Tiika Richard John, Wei Jia, Ma Rui, Yang Hongshan, Cui Guangxin, Duan Huirong, Ma Yanjun
College of Forestry, Gansu Agricultural University, Lanzhou, Gansu Province, China.
Lanzhou Institute of Husbandry and Pharmaceutical Science, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu Province, China.
PeerJ. 2020 Oct 28;8:e10207. doi: 10.7717/peerj.10207. eCollection 2020.
The gene family, one of the major transcription factor families in plants, plays crucial regulatory roles in physiological and biological developmental processes, and the adaptation of plants to the environment. However, the systematic study of WRKY structure, expression profiling, and regulatory functions has not been extensively reported in , although these aspects have been comprehensively studied in most plant species.
In this study, the genes were identified from a transcriptome database by using bioinformatics. The identification, phylogenetic analysis, zinc-finger structures, and conserved motif prediction were extensively explored. Moreover, the expression levels of 23 selected genes with fragments per kilobase of exons per million mapped reads (FPKM) >5 were assayed during different fruit developmental stages with real-time quantitative polymerase chain reaction (RT-qPCR).
A total of 73 putative WRKY proteins in the transcriptome database were identified and examined. Forty-four proteins with the WRKY domain were identified and divided into three major groups with several subgroups, in accordance with those in other plant species. All 44 LrWRKY proteins contained one or two conserved WRKY domains and a zinc-finger structure. Conserved motif prediction revealed conservation of the WRKY DNA-binding domain in proteins. The selected genes exhibited discrete expression patterns during different fruit developmental stages. Interestingly, five (-, -, -, -, and -) were expressed remarkably throughout the fruit developmental stages.
Our results reveal the characteristics of the gene family, thus laying a foundation for further functional analysis of the family in
WRKY基因家族是植物中主要的转录因子家族之一，在植物生理和生物发育过程以及植物对环境的适应性方面发挥着关键的调控作用。然而，尽管在大多数植物物种中已对WRKY的结构、表达谱和调控功能进行了全面研究，但在番茄中尚未广泛报道对其进行的系统研究。
在本研究中，通过生物信息学从番茄转录组数据库中鉴定WRKY基因。广泛探索了其鉴定、系统发育分析、锌指结构和保守基序预测。此外，使用实时定量聚合酶链反应（RT-qPCR）测定了23个选定的每百万映射 reads 中外显子每千碱基片段数（FPKM）>5的基因在不同果实发育阶段的表达水平。
在番茄转录组数据库中总共鉴定并检测了73个假定的WRKY蛋白。鉴定出44个具有WRKY结构域的蛋白，并根据其他植物物种中的分类将其分为三个主要组和几个亚组。所有44个LrWRKY蛋白均包含一个或两个保守的WRKY结构域和一个锌指结构。保守基序预测揭示了番茄蛋白中WRKY DNA结合结构域的保守性。选定的基因在不同果实发育阶段表现出不同的表达模式。有趣的是，五个基因（LrWRKY2、LrWRKY4、LrWRKY6、LrWRKY7和LrWRKY11）在整个果实发育阶段均有显著表达。
我们的结果揭示了番茄WRKY基因家族的特征，从而为进一步对番茄中WRKY家族进行功能分析奠定了基础。
