[1]赵森,邓力华,陈芬.不同植物FERONIA基因密码子使用偏好性分析[J].江苏农业学报,2020,(05):1073-1081.[doi:doi:10.3969/j.issn.1000-4440.2020.05.001]
　ZHAO Sen,DENG Li-hua,CHEN Fen.Analysis on codon usage preference of FERONIA genes in different plants[J].,2020,(05):1073-1081.[doi:doi:10.3969/j.issn.1000-4440.2020.05.001]
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不同植物FERONIA基因密码子使用偏好性分析()
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江苏农业学报[ISSN:1006-6977/CN:61-1281/TN]

卷:
期数:
2020年05期
页码:
1073-1081
栏目:
遗传育种·生理生化
出版日期:
2020-10-31

文章信息/Info

Title:
Analysis on codon usage preference of FERONIA genes in different plants
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 Li-hua2; CHEN Fen1
(1.Beibu Gulf University/Key Laboratory of Marine Biodiversity Conservation in Beibu Gulf of Guangxi, Qinzhou 535011, China;2.Institute of Subtropical Agriculture, Chinese Academy of Sciences/Key Laboratory of Agro-Ecological Processes in Subtropical Region, Changsha 410125, China)
关键词:
FERONIA基因; 密码子使用偏好性; 分子进化
Keywords:
FERONIA gene; codon usage preference; molecular evolution
分类号:
Q754；Q755
DOI:
doi:10.3969/j.issn.1000-4440.2020.05.001
文献标志码:
A
摘要:
为了了解植物FERONIA（FER）基因在长期进化过程中所形成的密码子使用模式及它们之间的亲缘关系，采用Codon W、CUSP在线程序和SPSS等分析软件对不同植物的FER基因密码子进行碱基组成分析、对应性分析、PR2-Plot分析、中性绘图分析和ENC-Plot分析并进行聚类分析。结果表明，单子叶植物FER基因密码子的平均G+C含量高于双子叶植物，且单子叶植物偏好使用以G/C结尾的密码子，而双子叶植物偏好使用以A/T结尾的密码子。对应性分析结果显示，在单子叶植物、双子叶植物中，向量轴1（Axis 1）可解释的变异分别占总变异的42.25%、28.56%。在单子叶植物中，Axis 1与总G+C含量、GC3含量、G3含量、C3含量呈极显著正相关（P<0.01），而在双子叶植物中则呈极显著负相关（P<0.01）。不同的碱基组成是单子叶植物和双子叶植物形成密码子使用偏好性的重要原因。PR2-Plot分析结果、中性绘图结果和ENC-Plot分析结果表明，自然选择是形成植物FER基因密码子使用偏好性的主要驱动力。基于编码序列（Coding sequence，CDS）构建的系统进化树比基于同义密码子相对使用度(RSCU)得出的聚类分析结果更接近传统的分类结果。本研究结果可为进一步开展植物分子进化和基因工程研究奠定基础。
Abstract:
To understand the usage pattern of codons formed in the long-term evolutionary process of FERONIA (FER) genes in plants and their genetic relationships, base composition analysis, correspondence analysis, PR2-Plot analysis, neutral plotting analysis and ENC-Plot analysis on FER gene codons of different plants were conducted by using Codon W, on line program of CUSP and analysis software like SPSS, and the cluster analysis was conducted. The results showed that the average content of G and C in FER gene codons of monocots was higher than that of dicots, and the monocots preferred G/C ending codons while dicots preferred A/T ending codons. The results of correspondence analysis showed that, Axis 1 accounted for 42.25% and 28.56% of the total variation in monocots and dicots respectively. Axis 1 presented significantly positive correlation (P<0.01) with contents of total G+C, GC3, G3 and C3 in monocots, while in dicots the correlation between Axis 1 and contents of total G+C, GC3, G3, C3 was significantly negative respectively. Different nucleotide composition is the important reason in the formation of codon usage preference in monocots and dicots. Results of PR2-Plot analysis, neutral plotting analysis as well as ENC-Plot analysis showed that, natural selection was the main driving force in the forming of codon usage preference of FER genes in plants. Phylogenetic tree constructed by coding sequence (CDS) was more similar with traditional classification results than the phylogenetic tree constructed by relative synonymous codon usage (RSCU). The results can lay foundation for further research on molecular evolution and gene engineering.

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备注/Memo

备注/Memo:
收稿日期：2020-04-14基金项目：广西高校中青年教师基础能力提升项目(KY2016YB496);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，山东临沂人，博士，讲师，主要从事植物分子遗传学研究。(E-mail)zhaosen@bbgu.edu.cn
更新日期/Last Update: 2020-11-16