌,其主要侵染宿主醉马草,一方面能提高宿主醉马草对生物与非生物的抗性;另一方面产生的有毒生物碱类次生代谢产物毒害家畜。以甘肃内生真菌核基因组为研究对象,通过分析该基因组的基本组成及密码子使用模式,确定最优密码子。同时对各密码子相关指标与基因长度、氨基酸的使用频率等进行相关性分析,明确影响基因组对密码子使用偏好性的主要因素。结果显示,GC3的分布范围主要集中在40%~60%,62.7%的基因有效密码子数使用频率分布在0~0.1,95.4%的有效密码子数低于期望值而且位于期望曲线的右下方,这意味着突变压力是影响甘肃内生真菌密码子使用偏好性的因素之一。然而,中性分析结果显示,GC12和GC3之间呈显著正相关(r=0.110, P<0.01)、回归线斜率为0.2729,表明突变对密码子使用偏好性的影响仅为27.29%,其他因素的影响所占比例约为82.71%。相关性分析结果显示,疏水性氨基酸对甘肃内生真菌密码子使用偏好性的影响系数最大,其次是芳香族氨基酸。此外,在甘肃内生真菌基因组中总共鉴定到26个以C或G结尾的最优密码子,表明甘肃内生真菌偏好使用的密码子可能与第3位的GC含量有关。

关键词: 甘肃内生真菌, 密码子偏好性, 突变, 自然选择, 氨基酸

Abstract: The sequence of multiple sets of triplet adjacent DNA or RNA nucleotides (codon) determines amino acid sequence. In the long process of adaptive evolution, the codon usage of organisms has developed certain biases. Two major factors affect codon usage bias. The species ‘Epichloё gansuensis’ is an important endophytic fungus. E. gansuensis infection can improve the host resistance to biotic and abiotic stress, but the fungus produces secondary alkaloid metabolites that may poison livestock. This study aimed to analyze the basic composition of the genome of E. gansuensis and the pattern of codon usage, and to determine the optimal codon. Correlation of each codon index with gene length, amino acid usage frequency and other indicators was analyzed, to identify the main factors affecting codon usage. We found that the GC3 is mainly distributed between 40%-60%, the effective codon number of 62.7% genes distributed between 0-0.1, 95.4% effective codon numbers are lower than the expected and lie to the lower right of the expectation curve. These results suggest that mutation pressure is one of the main influencing factors on codon usage of E. gansuensis. However, the neutral analysis showed a significant positive correlation between GC12 and GC3 (r=0.110, P<0.01), with a slope of the regression line 0.2729. It suggests that the effect of mutation on codon usage was only 27.29%, 82.71% for other factors. Correlation analysis also showed that hydrophobic amino acids had the greatest effect on the codon usage of E. gansuensis, greater than that of aromatic amino acids. In addition, 26 optimal codon that end with a G or C residue from E. gansuensis were identified, indicating that codon usage in E. gansuensis may relate to the presence of a GC residue at the third position of the triplet codon. These optimal codon are significantly correlated with transcription level, and may help in the design of degenerative primers, for tracing the evolutionary origin of endophytic fungi.

Key words: Epichloë, gansuensis, codon usage bias, mutation, natural selection, amino acid

李秀璋, 宋辉, 张宗豪, 徐海峰, 刘欣, 李玉玲, 李春杰. 甘肃内生真菌基因组密码子使用的偏好性分析[J]. 草业学报, 2020, 29(5): 67-77.

LI Xiu-zhang, SONG Hui, ZHANG Zong-hao, XU Hai-feng, LIU Xin, LI Yu-ling, LI Chun-jie. Analysis of codon usage bias in the genome of Epichloё gansuensis[J]. Acta Prataculturae Sinica, 2020, 29(5): 67-77.

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甘肃内生真菌基因组密码子使用的偏好性分析

Analysis of codon usage bias in the genome of Epichloё gansuensis

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