生物学杂志

生物学杂志 ›› 2021, Vol. 38 ›› Issue (6): 15-.doi: 10.3969/j.issn.2095-1736.2021.06.015

• 研究报告 • 上一篇    下一篇

独行菜LaAP2基因密码子偏性与进化分析

  

  1. 1. 喀什大学 生命与地理科学学院叶尔羌绿洲生态与生物资源研究高校重点实验室， 喀什 844000；
    2. 新疆师范大学 新疆特殊环境物种保护与调控生物学实验室干旱区植物逆境生物学实验室， 乌鲁木齐 830054
  • 出版日期:2021-12-18 发布日期:2021-12-15
  • 通讯作者: 赵惠新，教授，硕士生导师，从事植物抗逆生理生态与分子生物学研究，E-mail：zhaohuixin101@sina.com
  • 作者简介:周茜，硕士研究生，主要从事植物抗逆生理生态与分子生物学研究，E-mail：zhouqian19900713@sina.com
  • 基金资助:
    国家自然科学基金项目（31660079，U1703112）;喀什大学校级科研项目（022019110）

Codon usage bias and evolution analysis of the LaAP2 genein Lepidium apetalum Willd.

  1. 1. Key Laboratory of Ecology and Biological Resources in Yarkand Oasis, College of Life and Geography Science,Kashi University, Kashi 844000, China; 2. Xinjiang Key Laboratory of Special Species Conservation and Regulatory Biology, Key Laboratory of Plant Stress Biology in Arid Land, College of Life Science,Xinjiang Normal University, Urumqi 830054, China
  • Online:2021-12-18 Published:2021-12-15

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摘要： 为明确独行菜（Lepidium apetalum Willd.）LaAP2基因密码子的使用特性，运用CodonW与EMBOSS等程序软件，分析了独行菜LaAP2基因密码子的使用偏好性，并比较了独行菜LaAP2基因与模式生物的密码子使用频率。通过中性绘图、ENc（有效密码子数）和差性分析，探讨AP2基因密码子使用偏性形成的原因。结果表明：独行菜LaAP2基因的ENc值为48-65，CAI（密码子适应指数）为0-214，GC含量为42-69%，表明其密码子使用偏性弱，密码子偏好使用AT；RSCU值计算独行菜LaAP2基因高频密码子有11个；不同物种间的AP2基因的密码子存在一定选用偏好性；RSCU聚类分析表明，独行菜LaAP2基因与双子叶植物中十字花科的植物使用偏性最相似；密码子碱基成分和相关性分析发现，LaAP2基因在进化过程中密码子偏好性的形成与突变和自然选择等诸多因素相关；比较密码子使用频率分析发现，原核生物大肠杆菌表达系统更适合作为独行菜LaAP2基因的异源表达受体，模式植物拟南芥是较适宜独行菜LaAP2基因的遗传转化受体。研究为今后独行菜LaAP2基因的异源表达以及相关基因功能的进一步研究提供了重要参考。

关键词: 行菜, LaAP2基因, 密码子偏性, 聚类分析

Abstract: To understand the codon bias of LaAP2 in Lepidium apetalum, LaAP2 gene codon bias was analyzed by Codon W, and EMBOSS programs was used to analyze the codon usage bias of the Lepidium apetalum LaAP2 gene. Correlation analysis was conducted to compare the bias of the Lepidium apetalum LaAP2 gene in model organisms for which relatively mature genetic transformation systems are available. Neutral drawing, ENc plots and parity rule 2 polt were subsequently used for the exploration of possible factors that affect the formation of the bias. The results showed that the ENc, CAI, and GC content of LaAP2 were respectively 48-65, 0-214, and 42-69%, indicating that the codon bias level of LaAP2 in Lepidium apetalum was low and biased toward the synonymous codons with A or T. According to the RSCU value, 11 codons showed high-frequency. Comparison of the codon usage preference of homolongous genes with other crops suggested that there was a certain difference in codon usage preference among AP2 genes in different species. The RSCU cluster analysis showed that the preference of LaAP2 gene was the closest to that of brassicaceae burnett in dicotyledonous plants. The codon base composition and correlation analysis showed that the codon bias of the Lepidium apetalum LaAP2 gene had many factors such as mutation and selective pressure playing an important role in shaping codon usage bias. Based on the analysis of the frequency of codon usage across species, the prokaryote E. coli expression system was found to be the most suitable for use with the LaAP2 gene, and the model plant Arabidopsis was the most ideal genetic transformation receptor of the LaAP2 gene. This study provided important reference information for further studies on the heterologous sexpression and the function of the LaAP2 gene in Lepidium apetalum.

Key words: Lepidium apetalum Willd., LaAP2 gene, codon usage bias, cluster analysis

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