棉花苯丙氨酸解氨酶基因家族的生物信息学分析

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

【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。

[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.