[1]赵森,邓力华,陈芬.秋茄叶绿体基因组密码子使用偏好性分析[J].森林与环境学报,2020,40(05):534-541.[doi:10.13324/j.cnki.jfcf.2020.05.011]
 ZHAO Sen,DENG Lihua,CHEN Fen.Codon usage bias of chloroplast genome in Kandelia obovata[J].,2020,40(05):534-541.[doi:10.13324/j.cnki.jfcf.2020.05.011]
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秋茄叶绿体基因组密码子使用偏好性分析()
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《森林与环境学报》[ISSN:2096-0018/CN:35-1327/S]

卷:
40
期数:
2020年05期
页码:
534-541
栏目:
出版日期:
2020-09-15

文章信息/Info

Title:
Codon usage bias of chloroplast genome in Kandelia obovata
作者:
赵森1 邓力华2 陈芬1
1. 北部湾大学广西北部湾海洋生物多样性养护重点实验室, 广西 钦州 535011;
2. 中国科学院亚热带农业生态研究所亚热带农业生态过程重点实验室, 湖南 长沙 410125
Author(s):
ZHAO Sen1 DENG Lihua2 CHEN Fen1
1. Guangxi Key Laboratory of Beibu Gulf Marine Biodiversity Conservation, Beibu Gulf University, Qinzhou, Guangxi 535011, China;
2. Key Laboratory of Agro-ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, Hunan 410125, China
关键词:
秋茄叶绿体基因密码子偏好性最优密码子
Keywords:
Kandelia obovatachloroplast genecodon usage biasoptimal codons
分类号:
S718.3
DOI:
10.13324/j.cnki.jfcf.2020.05.011
摘要:
为了确定秋茄叶绿体基因组密码子的使用模式及其成因,以筛选到的50条蛋白质编码序列为研究对象,利用CodonW 1.4.2和CUSP在线程序对其密码子使用偏好性进行分析。结果表明:秋茄叶绿体基因组密码子第3位的GC含量(GC3)较低,平均值为27.62%,有30个密码子的相对同义密码子使用度(URSC)>1,其中以A/U结尾的密码子29个,说明秋茄叶绿体基因组偏向使用以A/U结尾的密码子;有效密码子数(Nec)的平均值为47.02,密码子使用偏好性较弱;Nec和GC3之间呈显著正相关(r=0.329,P<0.05),表明密码子第3位上的碱基组成影响密码子使用偏好性。中性分析结果显示,GC3和GC12相关性显著(r=0.464,P<0.01),回归系数为0.706 4,说明突变对密码子使用偏好性有重要影响。Nec-plot分析和奇偶偏好性分析表明,自然选择也是重要的影响因素。基于rbcL基因序列的系统进化树和基于URSC值的聚类分析有一定的相似性,表明密码子使用偏好性与物种之间的亲缘关系有关。综合分析表明,突变是秋茄叶绿体基因组密码子使用偏好性的重要因素,同时自然选择和碱基组成也有一定影响。ACC、ACA和GCA为最优密码子。
Abstract:
To determine the codon usage pattern of chloroplast genome and its shaping factors in the mangrove plant, Kandelia obovata, a total of 50 selected protein-coding sequences were analyzed using Codon W 1.4.2 and CUSP software. The results demonstrated that the GC content at the third codon position(GC3) was relatively low, with an average of 27.62%. There were 30 codons with a relative synonymous codon usage(URSC)>1, in which 29 of them ended with A/U. This suggests that the protein-coding genes in the chloroplast genome tend to use the codons ending with A/U. The effective number of codons(Nec) was 47.02; therefore, their codon usage bias was weaker. The Nec was found to have significant correlation with GC3 (r=0.329, P<0.05), implying the potential effect of third codon composition in codon usage bias. The neutral plot analysis revealed the significant correlation between GC3 and GC12(r=0.464, P<0.01) with a regression coefficient of 0.706 4, indicating the important role of mutation in codon usage bias. According to the Nec-plot and parity rule 2 analysis, the codon usage bias was also influenced by natural selection. The consistencies between the rbcL gene-based phylogenetic tree and URSC-based chloroplast gene analyses suggest that codon usage bias is related to the phylogenetic relationship among species. Therefore, based on the above mentioned findings, it can be concluded that mutation is a crucial factor of codon usage bias in K. obovata chloroplast genome, but natural selection and nucleotide constitution are also crucial for determining codon usage bias. ACC, ACA and GCA were found to be the optimal codons.

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备注/Memo

备注/Memo:
收稿日期:2020-06-11;改回日期:2020-07-02。
基金项目:广西高校中青年教师基础能力提升项目(KY2016YB496;2018KY0621);广西北部湾海洋生物多样性养护重点实验室项目(2019ZB01)。
作者简介:赵森(1982-),男,讲师,从事植物分子遗传学研究。Email:zhaosen@bbgu.edu.cn。
更新日期/Last Update: 1900-01-01