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棉花学报 ›› 2021, Vol. 33 ›› Issue (1): 66-74.doi: 10.11963/1002-7807.lyzlz.20210108

• 研究与进展 • 上一篇    下一篇

棉花苯丙氨酸解氨酶基因家族的生物信息学分析

李雨哲(),邢淋雪,刘梦洁,刘苏瑶,鲍梦楠,刘震()   

  1. 安阳工学院,河南安阳 45500
  • 收稿日期:2020-04-21 出版日期:2021-01-15 发布日期:2021-02-25
  • 通讯作者: 刘震 E-mail:liyuzhe0617@163.com;liuzhen378@163.com
  • 作者简介:李雨哲(1999―), liyuzhe0617@163.com
  • 基金资助:
    中国博士后科学基金(2018M632761)

Bioinformatics analysis of the phenylalanine ammonia lyase (PAL) gene family in cotton

Li Yuzhe(),Xing Linxue,Liu Mengjie,Liu Suyao,Bao Mengnan,Liu Zhen()   

  1. Anyang Institute of Technology, Anyang, Henan 455000 China
  • Received:2020-04-21 Online:2021-01-15 Published:2021-02-25
  • Contact: Liu Zhen E-mail:liyuzhe0617@163.com;liuzhen378@163.com

摘要:

【目的】 苯丙氨酸解氨酶是苯丙烷类代谢的关键酶,对调节植物生长和抗逆有重要作用。从全基因组层次了解棉花苯丙氨酸解氨酶基因家族的进化和功能,可为相关研究提供数据支撑。【方法】 利用HMMER和BLASTP从棉花基因组筛选苯丙氨酸解氨酶基因家族,利用MEGA-X进行进化分析,利用MCScanX进行共线性分析,并利用NCBI SRA的数据进行表达分析。【结果】 本研究分别从陆地棉、海岛棉、亚洲棉和雷蒙德氏棉基因组中筛选到12、13、7、8个苯丙氨酸解氨酶基因,依据进化分析和共线性关系数据,我们推测四种棉花的二倍体祖先起初应有6个苯丙氨酸解氨酶基因。顺式作用元件分析结果表明,苯丙氨酸解氨酶基因家族含有较多的光响应、激素响应、胁迫响应和生长发育相关的元件。苯丙氨酸解氨酶的蛋白序列具有保守的基序。陆地棉的12个苯丙氨酸解氨酶在低温、高温、盐和PEG胁迫下有不同的表达方式。【结论】 本研究明确了苯丙氨酸解氨酶在棉花基因组中的数量、理化性质、进化和表达特征,为苯丙氨酸解氨酶的深入研究提供了参考。

关键词: 苯丙氨酸解氨酶; 棉花; 基因家族; 表达; 生物信息学

Abstract:

[Objective] Phenylalanine ammonia-lyase is a key enzyme in the metabolism of phenylpropanoids and plays an important role in plant growth regulation and stress tolerance. The evolution and function study of cotton phenylalanine ammonia-lyase gene family at the whole genome level will provide data support for related researches. [Method] HMMER and BLASTP were used to search phenylalanine ammonia-lyase genes from cotton genomes, and MEGA was used for evolutionary analysis, MCScanX was used for collinear analysis; in addition, NCBI SRA data were used for expression analysis. [Result] In this study, 12, 13, 7, and 8 phenylalanine ammonia-lyase genes were obtained from Gossypium hirsutum, G. barbadense, G. arboreum, G. raimondii, respectively. According to the evolutionary analysis and collinearity results, we speculated that the diploid ancestors of the four cotton species should have six phenylalanine ammonia-lyase genes initially. The results of the cis-element analysis indicated that the phenylalanine ammonia-lyase gene family contains cis-elements related to light, hormone, stress, and development. The protein sequence of phenylalanine ammonia-lyase has a conserved motif. Twelve phenylalanine ammonia-lyases in G. hirsutum have different expression patterns under cold, hot, salt, and PEG stress. [Conclusion] The results of this study are helpful to understand the evolution and function of the phenylalanine ammonia-lyase gene family in cotton, and provide a theoretical basis and reference for the follow-up study of their specific functions in cotton. In this study, the numbers, physicochemical properties, evolution, and expression characteristics of phenylalanine ammonia-lyase of cotton were determined, which will provide resources for further study of phenylalanine ammonia-lyase.

Key words: phenylalanine ammonia-lyase; cotton; gene family; expression; bioinformatics