摘要
【目的】在大蒜(Allium sativum)全基因组中鉴定WOX基因家族,并进行密码子使用偏性分析,为进一步研究大蒜WOX基因家族的功能提供重要依据。【方法】利用生物信息学方法,鉴定分析大蒜WOX基因家族及其密码子使用偏性。基于GEO测序(RNA-seq)数据,分析大蒜WOX基因家族在大蒜鳞茎不同发育时期及其他组织中的表达模式。【结果】从大蒜基因组中鉴定到16个大蒜WOX基因家族。系谱进化分析发现:大蒜WOX基因家族被划分为3个进化支,分别属于远古支、中间支和WUS支。保守结构域分析发现:它们均含有68个氨基酸组成的保守结构域。密码子使用偏性分析发现:该基因家族密码子使用偏性较弱并受GC3s的影响,同时,该基因家族存在27个高频密码子和14个最优密码子,且大多数偏向于A/U结尾。基于RSCU值和CDS序列聚类发现:基于CDS序列聚类能更加准确表达该基因家族之间的进化关系。ENC-Plot和PR2-plot分析发现:该基因家族密码子使用偏性主要受选择压力的影响。最佳外源表达系统发现:拟南芥更适合用于该基因家族的外源表达系统。表达谱分析发现:该基因家族在鳞茎发育不同时期、叶片、假茎和根中存在差异表达。【结论】本研究为进一步弄清大蒜WOX基因家族在大蒜生长发育过程中的作用提供了科学依据。
[Objective]WOX genes family were identified in the genome of garlic(Allium sativum)and codon bias analysis was carried out,which provided an important basis for further research on the function of garlic WOX genes family.[Method]The methods of bioinformatics were used to identify and analyze garlic WOX genes family and their codon usage bias.Based on GEO sequencing(RNA-seq)data,the expression patterns of garlic WOX genes family in different developmental stages of garlic bulbs and other tissues were analyzed.[Result]Sixteen garlic WOX genes family were identified from the garlic genome.The pedigree evolution analysis revealed that the WOX genes family of garlic were divided into three clades,which respectively could be categorized as the ancient clade,the intermediate clade and the WUS clade.The analysis of the conserved domains showed that they all contained a conserved domain composed of 68 amino acids.Analysis of codon usage bias indicated that the gene codon usage bias of this family was weakened and affected by GC3s.Meanwhile,27 high-frequency codons and 14 optimal codons were revealed in this gene family,and most of them were biased towards A/U ends.Based on RSCU value and CDS sequence clustering,it was found that clustering based on CDS sequence could more accurately show the evolutionary relationship between genes in this family.ENC-Plot and PR2-plot analysis found that the codon usage bias of this family gene was mainly affected by selection pressure.The best exogenous expression system found:Arabidopsis was more suitable for the exogenous expression system of this genes family.Expression profile analysis revealed that the genes family were differentially expressed in different stages of bulb development,leaves,pseudostems and roots.[Conclusion]The study provided a scientific basis for further understanding the role of garlic WOX qenes genes family in the growth and development of garlic.
作者
董新玉
邓浪
张亚春
陈国发
李树锋
DONG Xin-yu;DENG Lang;ZHANG Ya-chun;CHEN Guo-fa;LI Shu-feng(Economic Crops Institute of Dali Academy of Agricultural Science and Extension,Dali,Yunnan 671000,China;Yunnan Vocational and Technical College of Agriculture,Kunming 650031,China)
出处
《西南农业学报》
CSCD
北大核心
2022年第2期285-293,共9页
Southwest China Journal of Agricultural Sciences
基金
财政部、农业农村部项目(CARS-24-G)。
