生物学杂志

生物学杂志 ›› 2022, Vol. 39 ›› Issue (3): 36-.doi: 10.3969/j.issn.2095-1736.2022.03.036

• 研究报告 • 上一篇    下一篇

苯丙氨酸解氨酶基因密码子偏好性与进化分析

  

  1. 西南交通大学生命科学与工程学院，成都610031
  • 出版日期:2022-06-18 发布日期:2022-06-17
  • 通讯作者: 廖海，博士，副教授，研究方向为生物化学和分子生物学，E-mail: ddliaohai@home.swjtu.edu.cn；周嘉裕，博士，副教授，研究方向为植物学和分子生物学，E-mail: spinezhou@home.swjtu.edu.cn
  • 作者简介:李秋娥，硕士研究生，研究方向为药用植物学，E-mail: 1803620921@qq.com
  • 基金资助:
    国家自然科学基金青年科学基金项目(31500276)；四川省重点研发项目(2018SZ0061)；四川省应用基础研究项目(2017JY0222)；大学生科研训练项目(200907)

Codon bias and evolution analysis of phenylalanine ammonia-lyase gene #br# #br#

  1. School of Life and Science, Southwest Jiaotong University, Chengdu 610031, China
  • Online:2022-06-18 Published:2022-06-17

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摘要： 利用Codon W与EMBOSS等程序，分析42种不同植物来源的PAL基因序列密码子偏好性及可能形成机制，旨在为植物PAL基因的表达提高提供理论指导。RSCU结果显示，相比其他植物单子叶植物的密码子偏好性较高，CUC是其最优密码子。单子叶等植物偏好以G/C编码，双子叶植物偏好以A/T编码。ENc-plot结果表明，双子叶植物的偏好性主要受自然选择的影响，而单子叶植物的偏好性受到突变与自然选择的双重影响。聚类分析表明，基于CDS序列的聚类比基于RSCU聚类更适合作为植物系统发育分析。绝大多数单子叶植物适合在大肠杆菌中表达，而双子叶植物的PAL基因适合在酵母中表达；拟南芥相比烟草更适合作为所有42种植物PAL基因的遗传转化宿主。研究结果可为植物PAL基因的遗传进化研究与功能验证等奠定理论基础。

关键词: 贝母, 苯丙氨酸解氨酶, 密码子偏好性, 进化分析

Abstract: 　Codon W and EMBOSS were used to analyze the codon usage bias of PAL genes and possible formation mechanism from 42 different plant species, to provide theoretical guidance for the improvement of PAL gene expression in plants. RSCU results indicated that PAL genes from monocotyledonous plants had stronger codon usage bias than those from dicotyledons and other plants, with CUC as the optimal codon. PAL genes in monocotyledons prefer G/C codes, whereas PAL in dicotyledons prefer A/T codes. Enc-plot results showed that the codon usage bias of dicotyledons and other plants was mainly influenced by natural selection, while the codon usage bias of monocotyledons was influenced by both mutation and natural selection. Cluster analysis showed that CDS sequence-based clustering was more suitable than RSCU based clustering in phylogenetic analysis. The PAL genes of most monocotyledons were suitable for expression in E. coli, whereas the PAL genes of dicotyledons were suitable for expression in yeast. Furthermore, Arabidopsis thaliana might be the more appropriate genetic transformation receptor for genetic transformation of the PAL genes from 42 different plant species than tobacco. These results laid the theoretical foundation for genetic evolution investigation and functional validation of PAL genes.

Key words: Fritillaria, phenylalanine ammonia-lyase, codon usage bias, evolution analysis

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