绿豆WRKY基因家族的全基因组鉴定及生物信息学分析  

Genome-wide identification and bio-informatics analysis of WRKY gene family in Vigna radiata

作　　者：郝青婷[1] 高伟 闫虎斌 张泽燕 朱慧珺 王茜 赵雪英 张耀文 HAO Qingting;GAO Wei;YAN Hubin;ZHANG Zeyan;ZHU Huijun;WANG Qian;ZHAO Xueying;ZHANG Yaowen(College of Agronomy,Shanxi Agriculture University,Taiyuan,Shanxi 030031,China)

机构地区：[1]山西农业大学农学院,山西太原030031

出　　处：《西北农林科技大学学报（自然科学版）》2023年第5期59-71,81,共14页Journal of Northwest A&F University(Natural Science Edition)

基　　金：国家现代农业产业技术体系项目(CARS-08-G10);国家重点研发计划项目子课题(2021YFD1600602-08);山西省重大专项重点实验室课题(202105D121010-19);山西省基础研究计划项目(20210302124504);山西省现代农业产业技术建设(杂粮)项目(2022-03)。

摘　　要：【目的】对绿豆WRKY转录因子在全基因组上进行鉴定及生物信息学分析,为绿豆WRKY基因功能的研究以及高抗绿豆品种培育奠定理论基础。【方法】利用Hmmer软件同源搜索,并通过在线工具SMART、NCBI-CDD和Pfam数据库进行结构域再确认获得79个绿豆WRKY基因,然后通过在线软件ProtParam、ProtScale、SWISS-MODEL分析绿豆WRKY家族蛋白的理化性质、亲疏水性并构建3D立体模型,使用MEGA X、McScanX软件构建进化树和绘制共线性图,利用MEME、PlantCARE在线工具分析WRKY转录因子的保守基序并预测基因上游的顺式作用元件。【结果】鉴定得到的79个VrWRKY蛋白的氨基酸数量为64~746,分子量为7.42~80.93 ku,等电点为4.49~10.41,大多数成员为亲水性不稳定蛋白。系统进化树分析表明,绿豆WRKY基因家族的79个成员可分为Ⅰ、Ⅱ和Ⅲ3组,其成员数量分别为16,51和12,Ⅱ组进一步划分为Ⅱ-a、Ⅱ-b、Ⅱ-c、Ⅱ-d和Ⅱ-e 5个亚组,其成员数量依次为2,17,17,7和8,其中Ⅱ-a、Ⅱ-b、Ⅱ-d和Ⅱ-e亲缘关系更近,而Ⅱ-c在进化树上的分布整体更靠近Ⅲ组。基因结构及保守基序分析显示,该家族基因均为间隔基因,且都含有保守基序WRKYGQK。基因染色体定位分析表明,所有成员在11条染色体上均有分布。顺式作用元件分析表明,绿豆WRKY基因启动子区存在丰富的激素及胁迫响应相关的元件。基因组间共线性分析结果表明,绿豆WRKY基因与拟南芥WRKY基因之间存在同源关系。基因复制结果表明,绿豆基因组有1对串联重复基因,15对大片段复制基因,片段复制在绿豆WRKY基因家族扩张中起主要作用。绿豆WRKY蛋白3D结构模拟表明,所有成员具有相似的两种蛋白结构,其中一种立体结构中心含有1个Zn^(2+)。【结论】鉴定得到79个含典型WRKY保守结构域的绿豆WRKY蛋白,其生物信息学分析丰富了绿豆WRKY转录因子的分子生物学理论。【Objective】The genome-wide identification and bioinformatics analysis of mungbean WRKY transcription factors were carried out to lay a theoretical foundation for the research of mungbean WRKY gene function and the cultivation of mungbean varieties with high resistance.【Method】The Hmmer software was used for homology search and 79 mungbean WRKY genes were reconfirmed by online SMART,NCBI-CDD and Pfam databases.Then,ProtParam,ProtScale and SWISS-MODEL were used to analyze physicochemical properties,hydrophilicity and hydrophobicity of mungbean WRKY family proteins and construct 3D three-dimensional models.MEGA X and McScanX software were used to construct phylogenetic tree and draw collinearity map,while MEME and PlantCARE online tools were used to analyze the conserved motifs of WRKY transcription factors and predict the cis-acting elements of genes upstream.【Result】A total of 79 VrWRKY proteins were identified with amino acids member of 64-746,molecular weight of 7.42-80.93 ku and isoelectric point of 4.49-10.41.Most of the members were hydrophilic labile proteins.The phylogenetic tree indicated that mungbean WRKY proteins were divided into 3 groups of I,Ⅱand III with numbers of 16,51 and 12,respectively.GroupⅡwas further divided into 5 subgroups ofⅡ-a,Ⅱ-b,Ⅱ-c,Ⅱ-d andⅡ-e with numbers of 2,17,17,7 and 8.Ⅱ-a,Ⅱ-b,Ⅱ-d andⅡ-e had close relationship whileⅡ-c was close to groupⅢ.The gene structure and conserved motifs showed that the family genes were all gap genes and contained the conserved motif of WRKYGQK.All members were distributed on 11 chromosomes,and the analysis of cis-acting elements showed that there were abundant elements related to hormone and stress response in the promoter region of mungbean WRKY gene.The gene duplication results showed that the mungbean genome had a pair of tandem duplication genes and 15 pairs of large segment duplication genes.Fragment duplication played a major role in the expansion of the mungbean WRKY gene family.The synteny analysis showed tha

关 键 词：绿豆 WRKY基因家族 顺式作用元件 基因结构 共线性分析 

分 类 号：S522.03[农业科学—作物学]