生物学杂志

生物学杂志 ›› 2020, Vol. 37 ›› Issue (6): 68-.doi: 10.3969/j.issn.2095-1736.2020.06.068

• 研究报告 • 上一篇    下一篇

百合科植物psbA基因密码子偏好性分析

  

  1. 西南交通大学 生命科学与工程学院， 成都 610031
  • 出版日期:2020-12-18 发布日期:2020-12-21
  • 通讯作者: 周嘉裕，博士，副教授，主要从事植物学和分子生物学研究，E-mail：spinezhou@home.swjtu.edu.cn； 廖海，博士，副教授，主要从事生物化学和分子生物学研究,E-mail：ddliaohai@home.swjtu.edu.cn
  • 作者简介:倪典墨，主要从事药用植物学方面研究,E-mail：1310383347@qq.com
  • 基金资助:
    国家自然科学基金（31500276)；四川省应用基础研究项目（2017JY0222）；四川省重点研发项目(2018SZ0061)；成都市科技技术研发项目（2016-HM01-00260-SF）；国家级大学生创新创业训练计划资助项目（201910613082）；西南交通大学个性化实验（GX201913086）

Codon bias analysis of psbA gene in Liliaceae

  1. School of Life Science and Engineering, Southwest Jiaotong University, Chengdu 610031, China
  • Online:2020-12-18 Published:2020-12-21

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摘要： 利用CodonW、CHIPS与CUPS等程序对60种百合科植物psbA基因的密码子偏好性展开分析，结果发现有26种密码子具有偏好性，其中12个极强，10个密码子在psbA中出现率极低，13个密码子没有出现。ENc平均值为37.84，显示出密码子偏好性较弱。GC和GC3s平均值分别为42.5%和48.0%，表明密码子组成偏向A与U碱基，且倾向于以A/U结尾。CAI的平均值为0.218，说明密码子的表达水平偏低。ENc-plot表明密码子偏好性主要受到自然选择的影响。聚类分析表明，基于CDS序列的聚类比基于RSCU更适合作为百合科植物系统发育分析。

关键词: 密码子偏好性, 聚类分析, 百合科, psbA基因

Abstract: CodonW, CHIPS and CUPS programs were used to analyze the codon bias of psbA gene from 60 species of Liliaceous plants. As a result, 26 codons were preferable, of which 12 codons were very strong; whereas 10 codons were seldom used and 13 codons did not appear. The average ENc value of 37.84 indicated that the overall preference was weak. The average values of GC and GC3s were 42.5% and 48.0%, respectively, indicating that A and U were frequently used in both the total composition and the 3rd codon position. The CAI value of 0.218 indicated that the codon expression level was low. ENc-plot analysis showed that codon preference was mainly due to selection．The cluster analysis showed that the clustering based on the CDS sequence was better than that based on the RSCU value in the genetic relationship among all the Liliaceae plants, and it was more suitable as a reference for phylogenetic analysis of the family of the Liliaceae.

Key words: codon bias, cluster analysis, Liliaceae, psbA gene

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