Open AccessIdentification and expression analysis of the WRKY gene family during different developmental stages in Lycium ruthenicum Murr. fruit
Author(s) -
Richard John Tiika,
Wei Jia,
Rui Ma,
Hongshan Yang,
Guangxin Cui,
Huirong Duan,
Yupo Ma
Publication year - 2020
Publication title -
peerj
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.927
H-Index - 70
ISSN - 2167-8359
DOI - 10.7717/peerj.10207
Subject(s) - wrky protein domain , biology , transcriptome , gene , genetics , gene family , zinc finger , phylogenetic tree , gene expression , gene expression profiling , homology (biology) , protein family , transcription factor
Background The WRKY 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 Lycium ruthenicum , although these aspects have been comprehensively studied in most plant species. Methods In this study, the WRKY genes were identified from a L. ruthenicum 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). Results A total of 73 putative WRKY proteins in the L. ruthenicum 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 L. ruthenicum proteins. The selected LrWRKY genes exhibited discrete expression patterns during different fruit developmental stages. Interestingly, five LrWRKYs (- 20 , - 21 , - 28 , - 30 , and - 31 ) were expressed remarkably throughout the fruit developmental stages. Discussion Our results reveal the characteristics of the LrWRKY gene family, thus laying a foundation for further functional analysis of the WRKY family in L. ruthenicum.